1
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Potok P, Kola A, Valensin D, Capdevila M, Potocki S. Copper Forms a PPII Helix-Like Structure with the Catalytic Domains of Bacterial Zinc Metalloproteases. Inorg Chem 2023; 62:18425-18439. [PMID: 37909295 PMCID: PMC10647932 DOI: 10.1021/acs.inorgchem.3c02391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 11/03/2023]
Abstract
The rapid spread of antibiotic-resistant bacteria continuously raises concerns about the future ineffectiveness of current antimicrobial treatments against infectious diseases. To address this problem, new therapeutic strategies and antimicrobial drugs with unique modes of action are urgently needed. Inhibition of metalloproteases, bacterial virulence factors, is a promising target for the development of antibacterial treatments. In this study, the interaction among Zn(II), Cu(II), and the metal-binding domains of two metalloproteases, AprA (Pseudomonas aureginosa) and CpaA (Acinetobacter baumanii), was investigated. The objective was to determine the coordination sphere of Zn(II) with a peptide model of two zinc-dependent metalloproteases. Additionally, the study explored the formation of Cu(II) complexes with the domains, as Cu(II) has been shown to inhibit metalloproteases. The third aim was to understand the role of nonbinding amino acids in stabilizing the metal complexes formed by these proteases. This work identified specific coordination patterns (HExxHxxxxxH) for both Zn(II) and Cu(II) complexes, with AprA and CpaA exhibiting a higher affinity for Cu(II) compared to Zn(II). The study also found that the CpaA domain has greater stability for both Zn(II) and Cu(II) complexes compared to AprA. The nonbinding amino acids of CpaA surrounding the metal ion contribute to the increased thermodynamic stability of the metal-peptide complex through various intramolecular interactions. These interactions can also influence the secondary structures of the peptides. The presence of certain amino acids, such as tyrosine, arginine, and glutamic acid, and their interactions contribute to the stability and, only in the case of Cu(II) complexes, the formation of a rare protein structure called a left-handed polyproline II helix (PPII), which is known to play a role in the stability and function of various proteins. These findings provide valuable insights into the coordination chemistry of bacterial metalloproteases and expand our understanding of potential mechanisms for inhibiting these enzymes.
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Affiliation(s)
- Paulina Potok
- Faculty
of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Arian Kola
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Daniela Valensin
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Merce Capdevila
- Departament
de Química, Universitat Autònoma
de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Sławomir Potocki
- Faculty
of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
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2
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Scheithauer L, Karagöz MS, Mayer BE, Steinert M. Protein sociology of ProA, Mip and other secreted virulence factors at the Legionella pneumophila surface. Front Cell Infect Microbiol 2023; 13:1140688. [PMID: 36936764 PMCID: PMC10017501 DOI: 10.3389/fcimb.2023.1140688] [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: 01/09/2023] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
The pathogenicity of L. pneumophila, the causative agent of Legionnaires' disease, depends on an arsenal of interacting proteins. Here we describe how surface-associated and secreted virulence factors of this pathogen interact with each other or target extra- and intracellular host proteins resulting in host cell manipulation and tissue colonization. Since progress of computational methods like AlphaFold, molecular dynamics simulation, and docking allows to predict, analyze and evaluate experimental proteomic and interactomic data, we describe how the combination of these approaches generated new insights into the multifaceted "protein sociology" of the zinc metalloprotease ProA and the peptidyl-prolyl cis/trans isomerase Mip (macrophage infectivity potentiator). Both virulence factors of L. pneumophila interact with numerous proteins including bacterial flagellin (FlaA) and host collagen, and play important roles in virulence regulation, host tissue degradation and immune evasion. The recent progress in protein-ligand analyses of virulence factors suggests that machine learning will also have a beneficial impact in early stages of drug discovery.
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Affiliation(s)
- Lina Scheithauer
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Mustafa Safa Karagöz
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Benjamin E. Mayer
- Computational Biology & Simulation, Technische Universität Darmstadt, Darmstadt, Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
- *Correspondence: Michael Steinert,
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3
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Arakawa K, Yanai J, Watanabe K. Study of the Ca2+-dependent gene expression of EuPrt, an extracellular metalloprotease produced by the psychro-tolerant bacterium Exiguobacterium undae Su-1. Biosci Biotechnol Biochem 2022; 86:1308-1317. [PMID: 35776951 DOI: 10.1093/bbb/zbac109] [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: 04/28/2022] [Accepted: 05/31/2022] [Indexed: 11/14/2022]
Abstract
The effect of a Ca2+ ion on the gene expression of an on-demand type of metalloprotease from psychrotrophic Exiguobacterium undae Su-1 (EuPrt) was studied. We first established a modified mM9 medium for strain Su-1 to examine its effect in more detail. Then, when the strain was cultured in mM9 medium and 1.0 mM CaCl2 was added, we detected the mature EuPrt and its precursor proteins via Western blotting analysis and found the relative protease activity and its transcription increased by 50-fold and 7-fold, respectively, at the peak. Furthermore, the intracellular concentration of Ca2+ ions was analyzed using inductively coupled plasma atomic emission spectroscopy (ICP-AES) with other metal ions along the growth of strain Su-1. The intracellular concentration of Ca2+ ion was found to increase as much as 3-fold in response to the addition of an extracellular Ca2+ ions, indicating that euPrt gene expression is regulated by sensing its intracellular concentration.
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Affiliation(s)
- Kiyoaki Arakawa
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto, Japan
| | - Junta Yanai
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto, Japan
| | - Kunihiko Watanabe
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto, Japan
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4
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Enhanced Production Process of Recombinant Mature Serratiopeptidase in Escherichia coli Using Fed-Batch Culture by Self-Proteolytic Activity of Fusion Protein. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8070307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microbial enzymes are increasingly finding applications as therapeutics due to their targeted activity and minimal side effects. Serratiopeptidase, also known as a miracle enzyme, has already proved its potential as an anti-inflammatory, mucolytic, fibrinolytic, analgesic in many studies. A cost effective, bioreactor level production process has been described here comprising of the fed-batch fermentation to produce recombinant serratiopeptidase protein expressed as a fusion construct. High yield of cell mass as well as protein was obtained by the optimization of bioreactor parameters. The downstream solubilization and purification processes were also optimized to achieve maximum yield of pure, active serratiopeptidase protein. A final yield of 2.5 ± 0.764 g L−1 of protein was obtained, having 8382 ± 291 U mg−1 of specific caseinolytic activity. Additionally, a novel, unexpected self-proteolytic activity of the enzyme that cleaves the N-terminal 6× His-SUMO fusion tag along with the enzyme propeptide, thus yielding a mature serratiopeptidase, was also found.
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5
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The role of propeptide-mediated autoinhibition and intermolecular chaperone in the maturation of cognate catalytic domain in leucine aminopeptidase. J Struct Biol 2021; 213:107741. [PMID: 33989771 DOI: 10.1016/j.jsb.2021.107741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/23/2021] [Accepted: 05/03/2021] [Indexed: 11/24/2022]
Abstract
Leucyl aminopeptidase A from Aspergillus oryzae RIB40 (AO-LapA) is an exo-acting peptidase, widely utilised in food debittering applications. AO-LapA is secreted as a zymogen by the host and requires enzymatic cleavage of the autoinhibitory propeptide to reveal its full activity. Scarcity of structural data of zymogen aminopeptidases hampers a better understanding of the details of their molecular action of autoinhibition and how this might be utilised to improve the properties of such enzymes by recombinant methods for more effective bioprocessing. To address this gap in the literature, herein we report high-resolution crystal structures of recombinantly expressed AO-LapA precursor (AO-proLapA), mature LapA (AO-mLapA) and AO-mLapA complexed with reaction product l-leucine (AO-mLapA-Leu), all purified from Pichia pastoris culture supernatant. Our structures reveal a plausible molecular mechanism of LapA catalytic domain autoinhibition by propeptide and highlights the role of intramolecular chaperone (IMC). Our data suggest an absolute requirement for IMC in the maturation of cognate catalytic domain of AO-LapA. This observation is reinforced by our expression and refolding data of catalytic domain only (AO-refLapA) from Escherichia coli inclusion bodies, revealing a limited active conformation. Our work supports the notion that known synthetic aminopeptidase inhibitors and substrates mimic key polar contacts between propeptide and corresponding catalytic domain, demonstrated in our AO-proLapA zymogen crystal structure. Furthermore, understanding the atomic details of the autoinhibitory mechanism of cognate catalytic domains by native propeptides has wider reaching implications toward synthetic production of more effective inhibitors of bimetallic aminopeptidases and other dizinc enzymes that share an analogous reaction mechanism.
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6
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Scheithauer L, Thiem S, Schmelz S, Dellmann A, Büssow K, Brouwer RMHJ, Ünal CM, Blankenfeldt W, Steinert M. Zinc metalloprotease ProA of Legionella pneumophila increases alveolar septal thickness in human lung tissue explants by collagen IV degradation. Cell Microbiol 2021; 23:e13313. [PMID: 33491325 DOI: 10.1111/cmi.13313] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 01/25/2023]
Abstract
ProA is a secreted zinc metalloprotease of Legionella pneumophila causing lung damage in animal models of Legionnaires' disease. Here we demonstrate that ProA promotes infection of human lung tissue explants (HLTEs) and dissect the contribution to cell type specific replication and extracellular virulence mechanisms. For the first time, we reveal that co-incubation of HLTEs with purified ProA causes a significant increase of the alveolar septal thickness. This destruction of connective tissue fibres was further substantiated by collagen IV degradation assays. The moderate attenuation of a proA-negative mutant in A549 epithelial cells and THP-1 macrophages suggests that effects of ProA in tissue mainly result from extracellular activity. Correspondingly, ProA contributes to dissemination and serum resistance of the pathogen, which further expands the versatile substrate spectrum of this thermolysin-like protease. The crystal structure of ProA at 1.48 Å resolution showed high congruence to pseudolysin of Pseudomonas aeruginosa, but revealed deviations in flexible loops, the substrate binding pocket S1 ' and the repertoire of cofactors, by which ProA can be distinguished from respective homologues. In sum, this work specified virulence features of ProA at different organisational levels by zooming in from histopathological effects in human lung tissue to atomic details of the protease substrate determination.
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Affiliation(s)
- Lina Scheithauer
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stefanie Thiem
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stefan Schmelz
- Structure and Function of Proteins, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Ansgar Dellmann
- Institut für Pathologie, Städtisches Klinikum Braunschweig gGmbH, Braunschweig, Germany
| | - Konrad Büssow
- Structure and Function of Proteins, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - René M H J Brouwer
- Herz-, Thorax-, Gefäßchirurgie, Städtisches Klinikum Braunschweig gGmbH, Braunschweig, Germany.,Institut für Psychologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Can M Ünal
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Fen Fakültesi, Turkish-German University, Istanbul, Turkey
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
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7
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Chang SC, Lee CY. Quorum-Sensing Regulator OpaR Directly Represses Seven Protease Genes in Vibrio parahaemolyticus. Front Microbiol 2020; 11:534692. [PMID: 33193123 PMCID: PMC7658014 DOI: 10.3389/fmicb.2020.534692] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/08/2020] [Indexed: 01/25/2023] Open
Abstract
Proteases play a key role in numerous bacterial physiological events. Microbial proteases are used in the pharmaceutical industry and in biomedical applications. The genus Vibrio comprises protease-producing bacteria. Proteases transform polypeptides into shorter chains for easier utilization. They also function as a virulence factor in pathogens. The mechanism by which protease genes are regulated in Vibrio parahaemolyticus, an emerging world-wide human pathogen, however, still remains unclear. Quorum sensing is the communication system of bacteria. OpaR is the master quorum-sensing regulator in V. parahaemolyticus. In the present study, quantitative reverse transcriptase-polymerase chain reaction and protease gene promoter-fusion reporter assays revealed that OpaR represses seven protease genes—three metalloprotease genes and four serine protease genes—which are involved in environmental survival and bacterial virulence. Furthermore, the electrophoresis mobility shift assay demonstrated that OpaR is bound directly to the promoter region of each of the seven protease genes. DNase I footprinting identified the sequence of these OpaR-binding sites. ChIP-seq analyses revealed 435 and 835 OpaR-binding sites in the late-log and stationary phases, respectively. These OpaR-binding sequences indicated a conserved OpaR-binding motif: TATTGATAAAATTATCAATA. These results advance our understanding of the protease regulation system in V. parahaemolyticus. This study is the first to reveal the OpaR motif within V. parahaemolyticus in vivo, using ChIP-seq, and to provide a database for OpaR direct regulon.
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Affiliation(s)
- San-Chi Chang
- Microbiology Laboratory, Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Chia-Yin Lee
- Microbiology Laboratory, Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
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8
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Wang Y, Liu BX, Cheng JH, Su HN, Sun HM, Li CY, Yang L, Shen QT, Zhang YZ, Zhang X, Chen XL. Characterization of a New M4 Metalloprotease With Collagen-Swelling Ability From Marine Vibrio pomeroyi Strain 12613. Front Microbiol 2020; 11:1868. [PMID: 32849455 PMCID: PMC7426729 DOI: 10.3389/fmicb.2020.01868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/16/2020] [Indexed: 01/22/2023] Open
Abstract
The ocean harbors a variety of bacteria that contain huge protease resources and offer a great potential for industrial and biotechnological applications. Here, we isolated a protease-secreting bacterium Vibrio pomeroyi strain 12613 from Atlantic seawater and purified a protease VP9 from strain 12613. VP9 was identified as a metalloprotease of the M4 family. VP9 could hydrolyze casein and gelatin but not elastin and collagen. With gelatin as the substrate, VP9 showed the highest activity at 40°C and pH 6.0–8.0. It was stable at temperatures of 50°C and less and in the range of pH 5.0–11.0. VP9 also had good tolerance to NaCl, non-ionic detergents, and organic solvent methanol. Unlike other M4 metalloproteases, VP9 has distinct collagen-swelling ability, and its collagen-swelling effect was concentration dependent. The relative expansion volume of collagen increased by approximately eightfold after treatment with 10 μM VP9 at 37°C for 12 h. The collagen-swelling mechanism of VP9 on bovine-insoluble type I collagen was further studied. Atomic force microscopy observation and biochemical analyses showed that VP9 can degrade proteoglycans in collagen fibers, resulting in the release of collagen fibrils from collagen fibers and the swelling of the latter. In addition, VP9 can degrade glycoproteins, a non-collagenous constituent interacting with collagen in the skin. The characteristics of VP9, such as sufficient specificity toward proteoglycans and glycoproteins but no activity toward collagen, suggest its promising potential in the unhairing and fiber-opening processing in leather industry.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Bai-Xue Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jun-Hui Cheng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - He-Min Sun
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Chun-Yang Li
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Liuyan Yang
- School of Life Science and Technology, iHuman Institute, ShanghaiTech University, Shanghai, China.,Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Shanghai, China
| | - Qing-Tao Shen
- School of Life Science and Technology, iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xia Zhang
- Department of Molecular Biology, Qingdao Vland Biotech Inc., Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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9
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Okai M, Onoue C, Tsuda R, Ishigami C, Yoshida-Mishima C, Urano N, Kato C, Ishida M. Q301P mutant of Vibrio PR protease affects activities under low-temperature and high-pressure conditions. J Biosci Bioeng 2020; 130:341-346. [PMID: 32611521 DOI: 10.1016/j.jbiosc.2020.05.011] [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: 03/30/2020] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 10/24/2022]
Abstract
We characterized a protease of the M4 family from the cold-adapted Vibrio sp. Pr21 that was isolated from seawater at 320-m deep in Sagami Bay, Japan, and named it as PR protease based on the strain name Pr21. The PR protease had activities at 10-60 °C and 0.1-350 MPa, with the optimal temperature and pressure at 40 °C and 250 MPa. The mutant 10C9 (Q301P) obtained by error-prone PCR had higher activities than the wild-type enzyme at 10-60 °C, and the Q301P mutation contributed to the increase of the activity. The specific activity value of 10C9 was also higher than that of the wild-type enzyme at 0.1-200 MPa, but the specific activity ratios (1.28-1.59) of 10C9/wild-type enzyme at 50-200 MPa at 30 °C were smaller than those at 10-60 °C (1.73-4.39) at 0.1 MPa. The catalytic efficiency value of 10C9 was lower than that of the wild-type enzyme at 200 MPa. The homology models of PR protease suggested that the side chain of Q301 was hydrogen-bonded with the carbonyl oxygen atom of the main chain of N234 in the wild-type enzyme, and P301 had no contact with N234 in 10C9. The break of the hydrogen bond in 10C9 might strengthen the increase of the flexibility of the β-sheet near the substrate binding pocket under high-temperature conditions, whereas the flexibility of the β-sheet in 10C9 might be moderately increased compared to that in the wild-type enzyme under high-pressure conditions.
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Affiliation(s)
- Masahiko Okai
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Chiori Onoue
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Ryo Tsuda
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Chihiro Ishigami
- School of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Chie Yoshida-Mishima
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Naoto Urano
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Chiaki Kato
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa 237-0061, Japan
| | - Masami Ishida
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan.
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10
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Belluzo BS, Abriata LA, Giannini E, Mihovilcevic D, Dal Peraro M, Llarrull LI. An experiment-informed signal transduction model for the role of the Staphylococcus aureus MecR1 protein in β-lactam resistance. Sci Rep 2019; 9:19558. [PMID: 31862951 PMCID: PMC6925264 DOI: 10.1038/s41598-019-55923-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 12/04/2019] [Indexed: 11/13/2022] Open
Abstract
The treatment of hospital- and community-associated infections by methicillin-resistant Staphylococcus aureus (MRSA) is a perpetual challenge. This Gram-positive bacterium is resistant specifically to β-lactam antibiotics, and generally to many other antibacterial agents. Its resistance mechanisms to β-lactam antibiotics are activated only when the bacterium encounters a β-lactam. This activation is regulated by the transmembrane sensor/signal transducer proteins BlaR1 and MecR1. Neither the transmembrane/metalloprotease domain, nor the complete MecR1 and BlaR1 proteins, are isolatable for mechanistic study. Here we propose a model for full-length MecR1 based on homology modeling, residue coevolution data, a new extensive experimental mapping of transmembrane topology, partial structures, molecular simulations, and available NMR data. Our model defines the metalloprotease domain as a hydrophilic transmembrane chamber effectively sealed by the apo-sensor domain. It proposes that the amphipathic helices inserted into the gluzincin domain constitute the route for transmission of the β-lactam-binding event in the extracellular sensor domain, to the intracellular and membrane-embedded zinc-containing active site. From here, we discuss possible routes for subsequent activation of proteolytic action. This study provides the first coherent model of the structure of MecR1, opening routes for future functional investigations on how β-lactam binding culminates in the proteolytic degradation of MecI.
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Affiliation(s)
- Bruno S Belluzo
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, 2000, Rosario, Argentina
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling - École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Estefanía Giannini
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, 2000, Rosario, Argentina
| | - Damila Mihovilcevic
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, 2000, Rosario, Argentina
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling - École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
| | - Leticia I Llarrull
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, 2000, Rosario, Argentina. .,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, 2000, Rosario, Argentina.
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11
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YpeB dimerization may be required to stabilize SleB for effective germination of Bacillus anthracis spores. BMC Microbiol 2019; 19:169. [PMID: 31349814 PMCID: PMC6660665 DOI: 10.1186/s12866-019-1544-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/18/2019] [Indexed: 12/16/2022] Open
Abstract
Background Bacillus cells faced with unfavorable environmental conditions undergo an asymmetric division process ultimately leading to the formation of the bacterial spore. In some instances the spore serves as an infectious agent; such is the case with the spore of Bacillus anthracis and the disease anthrax. Spores are resistant to a variety of environment conditions including traditional decontamination techniques due to the formation of specialized cellular structures. One such structure, the spore cortex, is a thick layer of modified peptidoglycan that contributes to spore dormancy through maintenance of the dehydrated state of the spore core. During spore germination, degradation of the cortex is required to facilitate complete hydration of the core and a return to vegetative growth. Degradation of the cortex is accomplished through the action of germination-specific lytic enzymes. One of these enzymes, SleB, has been previously shown to require the presence of the YpeB protein for its stable incorporation and subsequent function in spores of B. anthracis. The focus of the present study is to identify protein interactions of YpeB through in vivo chemical cross-linking and two-hybrid analysis. Results Conserved residues within YpeB PepSY domains were altered to facilitate implementation of a site-specific chemical cross-linker, 4-Azidophenacyl bromide. Analyses of crosslinked-spore extracts suggests that YpeB exists as a dimer or larger multimer within the spore, potentially mediated through interactions of the C-terminal domains. Spores expressing stable truncated forms of YpeB were crosslinked and corresponding truncated dimers were detected. Further characterization of individual YpeB domains using bacterial two-hybrid analysis indicated a possible role for both N-and C-terminal domains in YpeB oligomerization. Conclusions The YpeB protein likely exists as dimer or higher-order multimer in the dormant spore. Both the N- and C-terminal YpeB domains contribute to multimerization. SleB likely also exists as an oligomer, and SleB and YpeB may be found together within a protein complex. Disassembly of this complex during spore germination likely allows SleB to become active in spore cortex degradation. Further study of this protein complex may contribute to the development of methods to inhibit or stimulate germination, allowing more effective spore decontamination. Electronic supplementary material The online version of this article (10.1186/s12866-019-1544-1) contains supplementary material, which is available to authorized users.
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12
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Chen XL, Yang JY, Zheng XY, Sheng Q, Wang L, Zhang YZ, Qin QL, Zhang XY. Tripeptides From Casein Are Signal Molecules to Induce the Expression of the Extracellular Protease MCP-01 Gene in Marine Bacterium Pseudoalteromonas sp. SM9913. Front Microbiol 2019; 10:1354. [PMID: 31293532 PMCID: PMC6606773 DOI: 10.3389/fmicb.2019.01354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/31/2019] [Indexed: 01/29/2023] Open
Abstract
Microbial extracellular proteases play crucial roles in marine protein degradation and nitrogen recycling. Although a large number of marine bacteria are found to produce extracellular proteases, it is still unknown how marine bacteria respond to environmental proteins to activate the expression of genes encoding extracellular proteases. The inducing signal molecule for marine bacterial extracellular proteases has never been identified. In this study, we identified tripeptides as the inducing signal molecules for the extracellular protease MCP-01 of the deep-sea bacterium Pseudoalteromonas sp. SM9913. We found that casein, but not casamino acids, can induce the gene expression and synthesis of MCP-01, suggesting that peptides rather than amino acids derived from casein induce the gene expression and synthesis of MCP-01 in SM9913. Then, casein was hydrolyzed by SM9913 extracellular proteases, and the peptides with inducing effect were isolated and characterized. Finally, four tripeptides, SPP, RYP, RQF and FRQ, were shown to have significant inducing effect on the expression of MCP-01 gene, indicating that they are likely the inducing signal molecules for the expression of protease MCP-01 gene in SM9913. This study sheds light on the induction mechanism for the gene expression and biosynthesis of marine microbial extracellular proteases, which is helpful in better understanding the adaptation of bacteria to deep-sea sedimental environment.
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Affiliation(s)
- Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jin-Yu Yang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Institute of Agro-Food Science and Technology, Shandong Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing Technology of Shandong Province/Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Xiao-Yu Zheng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Qi Sheng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Lei Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
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13
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Howell M, Dumitrescu DG, Blankenship LR, Herkert D, Hatzios SK. Functional characterization of a subtilisin-like serine protease from Vibrio cholerae. J Biol Chem 2019; 294:9888-9900. [PMID: 31076508 DOI: 10.1074/jbc.ra119.007745] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/07/2019] [Indexed: 11/06/2022] Open
Abstract
Vibrio cholerae, the causative agent of the human diarrheal disease cholera, exports numerous enzymes that facilitate its adaptation to both intestinal and aquatic niches. These secreted enzymes can mediate nutrient acquisition, biofilm assembly, and V. cholerae interactions with its host. We recently identified a V. cholerae-secreted serine protease, IvaP, that is active in V. cholerae-infected rabbits and human choleric stool. IvaP alters the activity of several host and pathogen enzymes in the gut and, along with other secreted V. cholerae proteases, decreases binding of intelectin, an intestinal carbohydrate-binding protein, to V. cholerae in vivo IvaP bears homology to subtilisin-like enzymes, a large family of serine proteases primarily comprised of secreted endopeptidases. Following secretion, IvaP is cleaved at least three times to yield a truncated enzyme with serine hydrolase activity, yet little is known about the mechanism of extracellular maturation. Here, we show that IvaP maturation requires a series of sequential N- and C-terminal cleavage events congruent with the enzyme's mosaic protein domain structure. Using a catalytically inactive reporter protein, we determined that IvaP can be partially processed in trans, but intramolecular proteolysis is most likely required to generate the mature enzyme. Unlike many other subtilisin-like enzymes, the IvaP cleavage pattern is consistent with stepwise processing of the N-terminal propeptide, which could temporarily inhibit, and be cleaved by, the purified enzyme. Furthermore, IvaP was able to cleave purified intelectin, which inhibited intelectin binding to V. cholerae These results suggest that IvaP plays a role in modulating intelectin-V. cholerae interactions.
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Affiliation(s)
- Matthew Howell
- From the Departments of Molecular, Cellular, and Developmental Biology and.,the Microbial Sciences Institute, Yale University, West Haven, Connecticut 06516
| | - Daniel G Dumitrescu
- From the Departments of Molecular, Cellular, and Developmental Biology and.,the Microbial Sciences Institute, Yale University, West Haven, Connecticut 06516.,Chemistry, Yale University, New Haven, Connecticut 06511 and
| | - Lauren R Blankenship
- From the Departments of Molecular, Cellular, and Developmental Biology and.,the Microbial Sciences Institute, Yale University, West Haven, Connecticut 06516
| | - Darby Herkert
- From the Departments of Molecular, Cellular, and Developmental Biology and.,the Microbial Sciences Institute, Yale University, West Haven, Connecticut 06516
| | - Stavroula K Hatzios
- From the Departments of Molecular, Cellular, and Developmental Biology and .,the Microbial Sciences Institute, Yale University, West Haven, Connecticut 06516.,Chemistry, Yale University, New Haven, Connecticut 06511 and
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14
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Towards functional characterization of archaeal genomic dark matter. Biochem Soc Trans 2019; 47:389-398. [PMID: 30710061 PMCID: PMC6393860 DOI: 10.1042/bst20180560] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/08/2019] [Accepted: 01/09/2019] [Indexed: 01/07/2023]
Abstract
A substantial fraction of archaeal genes, from ∼30% to as much as 80%, encode ‘hypothetical' proteins or genomic ‘dark matter'. Archaeal genomes typically contain a higher fraction of dark matter compared with bacterial genomes, primarily, because isolation and cultivation of most archaea in the laboratory, and accordingly, experimental characterization of archaeal genes, are difficult. In the present study, we present quantitative characteristics of the archaeal genomic dark matter and discuss comparative genomic approaches for functional prediction for ‘hypothetical' proteins. We propose a list of top priority candidates for experimental characterization with a broad distribution among archaea and those that are characteristic of poorly studied major archaeal groups such as Thaumarchaea, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota) and Asgard.
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15
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Fiebig D, Storka J, Roeder M, Meyners C, Schmelz S, Blankenfeldt W, Scrima A, Kolmar H, Fuchsbauer HL. Destructive twisting of neutral metalloproteases: the catalysis mechanism of the Dispase autolysis-inducing protein from Streptomyces mobaraensis DSM 40487. FEBS J 2018; 285:4246-4264. [PMID: 30171661 DOI: 10.1111/febs.14647] [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: 04/27/2018] [Revised: 07/27/2018] [Accepted: 08/28/2018] [Indexed: 12/18/2022]
Abstract
The Dispase autolysis-inducing protein (DAIP) is produced by Streptomyces mobaraensis to disarm neutral metalloproteases by decomposition. The absence of a catalytic protease domain led to the assumption that the seven-bladed β-propeller protein DAIP causes structural modifications, thereby triggering autolysis. Determination of protein complexes consisting of DAIP and thermolysin or DAIP and a nonfunctional E138A bacillolysin variant supported this postulation. Protein twisting was indicated by DAIP-mediated inhibition of thermolysin while bacillolysin underwent immediate autolysis under the same conditions. Interestingly, an increase in SYPRO orange fluorescence allowed tracking of the fast degradation process. Similarly rapid autolysis of thermolysin mediated by DAIP was only observed upon the addition of amphiphilic compounds, which probably amplify the induced structural changes. DAIP further caused degradation of FITC-labeled E138A bacillolysin by trypsin, as monitored by a linear decrease in fluorescence polarization. The kinetic model, calculated from the obtained data, suggested a three-step mechanism defined by (a) fast DAIP-metalloprotease complex formation, (b) slower DAIP-mediated protein twisting, and (c) fragmentation. These results were substantiated by crystallized DAIP attached to a C-terminal helix fragment of thermolysin. Structural superposition of the complex with thermolysin is indicative of a conformational change upon binding to DAIP. Importantly, the majority of metalloproteases, also including homologs from various pathogens, are highly conserved at the autolysis-prone peptide bonds, suggesting their susceptibility to DAIP-mediated decomposition, which may offer opportunities for pharmaceutical applications. DATABASES: The atomic coordinates and structure factors (PDB ID: 6FHP) have been deposited in the Protein Data Bank (http://www.pdb.org/). ENZYMES: Aureolysin, EC 3.4.24.29; bacillolysin (Dispase, Gentlyase), EC 3.4.24.28; lasB (elastase), EC 3.4.24.4; subtilisin, EC 3.4.21.62; thermolysin, EC 3.4.24.27; transglutaminase, EC 2.3.2.13; trypsin, EC 3.4.21.4; vibriolysin (hemagglutinin(HA)/protease), EC 3.4.24.25.
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Affiliation(s)
- David Fiebig
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany.,Department of Chemistry, Technische Universität Darmstadt, Germany
| | - Juliana Storka
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany
| | - Markus Roeder
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany
| | - Christian Meyners
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany
| | - Stefan Schmelz
- Structural Biology of Autophagy Group, Department Structure and Function of Proteins, Helmholtz-Centre for Infection Research, Braunschweig, Germany.,Department Structure and Function of Proteins, Helmholtz-Centre for Infection Research, Braunschweig, Germany
| | - Wulf Blankenfeldt
- Department Structure and Function of Proteins, Helmholtz-Centre for Infection Research, Braunschweig, Germany.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Germany
| | - Andrea Scrima
- Structural Biology of Autophagy Group, Department Structure and Function of Proteins, Helmholtz-Centre for Infection Research, Braunschweig, Germany.,Department Structure and Function of Proteins, Helmholtz-Centre for Infection Research, Braunschweig, Germany
| | - Harald Kolmar
- Department of Chemistry, Technische Universität Darmstadt, Germany
| | - Hans-Lothar Fuchsbauer
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences of Darmstadt, Germany
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16
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Na Pombejra S, Jamklang M, Uhrig JP, Vu K, Gelli A. The structure-function analysis of the Mpr1 metalloprotease determinants of activity during migration of fungal cells across the blood-brain barrier. PLoS One 2018; 13:e0203020. [PMID: 30161190 PMCID: PMC6117016 DOI: 10.1371/journal.pone.0203020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 08/14/2018] [Indexed: 12/21/2022] Open
Abstract
Cryptococcal meningoencephalitis, the most common form of cryptococcosis, is caused by the opportunistic fungal pathogen, Cryptococcus neoformans. Molecular strategies used by C. neoformans to invade the central nervous system (CNS) have been the focus of several studies. Recently, the role of a novel secreted metalloprotease (Mpr1) in the pathogenicity of C. neoformans was confirmed by studies demonstrating that Mpr1 mediated the migration of fungal cells into the CNS. Given this central function, the aim here was to identify the molecular determinants of Mpr1 activity and resolve their role in the migration of cryptococci across the blood-brain barrier (BBB). The Mpr1 protein belongs to an understudied group of metalloproteases of the M36 class of fungalysins unique to fungi. They are generally synthesized as propeptides with fairly long prodomains and highly conserved regions within their catalytic core. Through structure-function analysis of Mpr1, our study identified the prodomain cleavage sites of Mpr1 and demonstrated that when mutated, the prodomain appears to remain attached to the catalytic C-terminus of Mpr1 rendering a nonfunctional Mpr1 protein and an inability for cryptococci to cross the BBB. We found that proteolytic activity of Mpr1 was dependent on the coordination of zinc with two histidine residues in the active site of Mpr1, since amino acid substitutions in the HExxH motif abolished Mpr1 proteolytic activity and prevented the migration of cryptococci across the BBB. A phylogenetic analysis of Mpr1 revealed a distinct pattern likely reflecting the neurotropic nature of C. neoformans and the specific function of Mpr1 in breaching the BBB. This study contributes to a deeper understanding of the molecular regulation of Mpr1 activity and may lead to the development of specific inhibitors that could be used to restrict fungal penetration of the CNS and thus prevent cryptococcal meningoencephalitis-related deaths.
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Affiliation(s)
- Sarisa Na Pombejra
- Department of Pharmacology, School of Medicine, University of California, Davis, California, United States of America
| | - Mantana Jamklang
- Department of Pharmacology, School of Medicine, University of California, Davis, California, United States of America
| | - John P. Uhrig
- Department of Pharmacology, School of Medicine, University of California, Davis, California, United States of America
| | - Kiem Vu
- Department of Pharmacology, School of Medicine, University of California, Davis, California, United States of America
| | - Angie Gelli
- Department of Pharmacology, School of Medicine, University of California, Davis, California, United States of America
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17
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Meng F, Chen R, Zhu X, Lu Y, Nie T, Lu F, Lu Z. Newly Effective Milk-Clotting Enzyme from Bacillus subtilis and Its Application in Cheese Making. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:6162-6169. [PMID: 29847114 DOI: 10.1021/acs.jafc.8b01697] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A new effective milk-clotting enzyme (BY-1) was produced from Bacillus subtilis PNG27. The analysis of MALDI-TOF-MS/MS showed that it belongs to the peptidase M4 family and had 521 amino acids. It had a higher proteolytic activity on α-casein, β-casein, κ-casein, and β-lactoglobulin than Rennet. Besides, BY-1 could decrease the curd time of poor-curd, UHT, refrigerated, and reconstituted milk. Moreover, two kinds of cheese were, respectively, made by BY-1 and Rennet. The results showed that the protein hydrolysates (WSN, CTA-N, and PTA-N) of cheese made by BY-1 were higher than that of Rennet. Flavor compounds (28) were detected from the cheese made by BY-1, whereas 15 compounds were detected from Rennet. The sensory evaluation indicated that the cheese produced by BY-1 exhibited better flavor and overall acceptability. Therefore, BY-1 could be widely used in cheese production.
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Affiliation(s)
- Fanqiang Meng
- College of Food Science and Technology , Nanjing Agriculture University , 1 Weigang , Nanjing 210095 , China
| | - Rui Chen
- College of Food Science and Technology , Nanjing Agriculture University , 1 Weigang , Nanjing 210095 , China
| | - Xiaoyu Zhu
- College of Food Science and Technology , Nanjing Agriculture University , 1 Weigang , Nanjing 210095 , China
| | - Yingjian Lu
- Department of Nutrition and Food Science , University of Maryland , College Park , Maryland 20742 , United States
| | - Ting Nie
- College of Food Science and Technology , Nanjing Agriculture University , 1 Weigang , Nanjing 210095 , China
| | - Fengxia Lu
- College of Food Science and Technology , Nanjing Agriculture University , 1 Weigang , Nanjing 210095 , China
| | - Zhaoxin Lu
- College of Food Science and Technology , Nanjing Agriculture University , 1 Weigang , Nanjing 210095 , China
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18
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Chura-Chambi RM, Fraga TR, da Silva LB, Yamamoto BB, Isaac L, Barbosa AS, Morganti L. Leptospira interrogans thermolysin refolded at high pressure and alkaline pH displays proteolytic activity against complement C3. ACTA ACUST UNITED AC 2018; 19:e00266. [PMID: 29992100 PMCID: PMC6036645 DOI: 10.1016/j.btre.2018.e00266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/23/2018] [Accepted: 06/16/2018] [Indexed: 11/30/2022]
Abstract
Enzymes from the thermolysin family are crucial factors in the pathogenesis of several diseases caused by bacteria and are potential targets for therapeutic interventions. Thermolysin encoded by the gene LIC13322 of the causative agent of leptospirosis, Leptospira interrogans, was shown to cleave proteins from the Complement System. However, the production of this recombinant protein using traditional refolding processes with high levels of denaturing reagents for thermolysin inclusion bodies (TL-IBs) solubilization results in poor recovery and low proteolytic activity probably due to improper refolding of the protein. Based on the assumption that leptospiral proteases play a crucial role during infection, the aim of this work was to obtain a functional recombinant thermolysin for future studies on the role of these metalloproteases on leptospiral infection. The association of high hydrostatic pressure (HHP) and alkaline pH was utilized for thermolysin refolding. Incubation of a suspension of TL-IBs at HHP and a pH of 11.0 is non-denaturing but effective for thermolysin solubilization. Soluble protein does not reaggregate by dialysis to pH 8.0. A volumetric yield of 46 mg thermolysin/L of bacterial culture and a yield of near 100% in relation to the total thermolysin present in TL-IBs were obtained. SEC-purified thermolysin suffers fragmentation, likely due to autoproteolysis and presents proteolytic activity against complement C3 α-chain, possibly by a generation of a C3b-like molecule. The proteolytic activity of thermolysin against C3 was time and dose-dependent. The experience gained in this study shall help to establish efficient HHP-based processes for refolding of bioactive proteins from IBs.
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Affiliation(s)
- Rosa Maria Chura-Chambi
- Instituto de Pesquisas Energéticas e Nucleares IPEN-CNEN/SP, Centro de Biotecnologia, Av. Prof. Lineu Prestes, 2242, CEP 05508-000, São Paulo, SP, Brazil
| | - Tatiana Rodrigues Fraga
- Instituto de Ciências Biomédicas, Universidade de São Paulo, Departamento de Imunologia, Av. Prof. Lineu Prestes, 1374, CEP 05508-900, São Paulo, SP, Brazil
| | - Ludmila Bezerra da Silva
- Instituto Butantan, Laboratório de Bacteriologia, Av. Vital Brasil, 1500, CEP 05503-900, São Paulo, SP, Brazil
| | - Bruno Bernardi Yamamoto
- Instituto Butantan, Laboratório de Bacteriologia, Av. Vital Brasil, 1500, CEP 05503-900, São Paulo, SP, Brazil
| | - Lourdes Isaac
- Instituto de Ciências Biomédicas, Universidade de São Paulo, Departamento de Imunologia, Av. Prof. Lineu Prestes, 1374, CEP 05508-900, São Paulo, SP, Brazil
| | - Angela Silva Barbosa
- Instituto Butantan, Laboratório de Bacteriologia, Av. Vital Brasil, 1500, CEP 05503-900, São Paulo, SP, Brazil
| | - Ligia Morganti
- Instituto de Pesquisas Energéticas e Nucleares IPEN-CNEN/SP, Centro de Biotecnologia, Av. Prof. Lineu Prestes, 2242, CEP 05508-000, São Paulo, SP, Brazil
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19
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Jeszeová L, Bauerová-Hlinková V, Baráth P, Puškárová A, Bučková M, Kraková L, Pangallo D. Biochemical and proteomic characterization of the extracellular enzymatic preparate of Exiguobacterium undae, suitable for efficient animal glue removal. Appl Microbiol Biotechnol 2018; 102:6525-6536. [DOI: 10.1007/s00253-018-9105-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 12/13/2022]
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20
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Arolas JL, Goulas T, Cuppari A, Gomis-Rüth FX. Multiple Architectures and Mechanisms of Latency in Metallopeptidase Zymogens. Chem Rev 2018; 118:5581-5597. [PMID: 29775286 DOI: 10.1021/acs.chemrev.8b00030] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Metallopeptidases cleave polypeptides bound in the active-site cleft of catalytic domains through a general base/acid mechanism. This involves a solvent molecule bound to a catalytic zinc and general regulation of the mechanism through zymogen-based latency. Sixty reported structures from 11 metallopeptidase families reveal that prosegments, mostly N-terminal of the catalytic domain, block the cleft regardless of their size. Prosegments may be peptides (5-14 residues), which are only structured within the zymogens, or large moieties (<227 residues) of one or two folded domains. While some prosegments globally shield the catalytic domain through a few contacts, others specifically run across the cleft in the same or opposite direction as a substrate, making numerous interactions. Some prosegments block the zinc by replacing the solvent with particular side chains, while others use terminal α-amino or carboxylate groups. Overall, metallopeptidase zymogens employ disparate mechanisms that diverge even within families, which supports that latency is less conserved than catalysis.
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Affiliation(s)
- Joan L Arolas
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
| | - Theodoros Goulas
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
| | - Anna Cuppari
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
| | - F Xavier Gomis-Rüth
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
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21
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Huang J, Zeng B, Liu D, Wu R, Zhang J, Liao B, He H, Bian F. Classification and structural insight into vibriolysin-like proteases of Vibrio pathogenicity. Microb Pathog 2018; 117:335-340. [PMID: 29510206 DOI: 10.1016/j.micpath.2018.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 01/18/2018] [Accepted: 03/02/2018] [Indexed: 12/17/2022]
Abstract
Vibriolysin-like proteases (VLPs) are important virulence agents in the arsenal of Vibrio causing instant cytotoxic effects during infection. Most of Vibrio secreted VLPs show serious pathogenicity, while some species of Vibrio with VLPs are non-pathogenic, like Vibrio tasmaniensis and Vibrio pacinii. To investigate the relation between VLPs and Vibrio pathogenicity, one phylogenetic tree of VLPs was constructed and compared consensus sequences at the N-terminus of VLPs. Based on these results, VLPs were defined into nine phylogenetic clades. Pathogenicity analysis of Vibrio showed that Vibrio species with VLPs III, VI, VII or VIII are serious pathogenic bacteria, while species with VLPs I, II, IV or IX are opportunistic pathogens. Multiple sequence alignment showed that the N-terminal 5-16 nucleotides of each clade are highly conservative. Topological analysis of VLPs exhibited the structural differences in N-terminal regions of each VLP clade. These results suggest that structure of N-terminus might play a key role in the pathogenicity of VLPs. Our findings give new insights into the classification of VLPs and the relationship between VLPs and Vibrio pathogenicity.
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Affiliation(s)
- JiaFeng Huang
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, China
| | - BingQi Zeng
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, China
| | - Dan Liu
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, China
| | - RiBang Wu
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, China
| | - Jiang Zhang
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, China
| | - BinQiang Liao
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, China
| | - HaiLun He
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, China.
| | - Fei Bian
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250000, China.
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22
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Chen D, Wang D, Xu C, Chen C, Li J, Wu W, Huang X, Xie H. Nematicidal protease genes screened from a soil metagenomic library to control Radopholus similis mediated by Pseudomonas fluorescens pf36. Appl Microbiol Biotechnol 2018; 102:3301-3314. [DOI: 10.1007/s00253-018-8869-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/25/2018] [Accepted: 02/10/2018] [Indexed: 12/01/2022]
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23
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Preparation and functional evaluation of collagen oligopeptide-rich hydrolysate from fish skin with the serine collagenolytic protease from Pseudoalteromonas sp. SM9913. Sci Rep 2017; 7:15716. [PMID: 29146927 PMCID: PMC5691207 DOI: 10.1038/s41598-017-15971-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 11/06/2017] [Indexed: 11/09/2022] Open
Abstract
Although several serine collagenolytic proteases from bacteria were reported, none has been used to prepare bioactive collagen peptides. MCP-01 is the most abundant extracellular protease of deep-sea Pseudoalteromonas sp. SM9913 and is a serine collagenolytic protease with high efficiency on fish collagen hydrolysis. Here, we set up a pilot scale process to ferment SM9913 for extracellular protease production. With SM9913 extracellular protease as a tool, a process to prepare collagen oligopeptide-rich hydrolysate from codfish skin was set up, which was further scaled up to pilot (100 L) and plant (2000 L) levels with yields >66%. The hydrolysates from laboratory-, pilot- and plant-scales had quite similar quality, containing ~95% peptides with molecular weights lower than 3000 Da and approximately 60% lower than 1000 Da, in which collagen oilgopeptides account for approximately 95%. Bioactivity analyses showed that the hydrolysate had moisture-retention ability, antioxidant activity, and promoting effect on cell viability of human dermal fibroblasts. Safety evaluation showed that the hydrolysate was nontoxic and nonirritating to skin. Therefore, SM9913 extracellular protease is a good enzyme to prepare bioactive oligopeptides from fish skin. The results also suggest that the collagen oligopeptides-rich hydrolysate may have potentials in biomedical, functional food, pharmaceutical and cosmetic industries.
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Structural insight into a novel neutral metalloproteinase from Paenibacillus spp. BD3526: Implications for mechanisms of rapid inactivation and calcium-dependent stability. Int J Biol Macromol 2017; 95:1082-1090. [DOI: 10.1016/j.ijbiomac.2016.10.098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/21/2016] [Accepted: 10/27/2016] [Indexed: 11/23/2022]
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25
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Zhu F, Liu F, Wu B, He B. Efficient Extracellular Expression of Metalloprotease for Z-Aspartame Synthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:9631-9638. [PMID: 27966925 DOI: 10.1021/acs.jafc.6b04164] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Metalloprotease PT121 and its mutant Y114S (Tyr114 was substituted to Ser) are effective catalysts for the synthesis of Z-aspartame (Z-APM). This study presents the selection of a suitable signal peptide for improving expression and extracellular secretion of proteases PT121 and Y114S by Escherichia coli. Co-inducers containing IPTG and arabinose were used to promote protease production and cell growth. Under optimal conditions, the expression levels of PT121 and Y114S reached >500 mg/L, and the extracellular activity of PT121/Y114S accounted for 87/82% of the total activity of proteases. Surprisingly, purer protein was obtained in the supernatant, because arabinose reduced cell membrane permeability, avoiding cell lysis. Comparison of Z-APM synthesis and caseinolysis between proteases PT121 and Y114S showed that mutant Y114S presented remarkably higher activity of Z-APM synthesis and considerably lower activity of caseinolysis. The significant difference in substrate specificity renders these enzymes promising biocatalysts.
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Affiliation(s)
- Fucheng Zhu
- College of Biotechnology and Pharmaceutical Engineering and ‡School of Pharmaceutical Sciences, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
| | - Feng Liu
- College of Biotechnology and Pharmaceutical Engineering and ‡School of Pharmaceutical Sciences, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering and ‡School of Pharmaceutical Sciences, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
| | - Bingfang He
- College of Biotechnology and Pharmaceutical Engineering and ‡School of Pharmaceutical Sciences, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
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Huang J, Wu C, Liu D, Yang X, Wu R, Zhang J, Ma C, He H. C-terminal domains of bacterial proteases: structure, function and the biotechnological applications. J Appl Microbiol 2016; 122:12-22. [DOI: 10.1111/jam.13317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/21/2016] [Accepted: 10/03/2016] [Indexed: 12/28/2022]
Affiliation(s)
- J. Huang
- State Key Laboratory of Medical Genetics; School of Life Sciences; Central South University; Changsha China
| | - C. Wu
- State Key Laboratory of Medical Genetics; School of Life Sciences; Central South University; Changsha China
| | - D. Liu
- State Key Laboratory of Medical Genetics; School of Life Sciences; Central South University; Changsha China
| | - X. Yang
- State Key Laboratory of Medical Genetics; School of Life Sciences; Central South University; Changsha China
| | - R. Wu
- State Key Laboratory of Medical Genetics; School of Life Sciences; Central South University; Changsha China
| | - J. Zhang
- State Key Laboratory of Medical Genetics; School of Life Sciences; Central South University; Changsha China
| | - C. Ma
- State Key Laboratory of Medical Genetics; School of Life Sciences; Central South University; Changsha China
| | - H. He
- State Key Laboratory of Medical Genetics; School of Life Sciences; Central South University; Changsha China
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Liu R, Qiu L, Cheng Q, Zhang H, Wang L, Song L. Evidence for Cleavage of the Metalloprotease Vsm from Vibrio splendidus Strain JZ6 by an M20 Peptidase (PepT-like Protein) at Low Temperature. Front Microbiol 2016; 7:1684. [PMID: 27826294 PMCID: PMC5078317 DOI: 10.3389/fmicb.2016.01684] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/07/2016] [Indexed: 11/13/2022] Open
Abstract
Metalloprotease Vsm is a major extracellular virulence factor of Vibrio splendidus. The toxicity of Vsm from V. splendidus strain JZ6 has been characterized, and production of this virulence factor proved to be temperature-regulated. The present study provides evidence that two forms (JZE1 and JZE2) of Vsm protein exist in extracellular products (ECPs) of strain JZ6, and a significant conversion of these two forms was detected by SDS-PAGE and immunoblotting analyses of samples obtained from cells grown at 4, 10, 16, 20, 24, and 28°C. Mass spectroscopy confirmed that JZE1 was composed only of the peptidase_M4 domain of Vsm, and JZE2 contained both the PepSY domain and the peptidase_M4 domain. An M20 peptidase T-like protein (PepTL) was screened from the transcriptome data of strain JZ6, which was considered as a crucial molecule to produce the active Vsm (JZE1) by cleavage of the propeptide. Similar to that of Vsm, PepTL mRNA accumulation was highest at 4°C (836.82-fold of that at 28°C), decreased with increasing of temperature and reached its lowest level at 28°C. Deletion of the gene encoding the PepTL resulted in a mutant strain that did not produce the JZE1 cleavage product. The peptidase activity of PepTL recombinant protein (rPepTL) was confirmed by cleaving the Vsm in ECPs with an in vitro degradation reaction. These results demonstrate that PepTL participates in activating Vsm in strain JZ6 by proteolytic cleavage at low temperature.
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Affiliation(s)
- Rui Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences Qingdao, China
| | - Limei Qiu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences Qingdao, China
| | - Qi Cheng
- School of Food Science and Technology, Dalian Polytechnic University Dalian, China
| | - Huan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences Qingdao, China
| | - Lingling Wang
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University Dalian, China
| | - Linsheng Song
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University Dalian, China
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Bogdanović X, Palm GJ, Schwenteit J, Singh RK, Gudmundsdóttir BK, Hinrichs W. Structural evidence of intramolecular propeptide inhibition of the aspzincin metalloendopeptidase AsaP1. FEBS Lett 2016; 590:3280-94. [DOI: 10.1002/1873-3468.12356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 08/03/2016] [Accepted: 08/05/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Xenia Bogdanović
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
- Institute for Biochemistry and Molecular Biology; ZBMZ; Medical Faculty; University of Freiburg; Freiburg im Breisgau Germany
| | - Gottfried J. Palm
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
| | - Johanna Schwenteit
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
- Institute for Experimental Pathology; University of Iceland, Keldur; Reykjavík Iceland
| | - Rajesh K. Singh
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
| | | | - Winfried Hinrichs
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
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Yokoi KJ, Kuzuwa S, Iwasaki SI, Yamakawa A, Taketo A, Kodaira KI. Aureolysin of Staphylococcus warneri M accelerates its proteolytic cascade, and participates in biofilm formation. Biosci Biotechnol Biochem 2016; 80:1238-42. [PMID: 27008278 DOI: 10.1080/09168451.2016.1148576] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The aureolysin (Aur) gene of S. warneri M (aurWM) was cloned and sequenced. Analyses of the aurWM-inactivated mutant (S. warneri Mau) suggested that AurWM was probably associated with efficient processing of the PROM protease (homolog of V8/SspA serine protease), whereas considerable amount of mature-PROC protease (homolog of SspB cysteine protease) accumulated without AurWM. Additionally, AurWM appeared to affect biofilm formation in an uncertain suppressive way.
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Affiliation(s)
- Ken-Ji Yokoi
- a Food Biochemistry Division , Toyama prefectural Food Research Institute , Toyama , Japan
| | - Shinya Kuzuwa
- b Molecular Biology Group, Faculty of Engineering , Toyama University , Toyama , Japan
| | - Shu-Ichi Iwasaki
- c Quality Control Group , White Food Industry Co. Ltd. , Nanto , Japan
| | - Ayanori Yamakawa
- d Biochemistry Division, Department of Material Science , Wakayama National College of Technology , Wakayama , Japan
| | - Akira Taketo
- e Department of Applied Physics and Chemistry , Fukui University of Technology , Fukui , Japan
| | - Ken-Ichi Kodaira
- b Molecular Biology Group, Faculty of Engineering , Toyama University , Toyama , Japan
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Bian F, Yue S, Peng Z, Zhang X, Chen G, Yu J, Xuan N, Bi Y. A comprehensive alanine-scanning mutagenesis study reveals roles for salt bridges in the structure and activity of Pseudomonas aeruginosa elastase. PLoS One 2015; 10:e0121108. [PMID: 25815820 PMCID: PMC4376888 DOI: 10.1371/journal.pone.0121108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/12/2015] [Indexed: 11/18/2022] Open
Abstract
The relationship between salt bridges and stability/enzymatic activity is unclear. We studied this relationship by systematic alanine-scanning mutation analysis using the typical M4 family metalloprotease Pseudomonas aeruginosa elastase (PAE, also known as pseudolysin) as a model. Structural analysis revealed seven salt bridges in the PAE structure. We constructed ten mutants for six salt bridges. Among these mutants, six (Asp189Ala, Arg179Ala, Asp201Ala, Arg205Ala, Arg245Ala and Glu249Ala) were active and four (Asp168Ala, Arg198Ala, Arg253Ala, and Arg279Ala) were inactive. Five mutants were purified, and their catalytic efficiencies (kcat/Km), half-lives (t1/2) and thermal unfolding curves were compared with those of PAE. Mutants Asp189Ala and Arg179Ala both showed decreased thermal stabilities and increased activities, suggesting that the salt bridge Asp189-Arg179 stabilizes the protein at the expense of catalytic efficiency. In contrast, mutants Asp201Ala and Arg205Ala both showed slightly increased thermal stability and slightly decreased activity, suggesting that the salt bridge Asp201-Arg205 destabilizes the protein. Mutant Glu249Ala is related to a C-terminal salt bridge network and showed both decreased thermal stability and decreased activity. Furthermore, Glu249Ala showed a thermal unfolding curve with three discernable states [the native state (N), the partially unfolded state (I) and the unfolded state (U)]. In comparison, there were only two discernable states (N and U) in the thermal unfolding curve of PAE. These results suggest that Glu249 is important for catalytic efficiency, stability and unfolding cooperativity. This study represents a systematic mutational analyses of salt bridges in the model metalloprotease PAE and provides important insights into the structure-function relationship of enzymes.
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Affiliation(s)
- Fei Bian
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- * E-mail: (FB); (YB)
| | - Shousong Yue
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Zhenying Peng
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Xiaowei Zhang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Gao Chen
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Jinhui Yu
- Shandong Crop Germplasm Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ning Xuan
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Yuping Bi
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Graduate Education Center, Shandong Academy of Agricultural Sciences, Jinan, China
- * E-mail: (FB); (YB)
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31
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López-Pelegrín M, Ksiazek M, Karim AY, Guevara T, Arolas JL, Potempa J, Gomis-Rüth FX. A novel mechanism of latency in matrix metalloproteinases. J Biol Chem 2015; 290:4728-4740. [PMID: 25555916 DOI: 10.1074/jbc.m114.605956] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The matrix metalloproteinases (MMPs) are a family of secreted soluble or membrane-anchored multimodular peptidases regularly found in several paralogous copies in animals and plants, where they have multiple functions. The minimal consensus domain architecture comprises a signal peptide, a 60-90-residue globular prodomain with a conserved sequence motif including a cysteine engaged in "cysteine-switch" or "Velcro" mediated latency, and a catalytic domain. Karilysin, from the human periodontopathogen Tannerella forsythia, is the only bacterial MMP to have been characterized biochemically to date. It shares with eukaryotic forms the catalytic domain but none of the flanking domains. Instead of the consensus MMP prodomain, it features a 14-residue propeptide, the shortest reported for a metallopeptidase, which lacks cysteines. Here we determined the structure of a prokarilysin fragment encompassing the propeptide and the catalytic domain, and found that the former runs across the cleft in the opposite direction to a bound substrate and inhibits the latter through an "aspartate-switch" mechanism. This finding is reminiscent of latency maintenance in the otherwise unrelated astacin and fragilysin metallopeptidase families. In addition, in vivo and biochemical assays showed that the propeptide contributes to protein folding and stability. Our analysis of prokarilysin reveals a novel mechanism of latency and activation in MMPs. Finally, our findings support the view that the karilysin catalytic domain was co-opted by competent bacteria through horizontal gene transfer from a eukaryotic source, and later evolved in a specific bacterial environment.
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Affiliation(s)
- Mar López-Pelegrín
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Miroslaw Ksiazek
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Ul. Gronostajowa 7, 30-387 Kraków, Poland, and
| | - Abdulkarim Y Karim
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Ul. Gronostajowa 7, 30-387 Kraków, Poland, and
| | - Tibisay Guevara
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Joan L Arolas
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain,.
| | - Jan Potempa
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Ul. Gronostajowa 7, 30-387 Kraków, Poland, and; the Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202.
| | - F Xavier Gomis-Rüth
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain,.
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32
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Role of YpeB in cortex hydrolysis during germination of Bacillus anthracis spores. J Bacteriol 2014; 196:3399-409. [PMID: 25022853 DOI: 10.1128/jb.01899-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The infectious agent of the disease anthrax is the spore of Bacillus anthracis. Bacterial spores are extremely resistant to environmental stresses, which greatly hinders spore decontamination efforts. The spore cortex, a thick layer of modified peptidoglycan, contributes to spore dormancy and resistance by maintaining the low water content of the spore core. The cortex is degraded by germination-specific lytic enzymes (GSLEs) during spore germination, rendering the cells vulnerable to common disinfection techniques. This study investigates the relationship between SleB, a GSLE in B. anthracis, and YpeB, a protein necessary for SleB stability and function. The results indicate that ΔsleB and ΔypeB spores exhibit similar germination phenotypes and that the two proteins have a strict codependency for their incorporation into the dormant spore. In the absence of its partner protein, SleB or YpeB is proteolytically degraded soon after expression during sporulation, rather than escaping the developing spore. The three PepSY domains of YpeB were examined for their roles in the interaction with SleB. YpeB truncation mutants illustrate the necessity of a region beyond the first PepSY domain for SleB stability. Furthermore, site-directed mutagenesis of highly conserved residues within the PepSY domains resulted in germination defects corresponding to reduced levels of both SleB and YpeB in the mutant spores. These results identify residues involved in the stability of both proteins and reiterate their codependent relationship. It is hoped that the study of GSLEs and interacting proteins will lead to the use of GSLEs as targets for efficient activation of spore germination and facilitation of spore cleanup.
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Tzanis A, Dalton KA, Hesketh A, den Hengst CD, Buttner MJ, Thibessard A, Kelemen GH. A sporulation-specific, sigF-dependent protein, SspA, affects septum positioning in Streptomyces coelicolor. Mol Microbiol 2013; 91:363-80. [PMID: 24261854 PMCID: PMC4282423 DOI: 10.1111/mmi.12466] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2013] [Indexed: 01/17/2023]
Abstract
The RNA polymerase sigma factor SigF controls late development during sporulation in the filamentous bacterium Streptomyces coelicolor. The only known SigF-dependent gene identified so far, SCO5321, is found in the biosynthetic cluster encoding spore pigment synthesis. Here we identify the first direct target for SigF, the gene sspA, encoding a sporulation-specific protein. Bioinformatic analysis suggests that SspA is a secreted lipoprotein with two PepSY signature domains. The sspA deletion mutant exhibits irregular sporulation septation and altered spore shape, suggesting that SspA plays a role in septum formation and spore maturation. The fluorescent translational fusion protein SspA–mCherry localized first to septum sites, then subsequently around the surface of the spores. Both SspA protein and sspA transcription are absent from the sigF null mutant. Moreover, in vitro transcription assay confirmed that RNA polymerase holoenzyme containing SigF is sufficient for initiation of transcription from a single sspA promoter. In addition, in vivo and in vitro experiments showed that sspA is a direct target of BldD, which functions to repress sporulation genes, including whiG, ftsZ and ssgB, during vegetative growth, co-ordinating their expression during sporulation septation.
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Affiliation(s)
- Angelos Tzanis
- University of East Anglia, Norwich Research Park, Norwich, UK
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Fernández D, Russi S, Vendrell J, Monod M, Pallarès I. A functional and structural study of the major metalloprotease secreted by the pathogenic fungusAspergillus fumigatus. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1946-57. [DOI: 10.1107/s0907444913017642] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 06/26/2013] [Indexed: 01/09/2023]
Abstract
Fungalysins are secreted fungal peptidases with the ability to degrade the extracellular matrix proteins elastin and collagen and are thought to act as virulence factors in diseases caused by fungi. Fungalysins constitute a unique family among zinc-dependent peptidases that bears low sequence similarity to known bacterial peptidases of the thermolysin family. The crystal structure of the archetype of the fungalysin family,Aspergillus fumigatusmetalloprotease (AfuMep), has been obtained for the first time. The 1.8 Å resolution structure of AfuMep corresponds to that of an autoproteolyzed proenzyme with separate polypeptide chains corresponding to the N-terminal prodomain in a binary complex with the C-terminal zinc-bound catalytic domain. The prodomain consists of a tandem of cystatin-like folds whose C-terminal end is buried into the active-site cleft of the catalytic domain. The catalytic domain harbouring the key catalytic zinc ion and its ligands, two histidines and one glutamic acid, undergoes a conspicuous rearrangement of its N-terminal end during maturation. One key positively charged amino-acid residue and the C-terminal disulfide bridge appear to contribute to its structural–functional properties. Thus, structural, biophysical and biochemical analysis were combined to provide a deeper comprehension of the underlying properties ofA. fumigatusfungalysin, serving as a framework for the as yet poorly known metallopeptidases from pathogenic fungi.
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López-Pelegrín M, Cerdà-Costa N, Martínez-Jiménez F, Cintas-Pedrola A, Canals A, Peinado JR, Marti-Renom MA, López-Otín C, Arolas JL, Gomis-Rüth FX. A novel family of soluble minimal scaffolds provides structural insight into the catalytic domains of integral membrane metallopeptidases. J Biol Chem 2013; 288:21279-21294. [PMID: 23733187 PMCID: PMC3774397 DOI: 10.1074/jbc.m113.476580] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 05/13/2013] [Indexed: 11/06/2022] Open
Abstract
In the search for structural models of integral-membrane metallopeptidases (MPs), we discovered three related proteins from thermophilic prokaryotes, which we grouped into a novel family called "minigluzincins." We determined the crystal structures of the zymogens of two of these (Pyrococcus abyssi proabylysin and Methanocaldococcus jannaschii projannalysin), which are soluble and, with ∼100 residues, constitute the shortest structurally characterized MPs to date. Despite relevant sequence and structural similarity, the structures revealed two unique mechanisms of latency maintenance through the C-terminal segments previously unseen in MPs as follows: intramolecular, through an extended tail, in proabylysin, and crosswise intermolecular, through a helix swap, in projannalysin. In addition, structural and sequence comparisons revealed large similarity with MPs of the gluzincin tribe such as thermolysin, leukotriene A4 hydrolase relatives, and cowrins. Noteworthy, gluzincins mostly contain a glutamate as third characteristic zinc ligand, whereas minigluzincins have a histidine. Sequence and structural similarity further allowed us to ascertain that minigluzincins are very similar to the catalytic domains of integral membrane MPs of the MEROPS database families M48 and M56, such as FACE1, HtpX, Oma1, and BlaR1/MecR1, which are provided with trans-membrane helices flanking or inserted into a minigluzincin-like catalytic domain. In a time where structural biochemistry of integral-membrane proteins in general still faces formidable challenges, the minigluzincin soluble minimal scaffold may contribute to our understanding of the working mechanisms of these membrane MPs and to the design of novel inhibitors through structure-aided rational drug design approaches.
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Affiliation(s)
- Mar López-Pelegrín
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona
| | - Núria Cerdà-Costa
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona
| | - Francisco Martínez-Jiménez
- the Genome Biology Group, Centre Nacional d'Anàlisi Genòmic, c/Baldiri Reixac, 4, 08028 Barcelona,; the Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation, c/Dr. Aiguader, 88, 08003 Barcelona
| | - Anna Cintas-Pedrola
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona
| | - Albert Canals
- the Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas and Institute for Research in Biomedicine, c/Baldiri Reixac, 10-12, 08028 Barcelona, and
| | - Juan R Peinado
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona
| | - Marc A Marti-Renom
- the Genome Biology Group, Centre Nacional d'Anàlisi Genòmic, c/Baldiri Reixac, 4, 08028 Barcelona,; the Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation, c/Dr. Aiguader, 88, 08003 Barcelona
| | - Carlos López-Otín
- the Departamento de Bioquímica y Biología Molecular and Instituto Universitario de Oncología, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Joan L Arolas
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona,.
| | - F Xavier Gomis-Rüth
- From the Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, c/Baldiri Reixac, 15-21, 08028 Barcelona,.
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36
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Yang J, Li J, Mai Z, Tian X, Zhang S. Purification, characterization, and gene cloning of a cold-adapted thermolysin-like protease from Halobacillus sp. SCSIO 20089. J Biosci Bioeng 2013; 115:628-32. [DOI: 10.1016/j.jbiosc.2012.12.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 12/04/2012] [Accepted: 12/13/2012] [Indexed: 10/27/2022]
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37
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Schwenteit J, Bogdanović X, Fridjonsson OH, Aevarsson A, Bornscheuer UT, Hinrichs W, Gudmundsdottir BK. Toxoid construction of AsaP1, a lethal toxic aspzincin metalloendopeptidase of Aeromonas salmonicida subsp. achromogenes, and studies of its activity and processing. Vet Microbiol 2013; 162:687-694. [PMID: 23031341 DOI: 10.1016/j.vetmic.2012.09.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 09/11/2012] [Accepted: 09/12/2012] [Indexed: 11/25/2022]
Abstract
AsaP1 is a toxic aspzincin metalloendopeptidase secreted by the fish pathogen Aeromonas salmonicida subsp. achromogenes. The protease is highly immunogenic and antibodies against AsaP1 evoke a passive protection against infection with A. salmonicida subsp. achromogenes. The protease is expressed as 37 kDa pre-pro-protein and processed to an active enzyme of 19kDa in A. salmonicida subsp. achromogenes. Recombinant expression of AsaP1(rec) in E. coli results in a protease of 22 kDa that is not secreted. AsaP1(rec) induces comparable pathological changes in Atlantic salmon (Salmo salar L.) to native AsaP1(wt). The aim of the study was to construct AsaP1 toxoids by exchanging catalytically important amino acids in the active site region of the protease. Four different AsaP1 mutants (AsaP1(E294A), AsaP1(E294Q), AsaP1(Y309A), and AsaP1(Y309F)) were successfully constructed by one step site directed mutagenesis, expressed in E. coli BL21 C43 as pre-pro-proteins and purified by His-tag affinity chromatography and gel filtration. Three of the resulting mutants (AsaP1(E294A), AsaP1(E294Q), and AsaP1(Y309A)) were not caseinolytic active and are detected as unprocessed pre-pro-proteins of 37 kDa. Caseinolytic active AsaP1(rec) and a mutant with reduced activity, AsaP1(Y309F), were processed to a size of 22 kDa. Furthermore, AsaP1(rec) is able to process the inactive mutants to the mature size of 22 kDa, allowing the conclusion that AsaP1 is autocatalytically processed. All four mutants AsaP1(E294A), AsaP1(E294Q), AsaP1(Y309A) and AsaP1(Y309F) are non-toxic in fish but induce a specific anti-AsaP1 antibody response in Arctic charr (Salvelinus alpinus L.) and are therefore true toxoids and possible vaccine additives.
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Affiliation(s)
- Johanna Schwenteit
- Institute for Experimental Pathology, University of Iceland, Keldur v/Vesturlandsveg, IS-112 Reykjavík, Iceland; Institute of Biochemistry, Department of Biotechnology and Enzyme Catalysis, Greifswald University, Felix Hausdorff-Str. 4, 17487 Greifswald, Germany.
| | - Xenia Bogdanović
- Department of Structural Biology, Greifswald University, Felix Hausdorff-Str. 4, 17487 Greifswald, Germany.
| | | | | | - Uwe T Bornscheuer
- Institute of Biochemistry, Department of Biotechnology and Enzyme Catalysis, Greifswald University, Felix Hausdorff-Str. 4, 17487 Greifswald, Germany.
| | - Winfried Hinrichs
- Department of Structural Biology, Greifswald University, Felix Hausdorff-Str. 4, 17487 Greifswald, Germany.
| | - Bjarnheidur K Gudmundsdottir
- Institute for Experimental Pathology, University of Iceland, Keldur v/Vesturlandsveg, IS-112 Reykjavík, Iceland.
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Ruf A, Stihle M, Benz J, Schmidt M, Sobek H. Structure of gentlyase, the neutral metalloprotease of Paenibacillus polymyxa. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:24-31. [PMID: 23275160 PMCID: PMC3532130 DOI: 10.1107/s0907444912041169] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/01/2012] [Indexed: 11/10/2022]
Abstract
Gentlyase is a bacterial extracellular metalloprotease that is widely applied in cell culture and for tissue dissociation and that belongs to the family of thermolysin-like proteases. The structure of thermolysin has been known since 1972 and that of Bacillus cereus neutral protease since 1992. However, the structure determination of other Bacillus neutral proteases has been hindered by their tendency to cannibalistic autolysis. High calcium conditions that allow the concentration and crystallization of the active Gentlyase metalloprotease without autoproteolysis were identified using thermal fluorescent shift assays. X-ray structures of the protease were solved in the absence and in the presence of the inhibitor phosphoramidon at 1.59 and 1.76 Å resolution, respectively. No domain movement was observed upon inhibitor binding, although such movement is thought to be a general feature of the thermolysin-like protease family. Further analysis of the structure shows that the observed calcium dependency of Gentlyase stability may arise from a partly degenerated calcium site Ca1-2 and a deletion near site Ca3.
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Affiliation(s)
- Armin Ruf
- pRED Pharma Research and Early Development, Small Molecule Research, Discovery Technologies, F. Hoffmann-La Roche Ltd, Basel, Switzerland.
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Menach E, Yasukawa K, Inouye K. Effects of site-directed mutagenesis of Asn116 in the -hairpin of the N-terminal domain of thermolysin on its activity and stability. J Biochem 2012; 152:231-9. [DOI: 10.1093/jb/mvs064] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Berzigotti S, Benlafya K, Sépulchre J, Amoroso A, Joris B. Bacillus licheniformis BlaR1 L3 loop is a zinc metalloprotease activated by self-proteolysis. PLoS One 2012; 7:e36400. [PMID: 22623956 PMCID: PMC3356374 DOI: 10.1371/journal.pone.0036400] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 04/04/2012] [Indexed: 11/26/2022] Open
Abstract
In Bacillus licheniformis 749/I, BlaP β-lactamase is induced by the presence of a β-lactam antibiotic outside the cell. The first step in the induction mechanism is the detection of the antibiotic by the membrane-bound penicillin receptor BlaR1 that is composed of two functional domains: a carboxy-terminal domain exposed outside the cell, which acts as a penicillin sensor, and an amino-terminal domain anchored to the cytoplasmic membrane, which works as a transducer-transmitter. The acylation of BlaR1 sensor domain by the antibiotic generates an intramolecular signal that leads to the activation of the L3 cytoplasmic loop of the transmitter by a single-point cleavage. The exact mechanism of L3 activation and the nature of the secondary cytoplasmic signal launched by the activated transmitter remain unknown. However, these two events seem to be linked to the presence of a HEXXH zinc binding motif of neutral zinc metallopeptidases. By different experimental approaches, we demonstrated that the L3 loop binds zinc ion, belongs to Gluzincin metallopeptidase superfamily and is activated by self-proteolysis.
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Affiliation(s)
- Stéphanie Berzigotti
- Centre for Protein Engineering, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Kamal Benlafya
- Centre for Protein Engineering, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Jérémy Sépulchre
- Centre for Protein Engineering, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Ana Amoroso
- Centre for Protein Engineering, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Bernard Joris
- Centre for Protein Engineering, Department of Life Sciences, University of Liège, Liège, Belgium
- * E-mail:
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Bhaumik P, Xiao H, Hidaka K, Gustchina A, Kiso Y, Yada RY, Wlodawer A. Structural insights into the activation and inhibition of histo-aspartic protease from Plasmodium falciparum. Biochemistry 2011; 50:8862-79. [PMID: 21928835 PMCID: PMC3501826 DOI: 10.1021/bi201118z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Histo-aspartic protease (HAP) from Plasmodium falciparum is a promising target for the development of novel antimalarial drugs. The sequence of HAP is highly similar to those of pepsin-like aspartic proteases, but one of the two catalytic aspartates, Asp32, is replaced with histidine. Crystal structures of the truncated zymogen of HAP and of the complex of the mature enzyme with inhibitor KNI-10395 have been determined at 2.1 and 2.5 Å resolution, respectively. As in other proplasmepsins, the propeptide of the zymogen interacts with the C-terminal domain of the enzyme, forcing the N- and C-terminal domains apart, thereby separating His32 and Asp215 and preventing formation of the mature active site. In the inhibitor complex, the enzyme forms a tight domain-swapped dimer, not previously seen in any aspartic proteases. The inhibitor is found in an unprecedented conformation resembling the letter U, stabilized by two intramolecular hydrogen bonds. Surprisingly, the location and conformation of the inhibitor are similar to those of the fragment of helix 2 comprising residues 34p-38p in the prosegments of the zymogens of gastric aspartic proteases; a corresponding helix assumes a vastly different orientation in proplasmepsins. Each inhibitor molecule is in contact with two molecules of HAP, interacting with the carboxylate group of the catalytic Asp215 of one HAP protomer through a water molecule, while also making a direct hydrogen bond to Glu278A' of the other protomer. A comparison of the shifts in the positions of the catalytic residues in the inhibitor complex presented here with those published previously gives further hints regarding the enzymatic mechanism of HAP.
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Affiliation(s)
- Prasenjit Bhaumik
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Huogen Xiao
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Koushi Hidaka
- Department of Medicinal Chemistry and Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607–8412, Japan
- Laboratory of Medicinal Chemistry, Kobe Gakuin University, 1-1–3 Minatojima, Chuo-ku, Kobe 650–8586, Japan
| | - Alla Gustchina
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Yoshiaki Kiso
- Department of Medicinal Chemistry and Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607–8412, Japan
- Laboratory of Medicinal Chemistry, Kobe Gakuin University, 1-1–3 Minatojima, Chuo-ku, Kobe 650–8586, Japan
- Laboratory of Peptide Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526–0829, Japan
| | - Rickey Y. Yada
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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Naumann TA, Wicklow DT, Price NPJ. Identification of a chitinase-modifying protein from Fusarium verticillioides: truncation of a host resistance protein by a fungalysin metalloprotease. J Biol Chem 2011; 286:35358-35366. [PMID: 21878653 PMCID: PMC3195611 DOI: 10.1074/jbc.m111.279646] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 08/23/2011] [Indexed: 11/06/2022] Open
Abstract
Chitinase-modifying proteins (cmps) are proteases secreted by fungal pathogens that truncate the plant class IV chitinases ChitA and ChitB during maize ear rot. cmp activity has been characterized for Bipolaris zeicola and Stenocarpella maydis, but the identities of the proteases are not known. Here, we report that cmps are secreted by multiple species from the genus Fusarium, that cmp from Fusarium verticillioides (Fv-cmp) is a fungalysin metalloprotease, and that it cleaves within a sequence that is conserved in class IV chitinases. Protein extracts from Fusarium cultures were found to truncate ChitA and ChitB in vitro. Based on this activity, Fv-cmp was purified from F. verticillioides. N-terminal sequencing of truncated ChitA and MALDI-TOF-MS analysis of reaction products showed that Fv-cmp is an endoprotease that cleaves a peptide bond on the C-terminal side of the lectin domain. The N-terminal sequence of purified Fv-cmp was determined and compared with a set of predicted proteins, resulting in its identification as a zinc metalloprotease of the fungalysin family. Recombinant Fv-cmp also truncated ChitA, confirming its identity, but had reduced activity, suggesting that the recombinant protease did not mature efficiently from its propeptide-containing precursor. This is the first report of a fungalysin that targets a nonstructural host protein and the first to implicate this class of virulence-related proteases in plant disease.
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Affiliation(s)
- Todd A Naumann
- Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Peoria, Illinois 61604.
| | - Donald T Wicklow
- Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Peoria, Illinois 61604
| | - Neil P J Price
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, Peoria, Illinois 61604
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Wu JW, Chen XL. Extracellular metalloproteases from bacteria. Appl Microbiol Biotechnol 2011; 92:253-62. [DOI: 10.1007/s00253-011-3532-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 07/25/2011] [Accepted: 08/04/2011] [Indexed: 10/17/2022]
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Eijsink VGH, Matthews BW, Vriend G. The role of calcium ions in the stability and instability of a thermolysin-like protease. Protein Sci 2011; 20:1346-55. [PMID: 21648000 PMCID: PMC3189520 DOI: 10.1002/pro.670] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 05/12/2011] [Indexed: 11/06/2022]
Abstract
Thermolysin and other secreted broad-specificity proteases, such as subtilisin or alpha-lytic protease, are produced as pre-pro-proteins that stay at least partially unfolded while in the cytosol. After secretion, the pro-proteases fold to their active conformations in a process that includes the autolytic removal of the pro-peptide. We review the life cycle of the thermolysin-like protease from Bacillus stearothermophilus in light of the calcium dependent stability and instability of the N-terminal domain. The protease binds calcium ions in the regions that are involved in the autolytic maturation process. It is generally assumed that the calcium ions contribute to the extreme stability of the protease, but experimental evidence for TLP-ste indicates that at least one of the calcium ions plays a regulatory role. We hypothesize that this calcium ion plays an important role as a switch that modulates the protease between stable and unstable states as appropriate to the biological need.
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Affiliation(s)
- VGH Eijsink
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life SciencesN-1432 Ås, Norway
| | - BW Matthews
- Institute of Molecular Biology, University of OregonEugene, 97403-1229 Oregon, USA
| | - G Vriend
- CMBI, NCMLS, Radboud University Nijmegen Medical Centre6525 GA 26-28 Nijmegen, The Netherlands
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Abstract
Listeria monocytogenes is an intracytosolic bacterial pathogen. Among the factors contributing to escape from vacuoles are a phosphatidylcholine phospholipase C (PC-PLC) and a metalloprotease (Mpl). Both enzymes are translocated across the bacterial membrane as inactive proproteins, whose propeptides serve in part to maintain them in association with the bacterium. We have shown that PC-PLC maturation is regulated by Mpl and pH and that Mpl maturation occurs by autocatalysis. In this study, we tested the hypothesis that Mpl activity is pH regulated. To synchronize the effect of pH on bacteria, the cytosolic pH of infected cells was manipulated immediately after radiolabeling de novo-synthesized bacterial proteins. Immunoprecipitation of secreted Mpl from host cell lysates revealed the presence of the propeptide and catalytic domain in samples treated at pH 6.5 but not at pH 7.3. The zymogen was present in small amounts under all conditions. Since proteases often remain associated with their respective propeptide following autocatalysis, we aimed at determining whether pH regulates autocatalysis or secretion of the processed enzyme. For this purpose, we used an Mpl construct that contains a Flag tag at the N terminus of its catalytic domain and antibodies that can distinguish N-terminal and non-N-terminal Flag. By fluorescence microscopy, we observed the Mpl zymogen associated with the bacterium at physiological pH but not following acidification. Mature Mpl was not detected in association with the bacterium at either pH. Using purified proteins, we determined that processing of the PC-PLC propeptide by mature Mpl is also pH sensitive. These results indicate that pH regulates the activity of Mpl on itself and on PC-PLC.
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