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Kim SY, Randall JR, Gu R, Nguyen QD, Davies BW. Antibacterial action, proteolytic immunity, and in vivo activity of a Vibrio cholerae microcin. Cell Host Microbe 2024:S1931-3128(24)00319-6. [PMID: 39260372 DOI: 10.1016/j.chom.2024.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/24/2024] [Accepted: 08/16/2024] [Indexed: 09/13/2024]
Abstract
Microcins are small antibacterial proteins that mediate interbacterial competition. Their narrow-spectrum activity provides opportunities to discover microbiome-sparing treatments. However, microcins have been found almost exclusively in Enterobacteriaceae. Their broader existence and potential implications in other pathogens remain unclear. Here, we identify and characterize a microcin active against pathogenic Vibrio cholerae: MvcC. We show that MvcC is reliant on the outer membrane porin OmpT to cross the outer membrane. MvcC then binds the periplasmic protein OppA to reach and disrupt the cytoplasmic membrane. We demonstrate that MvcC's cognate immunity protein is a protease, which precisely cleaves MvcC to neutralize its activity. Importantly, we show that MvcC is active against diverse cholera isolates and in a mouse model of V. cholerae colonization. Our results provide a detailed analysis of a microcin outside of Enterobacteriaceae and its potential to influence V. cholerae infection.
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Affiliation(s)
- Sun-Young Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Justin R Randall
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Richard Gu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Quoc D Nguyen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Bryan W Davies
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, TX, USA.
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2
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Chen SY, Fiedler MK, Gronauer TF, Omelko O, von Wrisberg MK, Wang T, Schneider S, Sieber SA, Zacharias M. Unraveling the mechanism of small molecule induced activation of Staphylococcus aureus signal peptidase IB. Commun Biol 2024; 7:895. [PMID: 39043865 PMCID: PMC11266668 DOI: 10.1038/s42003-024-06575-x] [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: 02/16/2024] [Accepted: 07/11/2024] [Indexed: 07/25/2024] Open
Abstract
Staphylococcus aureus signal peptidase IB (SpsB) is an essential enzyme for protein secretion. While inhibition of its activity by small molecules is a well-precedented mechanism to kill bacteria, the mode of activation is however less understood. We here investigate the activation mechanism of a recently introduced activator, the antibiotic compound PK150, and demonstrate by combined experimental and Molecular Dynamics (MD) simulation studies a unique principle of enzyme stimulation. Mass spectrometric studies with an affinity-based probe of PK150 unravel the binding site of PK150 in SpsB which is used as a starting point for MD simulations. Our model shows the localization of the molecule in an allosteric pocket next to the active site which shields the catalytic dyad from excess water that destabilizes the catalytic geometry. This mechanism is validated by the placement of mutations aligning the binding pocket of PK150. While the mutants retain turnover of the SpsB substrate, no stimulation of activity is observed upon PK150 addition. Overall, our study elucidates a previously little investigated mechanism of enzyme activation and serves as a starting point for the development of future enzyme activators.
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Affiliation(s)
- Shu-Yu Chen
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 2, Zurich, 8093, Switzerland
- TUM School of Natural Sciences, Department Biosciences, Theoretical Biophysics (T38), Center for Functional Protein Assemblies (CPA), Technical University Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching, 85748, Germany
| | - Michaela K Fiedler
- TUM School of Natural Sciences, Department Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technical University Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching, 85748, Germany
| | - Thomas F Gronauer
- TUM School of Natural Sciences, Department Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technical University Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching, 85748, Germany
| | - Olesia Omelko
- TUM School of Natural Sciences, Department Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technical University Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching, 85748, Germany
| | - Marie-Kristin von Wrisberg
- Department of Chemistry, Ludwig-Maximilians University Munich (LMU), Butenandtstr. 5-13, Munich, 81377, Germany
| | - Tao Wang
- TUM School of Natural Sciences, Department Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technical University Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching, 85748, Germany
| | - Sabine Schneider
- Department of Chemistry, Ludwig-Maximilians University Munich (LMU), Butenandtstr. 5-13, Munich, 81377, Germany
| | - Stephan A Sieber
- TUM School of Natural Sciences, Department Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technical University Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching, 85748, Germany.
| | - Martin Zacharias
- TUM School of Natural Sciences, Department Biosciences, Theoretical Biophysics (T38), Center for Functional Protein Assemblies (CPA), Technical University Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching, 85748, Germany.
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3
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Musik JE, Zalucki YM, Beacham IR, Jennings MP. The role of signal sequence proximal residues in the mature region of bacterial secreted proteins in E. coli. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184000. [PMID: 35798072 DOI: 10.1016/j.bbamem.2022.184000] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/18/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Secreted proteins contain an N-terminal signal peptide to guide them through the secretion pathway. Once the protein is translocated, the signal peptide is removed by a signal peptidase, such as signal peptidase I. The signal peptide has been extensively studied and reviewed; however, the mature region has not been the focus of review. Here we cover the experimental evidence that highlights the important role of the mature region amino acid residues in both the efficiency and the ability of secreted proteins to be successfully exported via secretion pathways and cleaved by signal peptidase I.
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Affiliation(s)
- Joanna E Musik
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, QLD, 4222, Australia
| | - Yaramah M Zalucki
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, QLD, 4222, Australia.
| | - Ifor R Beacham
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, QLD, 4222, Australia
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, QLD, 4222, Australia.
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4
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Benediktsdottir A, Lu L, Cao S, Zamaratski E, Karlén A, Mowbray SL, Hughes D, Sandström A. Antibacterial sulfonimidamide-based oligopeptides as type I signal peptidase inhibitors: Synthesis and biological evaluation. Eur J Med Chem 2021; 224:113699. [PMID: 34352713 DOI: 10.1016/j.ejmech.2021.113699] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/18/2021] [Accepted: 07/10/2021] [Indexed: 10/20/2022]
Abstract
Oligopeptide boronates with a lipophilic tail are known to inhibit the type I signal peptidase in E. coli, which is a promising drug target for developing novel antibiotics. Antibacterial activity depends on these oligopeptides having a cationic modification to increase their permeation. Unfortunately, this modification is associated with cytotoxicity, motivating the need for novel approaches. The sulfonimidamide functionality has recently gained much interest in drug design and discovery, as a means of introducing chirality and an imine-handle, thus allowing for the incorporation of additional substituents. This in turn can tune the chemical and biological properties, which are here explored. We show that introducing the sulfonimidamide between the lipophilic tail and the peptide in a series of signal peptidase inhibitors resulted in antibacterial activity, while the sulfonamide isostere and previously known non-cationic analogs were inactive. Additionally, we show that replacing the sulfonamide with a sulfonimidamide resulted in decreased cytotoxicity, and similar results were seen by adding a cationic sidechain to the sulfonimidamide motif. This is the first report of incorporation of the sulfonimidamide functional group into bioactive peptides, more specifically into antibacterial oligopeptides, and evaluation of its biological effects.
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Affiliation(s)
- Andrea Benediktsdottir
- Department of Medicinal Chemistry, BMC, Uppsala University, Box 574, SE-75123, Uppsala, Sweden
| | - Lu Lu
- Department of Cell and Molecular Biology, BMC, Uppsala University, Box 596, SE-75123, Uppsala, Sweden
| | - Sha Cao
- Department of Medical Biochemistry and Microbiology, BMC, Box 582, SE-75123, Uppsala, Sweden
| | - Edouard Zamaratski
- Department of Medicinal Chemistry, BMC, Uppsala University, Box 574, SE-75123, Uppsala, Sweden
| | - Anders Karlén
- Department of Medicinal Chemistry, BMC, Uppsala University, Box 574, SE-75123, Uppsala, Sweden
| | - Sherry L Mowbray
- Department of Cell and Molecular Biology, BMC, Uppsala University, Box 596, SE-75123, Uppsala, Sweden; Uppsala University, Science for Life Laboratory, Department of Cell and Molecular Biology, Box 596, SE-751 24, Uppsala, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, BMC, Box 582, SE-75123, Uppsala, Sweden
| | - Anja Sandström
- Department of Medicinal Chemistry, BMC, Uppsala University, Box 574, SE-75123, Uppsala, Sweden.
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5
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Lather A, Sharma S, Khatkar A. Naringin derivatives as glucosamine-6-phosphate synthase inhibitors based preservatives and their biological evaluation. Sci Rep 2020; 10:20477. [PMID: 33235242 PMCID: PMC7686335 DOI: 10.1038/s41598-020-77511-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 11/02/2020] [Indexed: 11/25/2022] Open
Abstract
Glucosamine-6-Phosphate synthase enzyme has been targeted for development of better and safe preservative due to its role in microbial cell wall synthesis. In recent year's demand of preservatives for the food, cosmetics and pharmaceuticals have increased. Although, the available synthetic preservatives have associated unwanted adverse effects, soa chain of naringin derivatives were schemed synthesized and judged for antioxidant, antimicrobial, preservative efficacy, stability study and topical evaluation. Molecular docking resulted with excellent dock score and binding energy for compound 7, compound 6 and compound 1 as compared to standard drugs. Resultant data of antimicrobial activity revealed compound 7as most potent antimicrobial compound for P. mirabilis, P. aeruginosa, S. aureus, E. coli, C. albicans, and A. niger, respectively, as compared to the standard drugs. The preservative efficacy test of compound 7 in White Lotion USP showed the log cfu/mL value within prescribed limit of USP standard. Compound 7 stabilize the White lotion USP from microbial growth for a period of six months under accelerated storage condition. Compound 7 was further evaluated for toxicity by using the Draize test in rabbits and showed no sign of eye and skin irritation. The outcome demonstrated that synthesized naringin compounds showed glorious antioxidant, antimicrobial, preservative efficacy, stable and safe as compared to standards.
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Affiliation(s)
- Amit Lather
- Laboratory for Preservation Technology and Enzyme Inhibition Studies, Faculty of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Sunil Sharma
- Department of Pharmaceutical Sciences, G.J.U.S.&T., Hisar, India
| | - Anurag Khatkar
- Laboratory for Preservation Technology and Enzyme Inhibition Studies, Faculty of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana, India.
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6
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Amygdalin based G-6-P synthase inhibitors as novel preservatives for food and pharmaceutical products. Sci Rep 2020; 10:13903. [PMID: 32807915 PMCID: PMC7431536 DOI: 10.1038/s41598-020-70895-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 08/06/2020] [Indexed: 11/29/2022] Open
Abstract
G-6-P synthase enzyme has been involved in the synthesis of the microbial cell wall, and its inhibition may lead to the antimicrobial effect. In the present study, we designed a library of amygdalin derivatives, and two most active derivatives selected on the basis of various parameters viz. dock score, binding energy, and ADMET data using molecular docking software (Schrodinger’s Maestro). The selected derivatives were synthesized and evaluated for their antioxidant and antimicrobial potential against several Gram (+ ve), Gram (−ve), as well as fungal strains. The results indicated that synthesized compounds exhibited good antioxidant, antimicrobial, and better preservative efficacy in food preparation as compared to the standard compounds. No significant differences were observed in different parameters as confirmed by Kruskal–Wallis test (p < 0.05). Docking results have been found in good correlation with experimental wet-lab data. Moreover, the mechanistic insight into the docking poses has also been explored by binding interactions of amygdalin derivative inside the dynamic site of G-6-P synthase.
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7
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Lather A, Sharma S, Khatkar S, Khatkar A. Docking Related Survey on Heterocyclic Compounds Based on Glucosamine-6- Phosphate Synthase Inhibitors and their Antimicrobial Potential. Curr Pharm Des 2020; 26:1650-1665. [PMID: 32065087 DOI: 10.2174/1381612826666200217115211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/24/2020] [Indexed: 11/22/2022]
Abstract
The synthetic heterocyclic compounds have their importance due to their wide applications in various fields of science. The heterocyclic compounds have been reported for their anticancer, antitubercular, insecticides, analeptics, analgesic, anti-bacterial, anti-viral, anti-fungal, and weedicidal activity. Researchers have tried various newer targets in search of better antimicrobials acting via novel mechanisms. Glucosamine-6-Phosphate synthase is an enzyme present in microbial cells. The inactivation of G-6-P synthase may serve as a novel approach to find better antimicrobials. The increasing demands development of newer and effective antimicrobial drugs has reported in search of newer techniques for the generation of new drugs. Hence, the molecular docking technique shall be explored to find or investigate the newer target finding the novel compounds which can be an active antimicrobial compound. The present review has focused on the reported heterocyclic compounds which have been evaluated for their antimicrobial potential using G-6-P synthase as a target. The results of in silico methods and in vitro methods have been compared and critically discussed.
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Affiliation(s)
- Amit Lather
- Vaish Institute of Pharmaceutical Education & Research, Rohtak, Haryana, India
| | - Sunil Sharma
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science and Technology, Hisar, India
| | - Sarita Khatkar
- Vaish Institute of Pharmaceutical Education & Research, Rohtak, Haryana, India
| | - Anurag Khatkar
- Faculty of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana, India
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8
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Abstract
Signal peptidases are the membrane bound enzymes that cleave off the amino-terminal signal peptide from secretory preproteins . There are two types of bacterial signal peptidases . Type I signal peptidase utilizes a serine/lysine catalytic dyad mechanism and is the major signal peptidase in most bacteria. Type II signal peptidase is an aspartic protease specific for prolipoproteins. This chapter will review what is known about the structure, function and mechanism of these unique enzymes.
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Affiliation(s)
- Mark Paetzel
- Department of Molecular Biology and Biochemistry, Simon Fraser University, South Science Building 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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9
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Crane JM, Randall LL. The Sec System: Protein Export in Escherichia coli. EcoSal Plus 2017; 7:10.1128/ecosalplus.ESP-0002-2017. [PMID: 29165233 PMCID: PMC5807066 DOI: 10.1128/ecosalplus.esp-0002-2017] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Indexed: 11/20/2022]
Abstract
In Escherichia coli, proteins found in the periplasm or the outer membrane are exported from the cytoplasm by the general secretory, Sec, system before they acquire stably folded structure. This dynamic process involves intricate interactions among cytoplasmic and membrane proteins, both peripheral and integral, as well as lipids. In vivo, both ATP hydrolysis and proton motive force are required. Here, we review the Sec system from the inception of the field through early 2016, including biochemical, genetic, and structural data.
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Affiliation(s)
- Jennine M. Crane
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Linda L. Randall
- Department of Biochemistry, University of Missouri, Columbia, Missouri
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10
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Bonnett SA, Ollinger J, Chandrasekera S, Florio S, O’Malley T, Files M, Jee JA, Ahn J, Casey A, Ovechkina Y, Roberts D, Korkegian A, Parish T. A Target-Based Whole Cell Screen Approach To Identify Potential Inhibitors of Mycobacterium tuberculosis Signal Peptidase. ACS Infect Dis 2016; 2:893-902. [PMID: 27642770 PMCID: PMC5215716 DOI: 10.1021/acsinfecdis.6b00075] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Indexed: 12/31/2022]
Abstract
The general secretion (Sec) pathway is a conserved essential pathway in bacteria and is the primary route of protein export across the cytoplasmic membrane. During protein export, the signal peptidase LepB catalyzes the cleavage of the signal peptide and subsequent release of mature proteins into the extracellular space. We developed a target-based whole cell assay to screen for potential inhibitors of LepB, the sole signal peptidase in Mycobacterium tuberculosis, using a strain engineered to underexpress LepB (LepB-UE). We screened 72,000 compounds against both the Lep-UE and wild-type (wt) strains. We identified the phenylhydrazone (PHY) series as having higher activity against the LepB-UE strain. We conducted a limited structure-activity relationship determination around a representative PHY compound with differential activity (MICs of 3.0 μM against the LepB-UE strain and 18 μM against the wt); several analogues were less potent against the LepB overexpressing strain. A number of chemical modifications around the hydrazone moiety resulted in improved potency. Inhibition of LepB activity was observed for a number of compounds in a biochemical assay using cell membrane fraction derived from M. tuberculosis. Compounds did not increase cell permeability, dissipate membrane potential, or inhibit an unrelated mycobacterial enzyme, suggesting a specific mode of action related to the LepB secretory mechanism.
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Affiliation(s)
- Shilah A. Bonnett
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Juliane Ollinger
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Susantha Chandrasekera
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Stephanie Florio
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Theresa O’Malley
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Megan Files
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Jo-Ann Jee
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - James Ahn
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Allen Casey
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Yulia Ovechkina
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - David Roberts
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Aaron Korkegian
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
| | - Tanya Parish
- TB Discovery
Research, Infectious Disease Research Institute, 1616 Eastlake Avenue East, Suite
400, Seattle, Washington 98102, United States
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11
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Zer Aviv P, Shubely M, Moskovits Y, Viskind O, Albeck A, Vertommen D, Ruthstein S, Shokhen M, Gruzman A. A New Oxopiperazin-Based Peptidomimetic Molecule Inhibits Prostatic Acid Phosphatase Secretion and Induces Prostate Cancer Cell Apoptosis. ChemistrySelect 2016. [DOI: 10.1002/slct.201600987] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Pinchas Zer Aviv
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Moran Shubely
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Yoni Moskovits
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Olga Viskind
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Amnon Albeck
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Didier Vertommen
- de Duve Institute; Université catholique de Louvain; Brussels 1200 Belgium
| | - Sharon Ruthstein
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Michael Shokhen
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Arie Gruzman
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
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12
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Zhang W, Xia Y. ER type I signal peptidase subunit (LmSPC1) is essential for the survival of Locusta migratoria manilensis and affects moulting, feeding, reproduction and embryonic development. INSECT MOLECULAR BIOLOGY 2014; 23:269-285. [PMID: 24467622 DOI: 10.1111/imb.12080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The endoplasmic reticulum type I signal peptidase complex (ER SPC) is a conserved enzyme that cleaves the signal peptides of secretory or membrane preproteins. The deletion of this enzyme leads to the accumulation of uncleaved proteins in biomembranes and cell death. However, the physiological functions of ER SPC in insects are not fully understood. Here, a catalytic subunit gene of ER SPC, LmSPC1, was cloned from Locusta migratoria manilensis and its physiological functions were analysed by RNA interference (RNAi). The LmSPC1 open reading frame encoded a protein of 178 amino acids with all five conserved regions of signal peptidases. RNAi-mediated knockdown of LmSPC1 resulted in high mortality. Sixty-nine per cent of dead nymphs died of abnormal moulting, corresponding to decreased activity of moulting fluid protease. Moreover, insects in the RNAi group experienced a decline in food intake, and a decrease in the secretion of total protein and digestive enzymes from midgut tissues to the midgut lumen. Furthermore, the females produced fewer eggs and eggs with disrupted embryogenesis. These results indicate that LmSPC1 is required for the secretion of secretory proteins, affects physiological functions, including moulting, feeding, reproduction and embryonic development, and is essential for survival. Therefore, LmSPC1 may be a potential target for locust control.
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Affiliation(s)
- W Zhang
- Genetic Engineering Research Center, School of Life Science, Chongqing Engineering Research Center for Fungal Insecticide, The Key Laboratory of Gene Function and Expression Regulation, Chongqing University, Chongqing, China
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13
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Paetzel M. Structure and mechanism of Escherichia coli type I signal peptidase. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:1497-508. [PMID: 24333859 DOI: 10.1016/j.bbamcr.2013.12.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 11/26/2013] [Accepted: 12/04/2013] [Indexed: 12/16/2022]
Abstract
Type I signal peptidase is the enzyme responsible for cleaving off the amino-terminal signal peptide from proteins that are secreted across the bacterial cytoplasmic membrane. It is an essential membrane bound enzyme whose serine/lysine catalytic dyad resides on the exo-cytoplasmic surface of the bacterial membrane. This review discusses the progress that has been made in the structural and mechanistic characterization of Escherichia coli type I signal peptidase (SPase I) as well as efforts to develop a novel class of antibiotics based on SPase I inhibition. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Mark Paetzel
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.
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14
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Membrane proteases in the bacterial protein secretion and quality control pathway. Microbiol Mol Biol Rev 2012; 76:311-30. [PMID: 22688815 DOI: 10.1128/mmbr.05019-11] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Proteolytic cleavage of proteins that are permanently or transiently associated with the cytoplasmic membrane is crucially important for a wide range of essential processes in bacteria. This applies in particular to the secretion of proteins and to membrane protein quality control. Major progress has been made in elucidating the structure-function relationships of many of the responsible membrane proteases, including signal peptidases, signal peptide hydrolases, FtsH, the rhomboid protease GlpG, and the site 1 protease DegS. These enzymes employ very different mechanisms to cleave substrates at the cytoplasmic and extracytoplasmic membrane surfaces or within the plane of the membrane. This review highlights the different ways that bacterial membrane proteases degrade their substrates, with special emphasis on catalytic mechanisms and substrate delivery to the respective active sites.
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15
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Panicker IS, Kanci A, Chiu CJ, Veith PD, Glew MD, Browning GF, Markham PF. A novel transposon construct expressing PhoA with potential for studying protein expression and translocation in Mycoplasma gallisepticum. BMC Microbiol 2012; 12:138. [PMID: 22770122 PMCID: PMC3438114 DOI: 10.1186/1471-2180-12-138] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 06/04/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycoplasma gallisepticum is a major poultry pathogen and causes severe economic loss to the poultry industry. In mycoplasmas lipoproteins are abundant on the membrane surface and play a critical role in interactions with the host, but tools for exploring their molecular biology are limited. RESULTS In this study we examined whether the alkaline phosphatase gene (phoA ) from Escherichia coli could be used as a reporter in mycoplasmas. The promoter region from the gene for elongation factor Tu (ltuf) and the signal and acylation sequences from the vlhA 1.1 gene, both from Mycoplasma gallisepticum , together with the coding region of phoA , were assembled in the transposon-containing plasmid pISM2062.2 (pTAP) to enable expression of alkaline phosphatase (AP) as a recombinant lipoprotein. The transposon was used to transform M. gallisepticum strain S6. As a control, a plasmid containing a similar construct, but lacking the signal and acylation sequences, was also produced (pTP) and also introduced into M. gallisepticum . Using a colorimetric substrate for detection of alkaline phosphatase activity, it was possible to detect transformed M. gallisepticum . The level of transcription of phoA in organisms transformed with pTP was lower than in those transformed with pTAP, and alkaline phosphatase was not detected by immunoblotting or enzymatic assays in pTP transformants, eventhough alkaline phosphatase expression could be readily detected by both assays in pTAP transformants. Alkaline phosphatase was shown to be located in the hydrophobic fraction of transformed mycoplasmas following Triton X-114 partitioning and in the membrane fraction after differential fractionation. Trypsin proteolysis confirmed its surface exposure. The inclusion of the VlhA lipoprotein signal sequence in pTAP enabled translocation of PhoA and acylation of the amino terminal cysteine moiety, as confirmed by the effect of treatment with globomycin and radiolabelling studies with [14C]palmitate. PhoA could be identified by mass-spectrometry after separation by two-dimensional electrophoresis. CONCLUSION This is the first study to express PhoA as a lipoprotein in mycoplasmas. The pTAP plasmid will facilitate investigations of lipoproteins and protein translocation across the cell membrane in mycoplasmas, and the ease of detection of these transformants makes this vector system suitable for the simultaneous screening and detection of cloned genes expressed as membrane proteins in mycoplasmas.
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Affiliation(s)
- Indu S Panicker
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary Science, The University of Melbourne, Parkville, VIC, Australia
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Ollinger J, O'Malley T, Ahn J, Odingo J, Parish T. Inhibition of the sole type I signal peptidase of Mycobacterium tuberculosis is bactericidal under replicating and nonreplicating conditions. J Bacteriol 2012; 194:2614-9. [PMID: 22427625 PMCID: PMC3347204 DOI: 10.1128/jb.00224-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 03/07/2012] [Indexed: 02/02/2023] Open
Abstract
Proteins secreted by bacteria perform functions vital for cell survival and play a role in virulence in Mycobacterium tuberculosis. M. tuberculosis lepB (Rv2903c) encodes the sole homolog of the type I signal peptidase (SPase). The lepB gene is essential in M. tuberculosis, since we could delete the chromosomal copy only when a second functional copy was provided elsewhere. By placing expression under the control of an anhydrotetracycline-inducible promoter, we confirmed that reduced lepB expression was detrimental to growth. Furthermore, we demonstrated that a serine-lysine catalytic dyad, characteristic for SPase function, is required for LepB function. We confirmed the involvement of LepB in the secretion of a reporter protein fused to an M. tuberculosis signal peptide. An inhibitor of LepB (MD3; a beta-aminoketone) was active against M. tuberculosis, exhibiting growth inhibition and bactericidal activity. Overexpression of lepB reduced the susceptibility of M. tuberculosis to MD3, and downregulation resulted in increased susceptibility, suggesting that LepB is the true target of MD3. MD3 lead to a rapid loss of viability and cell lysis. Interestingly, the compound had increased potency in nonreplicating cells, causing a reduction in viable cell numbers below the detection limit after 24 h. These data suggest that protein secretion is required to maintain viability under starvation conditions and that secreted proteins play a critical role in generating and surviving the persistent state. We conclude that LepB is a promising novel target for drug discovery in M. tuberculosis, since its inhibition results in rapid killing of persistent and replicating organisms.
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Affiliation(s)
- J Ollinger
- Infectious Disease Research Institute, Seattle, Washington, USA
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17
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Pei Q, Christofferson A, Zhang H, Chai J, Huang N. Computational investigation of the enzymatic mechanisms of phosphothreonine lyase. Biophys Chem 2011; 157:16-23. [DOI: 10.1016/j.bpc.2011.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Revised: 04/02/2011] [Accepted: 04/03/2011] [Indexed: 11/29/2022]
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Mechanistic studies of the inactivation of TEM-1 and P99 by NXL104, a novel non-beta-lactam beta-lactamase inhibitor. Antimicrob Agents Chemother 2010; 54:5132-8. [PMID: 20921316 DOI: 10.1128/aac.00568-10] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
NXL104 is a potent inhibitor of class A and C serine β-lactamases, including KPC carbapenemases. Native and NXL104-inhibited TEM-1 and P99 β-lactamases analyzed by liquid chromatography-electrospray ionization-time of flight mass spectrometry revealed that the inactivated enzymes formed a covalent adduct with NXL104. The principal inhibitory characteristics of NXL104 against TEM-1 and P99 β-lactamases were determined, including partition ratios, dissociation constants (K), rate constants for deactivation (k(2)), and reactivation rates. NXL104 is a potent inhibitor of TEM-1 and P99, characterized by high carbamylation efficiencies (k(2)/K of 3.7 × 10(5) M(-1) s(-1) for TEM-1 and 1 × 10(4) M(-1) s(-1) for P99) and slow decarbamylation. Complete loss of β-lactamase activity was obtained at a 1/1 enzyme/NXL104 ratio, with a k(3) value (rate constant for formation of product and free enzyme) close to zero for TEM-1 and P99. Fifty percent inhibitory concentrations (IC(50)s) were evaluated on selected β-lactamases, and NXL104 was shown to be a very potent inhibitor of class A and C β-lactamases. IC(50)s obtained with NXL104 (from 3 nM to 170 nM) were globally comparable on the β-lactamases CTX-M-15 and SHV-4 with those obtained with the comparators (clavulanate, tazobactam, and sulbactam) but were far lower on TEM-1, KPC-2, P99, and AmpC than those of the comparators. In-depth studies on TEM-1 and P99 demonstrated that NXL104 had a comparable or better affinity and inactivation rate than clavulanate and tazobactam and in all cases an improved stability of the covalent enzyme/inhibitor complex.
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Calo D, Eichler J. Crossing the membrane in Archaea, the third domain of life. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:885-91. [PMID: 20347718 DOI: 10.1016/j.bbamem.2010.03.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 03/18/2010] [Accepted: 03/18/2010] [Indexed: 11/16/2022]
Abstract
Many of the recent advancements in the field of protein translocation, particularly from the structural perspective, have relied on Archaea. For instance, the solved structures of the translocon from the methanoarchaeon Methanocaldococcus jannaschii of the ribosomal large subunit from the haloarchaeon Haloarcula marismortui and of components of the SRP pathway from several archaeal species have provided novel insight into various aspects of the translocation event. Given the major contribution that Archaea have made to our understanding of how proteins enter and traverse membranes, it is surprising that relatively little is known of protein translocation in Archaea in comparison to the well-defined translocation pathways of Eukarya and Bacteria. What is known, however, points to archaeal translocation as comprising a mosaic of eukaryal and bacterial traits together with aspects of the process seemingly unique to this, the third domain of life. Here, current understanding of archaeal protein translocation is considered. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.
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Affiliation(s)
- Doron Calo
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva 84105, Israel
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20
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Bockstael K, Geukens N, Van Mellaert L, Herdewijn P, Anné J, Van Aerschot A. Evaluation of the type I signal peptidase as antibacterial target for biofilm-associated infections of Staphylococcus epidermidis. MICROBIOLOGY-SGM 2009; 155:3719-3729. [PMID: 19696105 DOI: 10.1099/mic.0.031765-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The development of antibacterial resistance is inevitable and is a major concern in hospitals and communities. Moreover, biofilm-grown bacteria are less sensitive to antimicrobial treatment. In this respect, the Gram-positive Staphylococcus epidermidis is an important source of nosocomial biofilm-associated infections. In the search for new antibacterial therapies, the type I signal peptidase (SPase I) serves as a potential target for development of antibacterials with a novel mode of action. This enzyme cleaves off the signal peptide from secreted proteins, making it essential for protein secretion, and hence for bacterial cell viability. S. epidermidis encodes three putative SPases I (denoted Sip1, Sip2 and Sip3), of which Sip1 lacks the catalytic lysine. In this report, we investigated the active S. epidermidis SPases I in more detail. Sip2 and Sip3 were found to complement a temperature-sensitive Escherichia coli lepB mutant, demonstrating their in vivo functional activity. In vitro functional activity of purified Sip2 and Sip3 proteins and inhibition of their activity by the SPase I inhibitor arylomycin A(2) were further illustrated using a fluorescence resonance energy transfer (FRET)-based assay. Furthermore, we demonstrated that SPase I not only is an attractive target for development of novel antibacterials against free-living bacteria, but also is a feasible target for biofilm-associated infections.
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Affiliation(s)
- Katrijn Bockstael
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Nick Geukens
- Laboratory of Bacteriology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Lieve Van Mellaert
- Laboratory of Bacteriology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Jozef Anné
- Laboratory of Bacteriology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Arthur Van Aerschot
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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Bockstael K, Geukens N, Rao CVS, Herdewijn P, Anné J, Van Aerschot A. An easy and fast method for the evaluation of Staphylococcus epidermidis type I signal peptidase inhibitors. J Microbiol Methods 2009; 78:231-7. [PMID: 19539664 DOI: 10.1016/j.mimet.2009.06.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 06/08/2009] [Accepted: 06/09/2009] [Indexed: 11/29/2022]
Abstract
In the framework of the search for new antimicrobial therapies to combat resistant bacteria, the type I signal peptidase (SPase I) serves as a potentially interesting target for the development of antibacterials with a new mode of action. Bacterial SPases I play a key role in protein secretion as they are responsible for the cleavage of signal peptides from secreted proteins. For the Gram-positive Staphylococcus epidermidis, an important source of biofilm-associated infections, three putative SPases I (denoted Sip1, Sip2, Sip3) have been described, of which Sip1 lacks the catalytic lysine. Here, we report the in vitro activity of purified Sip2 and Sip3 using pre-SceD as a native preprotein substrate of S. epidermidis and in a FRET-based assay. For the latter, a novel internally quenched fluorescent peptide substrate based on the signal peptide sequence of this native preprotein was developed and specific cleavage of this synthetic fluorogenic peptide substrate was demonstrated. The latter in vitro assay represents a rapid and reliable tool in future research for the identification and validation of potential SPase I inhibitors.
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Affiliation(s)
- Katrijn Bockstael
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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22
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Rao S, Bockstael K, Nath S, Engelborghs Y, Anné J, Geukens N. Enzymatic investigation of the Staphylococcus aureus type I signal peptidase SpsB - implications for the search for novel antibiotics. FEBS J 2009; 276:3222-34. [PMID: 19438721 DOI: 10.1111/j.1742-4658.2009.07037.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Staphylococcus aureus has one essential type I signal peptidase (SPase), SpsB, which has emerged as a potential target in the search for antibiotics with a new mode of action. In this framework, the biochemical properties of SpsB are described and compared with other previously characterized SPases. Two different substrates have been used to assess the in vitro processing activity of SpsB: (a) a native preprotein substrate immunodominant staphylococcal antigen A and (b) an intramolecularly quenched fluorogenic synthetic peptide based on the sequence of the SceD preprotein of Staphylococcus epidermidis for fluorescence resonance energy transfer-based analysis. Activity testing at different pH showed that the enzyme has an optimum pH of approximately 8. The pH-rate profile revealed apparent pK(a) values of 6.6 and 8.7. Similar to the other SPases, SpsB undergoes self-cleavage and, although the catalytic serine is retained in the self-cleavage product, a very low residual enzymatic activity remained. In contrast, a truncated derivative of SpsB, which was nine amino acids longer at the N-terminus compared to the self-cleavage product, retained activity. The specificity constants (k(cat)/K(m)) of the full-length and the truncated derivative were 1.85 +/- 0.13 x 10(3) m(-1).s(-1) and 59.4 +/- 6.4 m(-1).s(-1), respectively, as determined using the fluorogenic synthetic peptide substrate. These observations highlight the importance of the amino acids in the transmembrane segment and also those preceding the catalytic serine in the sequence of SpsB. Interestingly, we also found that the activity of the truncated SpsB increased in the presence of a non-ionic detergent.
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Affiliation(s)
- Smitha Rao
- Laboratory of Bacteriology, Katholieke Universiteit Leuven, Belgium
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Ekici OD, Paetzel M, Dalbey RE. Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration. Protein Sci 2008; 17:2023-37. [PMID: 18824507 DOI: 10.1110/ps.035436.108] [Citation(s) in RCA: 225] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Serine proteases comprise nearly one-third of all known proteases identified to date and play crucial roles in a wide variety of cellular as well as extracellular functions, including the process of blood clotting, protein digestion, cell signaling, inflammation, and protein processing. Their hallmark is that they contain the so-called "classical" catalytic Ser/His/Asp triad. Although the classical serine proteases are the most widespread in nature, there exist a variety of "nonclassical" serine proteases where variations to the catalytic triad are observed. Such variations include the triads Ser/His/Glu, Ser/His/His, and Ser/Glu/Asp, and include the dyads Ser/Lys and Ser/His. Other variations are seen with certain serine and threonine peptidases of the Ntn hydrolase superfamily that carry out catalysis with a single active site residue. This work discusses the structure and function of these novel serine proteases and threonine proteases and how their catalytic machinery differs from the prototypic serine protease class.
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Affiliation(s)
- Ozlem Doğan Ekici
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
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24
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Kim YT, Yoshida H, Kojima M, Kurita R, Nishii W, Muramatsu T, Ito H, Park SJ, Takahashi K. The Effects of Mutations in the Carboxyl-Terminal Region on the Catalytic Activity of Escherichia coli Signal Peptidase I. J Biochem 2008; 143:237-42. [DOI: 10.1093/jb/mvm212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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25
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Li T, Froeyen M, Herdewijn P. Computational alanine scanning and free energy decomposition for E. coli type I signal peptidase with lipopeptide inhibitor complex. J Mol Graph Model 2008; 26:813-23. [PMID: 17532654 DOI: 10.1016/j.jmgm.2007.04.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Revised: 04/24/2007] [Accepted: 04/28/2007] [Indexed: 11/18/2022]
Abstract
A thorough investigation of different roles of Escherichia coli type I signal peptidase residues binding to lipopeptide inhibitor has been performed by a combination of computational alanine scanning mutagenesis and free energy decomposition methods. PB and GB models are both used to evaluate the binding free energy in computational alanine scanning method and only GB model can be used to decompose the binding free energy on a per-residue basis. The regression analysis between the PB and GB model and also between the computational alanine scanning and free energy decomposition have been reported with a correlation coefficient of 0.96 and 0.83, respectively, which suggest they are both in fair agreement with each other. Moreover, the contribution components from van der Waals, electrostatic interaction, non-polar and polar energy of solvation, have been determined as well as the effects of backbones and side-chains. The results indicate that Lys145 is the most important residue for the binding but also acts as a general base, activating Ser90 to increase its nucleophility, recognizing and stabilizing the binding of lipopeptide inhibitor to the E. coli SPase. The hydroxyl group of Ser88 plays a key role for the binding of the inhibitor. Ser90 contributes more to the intramolecular interaction than to the intermolecular interaction. Tyr143 and Phe84 contribute larger van der Waals interaction energies, indicating that these residues can be important for the selection based on the shape of the inhibitors. The contributions from other several interfacial residues of the E. coli SPase are also analyzed. This study can be a guide for the optimization of lipopeptide inhibitors and future design of new therapeutic agents for the treatment of bacterial infections.
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Affiliation(s)
- Tong Li
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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26
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Abstract
Pili are a major surface feature of the human pathogen Streptococcus pyogenes (group A streptococcus [GAS]). The T3 pilus is composed of a covalently linked polymer of protein T3 (formerly Orf100 or Fct3) with an ancillary protein, Cpa, attached. A putative signal peptidase, SipA (also called LepA), has been identified in several pilus gene clusters of GAS. We demonstrate that the SipA2 allele of a GAS serotype M3 strain is required for synthesis of T3 pili. Heterologous expression in Escherichia coli showed that SipA2, along with the pilus backbone protein T3 and the sortase SrtC2, is required for polymerization of the T3 protein. In addition, we found that SipA2 is also required for linkage of the ancillary pilin protein Cpa to polymerized T3. Despite partial conservation of motifs of the type I signal peptidase family proteins, SipA lacks the highly conserved and catalytically important serine and lysine residues of these enzymes. Substitution of alanine for either of the two serine residues closest to the expected location of an active site serine demonstrated that these serine residues are both dispensable for T3 polymerization. Therefore, it seems unlikely that SipA functions as a signal peptidase. However, a T3 protein mutated at the P-1 position of the signal peptide cleavage site (alanine to arginine) was unstable in the presence of SipA2, suggesting that there is an interaction between SipA and T3. A possible chaperone-like function of SipA2 in T3 pilus formation is discussed.
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27
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Ekici OD, Karla A, Paetzel M, Lively MO, Pei D, Dalbey RE. Altered -3 substrate specificity of Escherichia coli signal peptidase 1 mutants as revealed by screening a combinatorial peptide library. J Biol Chem 2006; 282:417-25. [PMID: 17077081 DOI: 10.1074/jbc.m608779200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Signal peptidase functions to cleave signal peptides from preproteins at the cell membrane. It has a substrate specificity for small uncharged residues at -1 (P1) and aliphatic residues at the -3 (P3) position. Previously, we have reported that certain alterations of the Ile-144 and Ile-86 residues in Escherichia coli signal peptidase I (SPase) can change the specificity such that signal peptidase is able to cleave pro-OmpA nuclease A in vitro after phenylalanine or asparagine residues at the -1 position (Karla, A., Lively, M. O., Paetzel, M. and Dalbey, R. (2005) J. Biol. Chem. 280, 6731-6741). In this study, screening of a fluorescence resonance energy transfer-based peptide library revealed that the I144A, I144C, and I144C/I86T SPase mutants have a more relaxed substrate specificity at the -3 position, in comparison to the wild-type SPase. The double mutant tolerated arginine, glutamine, and tyrosine residues at the -3 position of the substrate. The altered specificity of the I144C/I86T mutant was confirmed by in vivo processing of pre-beta-lactamase containing non-canonical arginine and glutamine residues at the -3 position. This work establishes Ile-144 and Ile-86 as key P3 substrate specificity determinants for signal peptidase I and demonstrates the power of the fluorescence resonance energy transfer-based peptide library approach in defining the substrate specificity of proteases.
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Affiliation(s)
- Ozlem Dogan Ekici
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
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28
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Fine A, Irihimovitch V, Dahan I, Konrad Z, Eichler J. Cloning, expression, and purification of functional Sec11a and Sec11b, type I signal peptidases of the archaeon Haloferax volcanii. J Bacteriol 2006; 188:1911-9. [PMID: 16484202 PMCID: PMC1426568 DOI: 10.1128/jb.188.5.1911-1919.2006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Across evolution, type I signal peptidases are responsible for the cleavage of secretory signal peptides from proteins following their translocation across membranes. In Archaea, type I signal peptidases combine domain-specific features with traits found in either their eukaryal or bacterial counterparts. Eukaryal and bacterial type I signal peptidases differ in terms of catalytic mechanism, pharmacological profile, and oligomeric status. In this study, genes encoding Sec11a and Sec11b, two type I signal peptidases of the halophilic archaeon Haloferax volcanii, were cloned. Although both genes are expressed in cells grown in rich medium, gene deletion approaches suggest that Sec11b, but not Sec11a, is essential. For purification purposes, tagged versions of the protein products of both genes were expressed in transformed Haloferax volcanii, with Sec11a and Sec11b being fused to a cellulose-binding domain capable of interaction with cellulose in hypersaline surroundings. By employing an in vitro signal peptidase assay designed for use with high salt concentrations such as those encountered by halophilic archaea such as Haloferax volcanii, the signal peptide-cleaving activities of both isolated membranes and purified Sec11a and Sec11b were addressed. The results show that the two enzymes differentially cleave the assay substrate, raising the possibility that the Sec11a and Sec11b serve distinct physiological functions.
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Affiliation(s)
- Amir Fine
- Dept. of Life Sciences, Ben Gurion University, P.O. Box 653, Beersheva 84105, Israel
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29
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Tuteja R. Type I signal peptidase: An overview. Arch Biochem Biophys 2005; 441:107-11. [PMID: 16126156 DOI: 10.1016/j.abb.2005.07.013] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Accepted: 07/23/2005] [Indexed: 11/28/2022]
Abstract
The signal hypothesis suggests that proteins contain information within their amino acid sequences for protein targeting to the membrane. These distinct targeting sequences are cleaved by specific enzymes known as signal peptidases. There are various type of signal peptidases known such as type I, type II, and type IV. Type I signal peptidases are indispensable enzymes, which catalyze the cleavage of the amino-terminal signal-peptide sequences from preproteins, which are translocated across biological membranes. These enzymes belong to a novel group of serine proteases, which generally utilize a Ser-Lys or Ser-His catalytic dyad instead of the prototypical Ser-His-Asp triad. Despite having no distinct consensus sequence other than a commonly found 'Ala-X-Ala' motif preceding the cleavage site, signal sequences are recognized by type I signal peptidase with high fidelity. Type I signal peptidases have been found in bacteria, archaea, fungi, plants, and animals. In this review, I present an overview of bacterial type I signal peptidases and describe some of their properties in detail.
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Affiliation(s)
- Renu Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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van Roosmalen ML, Geukens N, Jongbloed JDH, Tjalsma H, Dubois JYF, Bron S, van Dijl JM, Anné J. Type I signal peptidases of Gram-positive bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1694:279-97. [PMID: 15546672 DOI: 10.1016/j.bbamcr.2004.05.006] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2003] [Accepted: 05/12/2004] [Indexed: 11/21/2022]
Abstract
Proteins that are exported from the cytoplasm to the periplasm and outer membrane of Gram-negative bacteria, or the cell wall and growth medium of Gram-positive bacteria, are generally synthesized as precursors with a cleavable signal peptide. During or shortly after pre-protein translocation across the cytoplasmic membrane, the signal peptide is removed by signal peptidases. Importantly, pre-protein processing by signal peptidases is essential for bacterial growth and viability. This review is focused on the signal peptidases of Gram-positive bacteria, Bacillus and Streptomyces species in particular. Evolutionary concepts, current knowledge of the catalytic mechanism, substrate specificity requirements and structural aspects are addressed. As major insights in signal peptidase function and structure have been obtained from studies on the signal peptidase LepB of Escherichia coli, similarities and differences between this enzyme and known Gram-positive signal peptidases are highlighted. Notably, while the incentive for previous research on Gram-positive signal peptidases was largely based on their role in the biotechnologically important process of protein secretion, present-day interest in these essential enzymes is primarily derived from the idea that they may serve as targets for novel anti-microbials.
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Affiliation(s)
- Maarten L van Roosmalen
- Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, Netherlands
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Karla A, Lively MO, Paetzel M, Dalbey R. The Identification of Residues That Control Signal Peptidase Cleavage Fidelity and Substrate Specificity. J Biol Chem 2005; 280:6731-41. [PMID: 15598653 DOI: 10.1074/jbc.m413019200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Signal peptidase, which removes signal peptides from preproteins, has a substrate specificity for small uncharged residues at -1 (P1) and small or larger aliphatic residues at the -3 (P3) position. Structures of the catalytic domain with a 5S-penem inhibitor and a lipopeptide inhibitor reveal candidate residues that make up the S1 and S3 pockets that bind the P1 and P3 specificity residues of the preprotein substrate. We have used site-directed mutagenesis, mass spectrometric analysis, and in vivo and in vitro activity assays as well as molecular modeling to examine the importance of the substrate pocket residues. Generally, we find that the S1 and S3 binding sites can tolerate changes that are expected to increase or decrease the size of the pocket without large effects on activity. One residue that contributes to the high fidelity of cleavage of signal peptidase is the Ile-144 residue. Changes of the Ile-144 residue to cysteine result in cleavage at multiple sites, as determined by mass spectrometry and Edman sequencing analysis. In addition, we find that signal peptidase is able to cleave after phenylalanine at the -1 residue in a double mutant in which both Ile-86 and Ile-144 were changed to an alanine. Also, alteration of the Ile-144 and Ile-86 residues to the corresponding residues found in the homologous Imp1 protease changes the specificity to promote cleavage following a -1 Asn residue. This work shows that Ile-144 and Ile-86 contribute to the signal peptidase substrate specificity and that Ile-144 is important for the accuracy of the cleavage reaction.
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Affiliation(s)
- Andrew Karla
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
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32
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Lammertyn E, Van Mellaert L, Meyen E, Lebeau I, De Buck E, Anné J, Geukens N. Molecular and functional characterization of type I signal peptidase from Legionella pneumophila. MICROBIOLOGY-SGM 2004; 150:1475-1483. [PMID: 15133109 DOI: 10.1099/mic.0.26973-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Legionella pneumophila is a facultative intracellular Gram-negative rod-shaped bacterium that has become an important cause of both community-acquired and nosocomial pneumonia. Numerous studies concerning the unravelling of the virulence mechanism of this important pathogen have been initiated. As evidence is now accumulating for the involvement of protein secretion systems in bacterial virulence in general, the type I signal peptidase (LepB) of L. pneumophila was of particular interest. This endopeptidase plays an essential role in the processing of preproteins carrying a typical amino-terminal signal peptide, upon translocation across the cytoplasmic membrane. This paper reports the cloning and the transcriptional analysis of the L. pneumophila lepB gene encoding the type I signal peptidase (SPase). Reverse transcription PCR experiments showed clear lepB expression when L. pneumophila was grown both in culture medium, and also intracellularly in Acanthamoeba castellanii, a natural eukaryotic host of L. pneumophila. In addition, LepB was shown to be encoded by a polycistronic mRNA transcript together with two other proteins, i.e. a LepA homologue and a ribonuclease III homologue. SPase activity of the LepB protein was demonstrated by in vivo complementation analysis in a temperature-sensitive Escherichia coli lepB mutant. Protein sequence and predicted membrane topology were compared to those of leader peptidases of other Gram-negative human pathogens. Most strikingly, a strictly conserved methionine residue in the substrate binding pocket was replaced by a leucine residue, which might influence substrate recognition. Finally it was shown by in vivo experiments that L. pneumophila LepB is a target for (5S,6S)-6-[(R)-acetoxyethyl]-penem-3-carboxylate, a specific inhibitor of type I SPases.
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Affiliation(s)
- Elke Lammertyn
- Laboratory of Bacteriology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Lieve Van Mellaert
- Laboratory of Bacteriology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Eef Meyen
- Laboratory of Bacteriology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Ilya Lebeau
- Laboratory of Bacteriology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Emmy De Buck
- Laboratory of Bacteriology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Jozef Anné
- Laboratory of Bacteriology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Nick Geukens
- Laboratory of Bacteriology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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33
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Kulanthaivel P, Kreuzman AJ, Strege MA, Belvo MD, Smitka TA, Clemens M, Swartling JR, Minton KL, Zheng F, Angleton EL, Mullen D, Jungheim LN, Klimkowski VJ, Nicas TI, Thompson RC, Peng SB. Novel lipoglycopeptides as inhibitors of bacterial signal peptidase I. J Biol Chem 2004; 279:36250-8. [PMID: 15173160 DOI: 10.1074/jbc.m405884200] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Signal peptidase (SPase) I is responsible for the cleavage of signal peptides of many secreted proteins in bacteria. Because of its unique physiological and biochemical properties, it serves as a potential target for development of novel antibacterial agents. In this study, we report the production, isolation, and structure determination of a family of structurally related novel lipoglycopeptides from a Streptomyces sp. as inhibitors of SPase I. Detailed spectroscopic analyses, including MS and NMR, revealed that these lipoglycopeptides share a common 14-membered cyclic peptide core, an acyclic tripeptide chain, and a deoxy-alpha-mannose sugar, but differ in the degree of oxidation of the N-methylphenylglycine residue and the length and branching of the fatty acyl chain. Biochemical analysis demonstrated that these peptides are potent and competitive inhibitors of SPase I with K(i) 50 to 158 nm. In addition, they showed modest antibacterial activity against a panel of pathogenic Gram-positive and Gram-negative bacteria with minimal inhibitory concentration of 8-64 microm against Streptococcus pneumonniae and 4-8 microm against Escherichia coli. Notably, they mechanistically blocked the protein secretion in whole cells as demonstrated by inhibiting beta-lactamase release from Staphylococcus aureus. Taken together, the present discovery of a family of novel lipoglycopeptides as potent inhibitors of bacterial SPase I may lead to the development of a novel class of broad-spectrum antibiotics.
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Kim YT, Kurita R, Kojima M, Nishii W, Tanokura M, Muramatsu T, Ito H, Takahashi K. Identification of arginine residues important for the activity of Escherichia coli signal peptidase I. Biol Chem 2004; 385:381-8. [PMID: 15195997 DOI: 10.1515/bc.2004.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Escherichia coil signal peptidase I (leader peptidase, SPase I) is an integral membrane serine protease that catalyzes the cleavage of signal (leader) peptides from pre-forms of membrane or secretory proteins. We previously demonstrated that E. coil SPase I was significantly inactivated by reaction with phenylglyoxal with concomitant modification of three to four of the total 17 arginine residues in the enzyme. This result indicated that several arginine residues are important for the optimal activity of the enzyme. In the present study, we have constructed 17 mutants of the enzyme by site-directed mutagenesis to investigate the role of individual arginine residues in the enzyme. Mutation of Arg127, Arg146, Arg198, Arg199, Arg226, Arg236, Arg275, Arg282, and Arg295 scarcely affected the enzyme activity in vivo and in vitro. However, the enzymatic activity toward a synthetic substrate was significantly decreased by replacements of Arg77, Arg222, Arg315, or Arg318 with alanine/lysine. The kcat values of the R77A, R77K, R222A, R222K, R315A, R318A, and R318K mutant enzymes were about 5.5-fold smaller than that of the wild-type enzyme, whereas the Km values of these mutant enzymes were almost identical with that of the wild-type. Moreover, the complementing abilities in E. Arg222, Arg315, coil IT41 were lost completely when Arg77, or Arg318 was replaced with alanine/lysine. The circular dichroism spectra and other enzymatic properties of these mutants were comparable to those of the wild-type enzyme, indicating no global conformational changes. However, the thermostability of R222A, R222K, R315A, and R318K was significantly lower compared to the wild type. Therefore, Arg77, Arg222, Arg315, and Arg318 are thought to be important for maintaining the proper and stable conformation of SPase I.
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Affiliation(s)
- Yong-Tae Kim
- Department of Chemistry, Aoyama Gakuin University, Sagamihara, Kanagawa 229-8558, Japan.
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35
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Kriakov J, Lee SH, Jacobs WR. Identification of a regulated alkaline phosphatase, a cell surface-associated lipoprotein, in Mycobacterium smegmatis. J Bacteriol 2003; 185:4983-91. [PMID: 12897018 PMCID: PMC166462 DOI: 10.1128/jb.185.16.4983-4991.2003] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although alkaline phosphatases are common in a wide variety of bacteria, there has been no prior evidence for alkaline phosphatases in Mycobacterium smegmatis. Here we report that transposon insertions in the pst operon, encoding homologues of an inorganic phosphate transporter, leads to constitutive expression of a protein with alkaline phosphatase activity. DNA sequence analysis revealed that M. smegmatis does indeed have a phoA gene that shows high homology to other phoA genes. The M. smegmatis phoA gene was shown to be induced by phosphate starvation and thus negatively regulated by the pst operon. Interestingly, the putative M. smegmatis PhoA has a hydrophobic N-terminal domain which resembles a lipoprotein signal sequence. The M. smegmatis PhoA was demonstrated to be an exported protein associated with the cell surface. Furthermore, immunoprecipitation of PhoA from [(14)C]acetate-labeled M. smegmatis cell lysates demonstrated that this phosphatase is a lipoprotein.
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Affiliation(s)
- Jordan Kriakov
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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36
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Rahman MS, Simser JA, Macaluso KR, Azad AF. Molecular and functional analysis of the lepB gene, encoding a type I signal peptidase from Rickettsia rickettsii and Rickettsia typhi. J Bacteriol 2003; 185:4578-84. [PMID: 12867468 PMCID: PMC165774 DOI: 10.1128/jb.185.15.4578-4584.2003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The type I signal peptidase lepB genes from Rickettsia rickettsii and Rickettsia typhi, the etiologic agents of Rocky Mountain spotted fever and murine typhus, respectively, were cloned and characterized. Sequence analysis of the cloned lepB genes from R. rickettsii and R. typhi shows open reading frames of 801 and 795 nucleotides, respectively. Alignment analysis of the deduced amino acid sequences reveals the presence of highly conserved motifs that are important for the catalytic activity of bacterial type I signal peptidase. Reverse transcription-PCR and Northern blot analysis demonstrated that the lepB gene of R. rickettsii is cotranscribed in a polycistronic message with the putative nuoF (encoding NADH dehydrogenase I chain F), secF (encoding protein export membrane protein), and rnc (encoding RNase III) genes in a secF-nuoF-lepB-rnc cluster. The cloned lepB genes from R. rickettsii and R. typhi have been demonstrated to possess signal peptidase I activity in Escherichia coli preprotein processing in vivo by complementation assay.
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Affiliation(s)
- M Sayeedur Rahman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
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37
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Affiliation(s)
- Mark Paetzel
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
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38
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Barbosa MDFS, Lin S, Markwalder JA, Mills JA, DeVito JA, Teleha CA, Garlapati V, Liu C, Thompson A, Trainor GL, Kurilla MG, Pompliano DL. Regulated expression of the Escherichia coli lepB gene as a tool for cellular testing of antimicrobial compounds that inhibit signal peptidase I in vitro. Antimicrob Agents Chemother 2002; 46:3549-54. [PMID: 12384363 PMCID: PMC128713 DOI: 10.1128/aac.46.11.3549-3554.2002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli under-expressing lepB was utilized to test cellular inhibition of signal peptidase I (SPase). For the construction of a lepB regulatable strain, the E. coli lepB gene was cloned into pBAD, with expression dependent on L-arabinose. The chromosomal copy of lepB was replaced with a kanamycin resistance gene, which was subsequently removed. SPase production by the lepB regulatable strain in the presence of various concentrations of L-arabinose was monitored by Western blot analysis. At lower arabinose concentrations growth proceeded more slowly, possibly due to a decrease of SPase levels in the cells. A penem SPase inhibitor with little antimicrobial activity against E. coli when tested at 100 micro M was utilized to validate the cell-based system. Under-expression of lepB sensitized the cells to penem, with complete growth inhibition observed at 10 to 30 micro M. Growth was rescued by increasing the SPase levels. The cell-based assay was used to test cellular inhibition of SPase by compounds that inhibit the enzyme in vitro. MD1, MD2, and MD3 are SPase inhibitors with antimicrobial activity against Staphylococcus aureus, although they do not inhibit growth of E. coli. MD1 presented the best spectrum of antimicrobial activity. Both MD1 and MD2 prevented growth of E. coli under-expressing lepB in the presence of polymyxin B nonapeptide, with growth rescue observed when wild-type levels of SPase were produced. MD3 and MD4, a reactive analog of MD3, inhibited growth of E. coli under-expressing lepB. However, growth rescue in the presence of these compounds following increased lepB expression was observed only after prolonged incubation.
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Affiliation(s)
- Maria D F S Barbosa
- Departments of Antimicrobial Research, Bristol-Myers Squibb Company, Wilmington, Delaware 19880, USA.
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39
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Zheng F, Angleton EL, Lu J, Peng SB. In vitro and in vivo self-cleavage of Streptococcus pneumoniae signal peptidase I. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:3969-77. [PMID: 12180973 DOI: 10.1046/j.1432-1033.2002.03083.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have previously demonstrated that Streptococcus pneumoniae signal peptidase (SPase) I catalyzes a self-cleavage to result in a truncated product, SPase37-204 [Peng, S.B., Wang, L., Moomaw, J., Peery, R.B., Sun, P.M., Johnson, R.B., Lu, J., Treadway, P., Skatrud, P.L. & Wang, Q.M. (2001) J. Bacteriol.183, 621-627]. In this study, we investigated the effect of phospholipid on invitro self-cleavage of S. pneumoniae SPase I. In the presence of phospholipid, the self-cleavage predominantly occurred at one cleavage site between Gly36-His37, whereas the self-cleavage occurred at multiple sites in the absence of phospholipid, and two additional self-cleavage sites, Ala65-His66 and Ala143-Phe144, were identified. All three self-cleavage sites strongly resemble the signal peptide cleavage site and follow the (-1, -3) rule for SPase I recognition. Kinetic analysis demonstrated that self-cleavage is a concentration dependent and intermolecular event, and the activity in the presence of phospholipid is 25-fold higher than that in the absence of phospholipid. Biochemical analysis demonstrated that SPase37-204, the major product of the self-cleavage totally lost activity to cleave its substrates, indicating that the self-cleavage resulted in the inactivation of the enzyme. More importantly, the self-cleavage was demonstrated to be happening in vivo in all the growth phases of S. pneumoniae cells. The bacterial cells keep the active SPase I at the highest level in exponential growth phase, suggesting that the self-cleavage may play an important role in regulating the activity of the enzyme under different conditions.
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Affiliation(s)
- Feng Zheng
- Infectious Diseases Research, Lilly Research Laboratories, Indianapolis, IN 46285, USA
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40
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Bacterial Type I Signal Peptidases. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s1874-6047(02)80003-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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41
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Gallagher J, Kaderbhai NN, Kaderbhai MA. Kinetic constants of signal peptidase I using cytochrome b5 as a precursor substrate. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1550:1-5. [PMID: 11738082 DOI: 10.1016/s0167-4838(01)00265-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A procedure is described for measuring Escherichia coli signal peptidase I activity which exploits an intact precursor protein composed of the alkaline phosphatase signal peptide fused to the full length mammalian cytochrome b5. This cytochrome b5 precursor protein has been extensively characterised and shown to be processed accurately by purified signal peptidase I [Protein Expr. Purif. 7 (1996) 237]. The amphipathic, chimaeric cytochrome b5 precursor was isolated in mg quantities in a highly homogeneous state under non-denaturing conditions. The processing of the cytochrome b5 precursor by signal peptidase displayed Michaelis-Menten kinetics with K(m)=50 microM and k(cat)=11 s(-1). The K(m) was 20-fold lower than that obtained with signal peptide substrates and 3-fold higher than that reported for pro-OmpA-nuclease A precursor fusion. The corresponding turnover number, k(cat), was four orders of magnitude greater than the peptide substrates but was 2-fold lower than pro-OmpA-nuclease A precursor fusion. These results confirm that both the affinities and the catalytic power of the signal peptidase are significantly higher for macromolecular precursor substrates than for the shorter signal peptide substrates.
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Affiliation(s)
- J Gallagher
- Institute of Biological Sciences, The University of Wales Aberystwyth, SY23 3DD, Aberystwyth, UK
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42
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Peng SB, Zheng F, Angleton EL, Smiley D, Carpenter J, Scott JE. Development of an Internally Quenched Fluorescent Substrate and a Continuous Fluorimetric Assay for Streptococcus pneumoniae Signal Peptidase I. Anal Biochem 2001; 293:88-95. [PMID: 11373083 DOI: 10.1006/abio.2001.5102] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Signal peptidase (SPase) I is responsible for the cleavage of signal peptides of many secreted proteins in bacteria and serves as a potential target for the development of novel antibacterial agents due to its unique physiological and biochemical properties. In this paper, we describe a novel fluorogenic substrate, KLTFGTVK(Abz)PVQAIAGY(NO2)EWL, in which 2-aminobenzoic acid (Abz) and 3-nitrotyrosine (Y(NO2)) were used as the fluorescent donor and acceptor, respectively. The substrate can be cleaved by both Streptococcus pneumoniae and Escherichia coli SPase I. Upon cleavage of the fluorogenic substrate by SPase I, the fluorescent intensity increases and can be monitored continuously by spectrofluorometer. Kinetic analysis with S. pneumoniae SPase I demonstrated that the K(m) value for the substrate is 118.1 microM, and the k(cat) value is 0.032 s(-1). Mass spectrometric analysis and peptide sequencing of the two cleaved products confirmed that the cleavage occurs specifically at the predicted site. More interestingly, the positively charged lysine in the N-terminus of the substrate was demonstrated to be important for effective cleavage. Phospholipids were found to stimulate the cleavage reaction. This stimulation by phospholipids is dependent upon the N-terminal charge of the substrate, indicating that the interaction of the positively charged substrate with anionic phospholipids is important for maintaining the substrate in certain conformation for cleavage. The substrate and assay described here can be readily automated and utilized for the identification of potential antibacterial agents.
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Affiliation(s)
- S B Peng
- Infectious Diseases Research, Lilly Research Laboratories, Indianapolis, IN 46285, USA.
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43
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Peng SB, Wang L, Moomaw J, Peery RB, Sun PM, Johnson RB, Lu J, Treadway P, Skatrud PL, Wang QM. Biochemical characterization of signal peptidase I from gram-positive Streptococcus pneumoniae. J Bacteriol 2001; 183:621-7. [PMID: 11133956 PMCID: PMC94918 DOI: 10.1128/jb.183.2.621-627.2001] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2000] [Accepted: 10/25/2000] [Indexed: 11/20/2022] Open
Abstract
Bacterial signal peptidase I is responsible for proteolytic processing of the precursors of secreted proteins. The enzymes from gram-negative and -positive bacteria are different in structure and specificity. In this study, we have cloned, expressed, and purified the signal peptidase I of gram-positive Streptococcus pneumoniae. The precursor of streptokinase, an extracellular protein produced in pathogenic streptococci, was identified as a substrate of S. pneumoniae signal peptidase I. Phospholipids were found to stimulate the enzymatic activity. Mutagenetic analysis demonstrated that residues serine 38 and lysine 76 of S. pneumoniae signal peptidase I are critical for enzyme activity and involved in the active site to form a serine-lysine catalytic dyad, which is similar to LexA-like proteases and Escherichia coli signal peptidase I. Similar to LexA-like proteases, S. pneumoniae signal peptidase I catalyzes an intermolecular self-cleavage in vitro, and an internal cleavage site has been identified between glycine 36 and histidine 37. Sequence analysis revealed that the signal peptidase I and LexA-like proteases show sequence homology around the active sites and some common properties around the self-cleavage sites. All these data suggest that signal peptidase I and LexA-like proteases are closely related and belong to a novel class of serine proteases.
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Affiliation(s)
- S B Peng
- Infectious Diseases Research, Lilly Research Laboratories, Indianapolis, Indiana 46285, USA.
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44
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Eisenbrandt R, Kalkum M, Lurz R, Lanka E. Maturation of IncP pilin precursors resembles the catalytic Dyad-like mechanism of leader peptidases. J Bacteriol 2000; 182:6751-61. [PMID: 11073921 PMCID: PMC111419 DOI: 10.1128/jb.182.23.6751-6761.2000] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The pilus subunit, the pilin, of conjugative IncP pili is encoded by the trbC gene. IncP pilin is composed of 78 amino acids forming a ring structure (R. Eisenbrandt, M. Kalkum, E.-M. Lai, C. I. Kado, and E. Lanka, J. Biol. Chem. 274:22548-22555, 1999). Three enzymes are involved in maturation of the pilin: LepB of Escherichia coli for signal peptide removal and a yet-unidentified protease for removal of 27 C-terminal residues. Both enzymes are chromosome encoded. Finally, the inner membrane-associated IncP TraF replaces a four-amino-acid C-terminal peptide with the truncated N terminus, yielding the cyclic polypeptide. We refer to the latter process as "prepilin cyclization." We have used site-directed mutagenesis of trbC and traF to unravel the pilin maturation process. Each of the mutants was analyzed for its phenotypes of prepilin cyclization, pilus formation, donor-specific phage adsorption, and conjugative DNA transfer abilities. Effective prepilin cyclization was determined by matrix-assisted laser desorption-ionization-mass spectrometry using an optimized sample preparation technique of whole cells and trans-3-indolyl acrylic acid as a matrix. We found that several amino acid exchanges in the TrbC core sequence allow prepilin cyclization but disable the succeeding pilus assembly. We propose a mechanism explaining how the signal peptidase homologue TraF attacks a C-terminal section of the TrbC core sequence via an activated serine residue. Rather than cleaving and releasing hydrolyzed peptides, TraF presumably reacts as a peptidyl transferase, involving the N terminus of TrbC in the aminolysis of a postulated TraF-acetyl-TrbC intermediate. Under formal loss of a C-terminal tetrapeptide, a new peptide bond is formed in a concerted action, connecting serine 37 with glycine 114 of TrbC.
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Affiliation(s)
- R Eisenbrandt
- Max-Planck-Institut für Molekulare Genetik, Dahlem, D-14195 Berlin, Germany
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45
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Tjalsma H, Stover AG, Driks A, Venema G, Bron S, van Dijl JM. Conserved serine and histidine residues are critical for activity of the ER-type signal peptidase SipW of Bacillus subtilis. J Biol Chem 2000; 275:25102-8. [PMID: 10827084 DOI: 10.1074/jbc.m002676200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Type I signal peptidases (SPases) are required for the removal of signal peptides from translocated proteins and, subsequently, release of the mature protein from the trans side of the membrane. Interestingly, prokaryotic (P-type) and endoplasmic reticular (ER-type) SPases are functionally equivalent, but structurally quite different, forming two distinct SPase families that share only few conserved residues. P-type SPases were, so far, exclusively identified in eubacteria and organelles, whereas ER-type SPases were found in the three kingdoms of life. Strikingly, the presence of ER-type SPases appears to be limited to sporulating Gram-positive eubacteria. The present studies were aimed at the identification of potential active site residues of the ER-type SPase SipW of Bacillus subtilis, which is required for processing of the spore-associated protein TasA. Conserved serine, histidine, and aspartic acid residues are critical for SipW activity, suggesting that the ER-type SPases employ a Ser-His-Asp catalytic triad or, alternatively, a Ser-His catalytic dyad. In contrast, the P-type SPases employ a Ser-Lys catalytic dyad (Paetzel, M., Dalbey, R. E., and Strynadka, N. C. J. (1998) Nature 396, 186-190). Notably, catalytic activity of SipW was not only essential for pre-TasA processing, but also for the incorporation of mature TasA into spores.
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Affiliation(s)
- H Tjalsma
- Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Haren, The Netherlands
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46
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Paetzel M, Dalbey RE, Strynadka NC. The structure and mechanism of bacterial type I signal peptidases. A novel antibiotic target. Pharmacol Ther 2000; 87:27-49. [PMID: 10924740 DOI: 10.1016/s0163-7258(00)00064-4] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Type I signal peptidases are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidases are unique serine proteases that utilize a Ser/Lys catalytic dyad mechanism in place of the classical Ser/His/Asp catalytic triad mechanism. They represent a potential novel antibiotic target at the bacterial membrane surface. This review will discuss the bacterial signal peptidases that have been characterized to date, as well as putative signal peptidase sequences that have been recognized via bacterial genome sequencing. We review the investigations into the mechanism of Escherichia coli and Bacillus subtilis signal peptidase, and discuss the results in light of the recent crystal structure of the E. coli signal peptidase in complex with a beta-lactam-type inhibitor. The proposed conserved structural features of Type I signal peptidases give additional insight into the mechanism of this unique enzyme.
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Affiliation(s)
- M Paetzel
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
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Klenotic PA, Carlos JL, Samuelson JC, Schuenemann TA, Tschantz WR, Paetzel M, Strynadka NC, Dalbey RE. The role of the conserved box E residues in the active site of the Escherichia coli type I signal peptidase. J Biol Chem 2000; 275:6490-8. [PMID: 10692453 DOI: 10.1074/jbc.275.9.6490] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Type I signal peptidases are integral membrane proteins that function to remove signal peptides from secreted and membrane proteins. These enzymes carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases. Site-directed scanning mutagenesis was used to obtain a qualitative assessment of which residues in the fifth conserved region, Box E, of the Escherichia coli signal peptidase I are critical for maintaining a functional enzyme. First, we find that there is no requirement for activity for a salt bridge between the invariant Asp-273 and the Arg-146 residues. In addition, we show that the conserved Ser-278 is required for optimal activity as well as conserved salt bridge partners Asp-280 and Arg-282. Finally, Gly-272 is essential for signal peptidase I activity, consistent with it being located within van der Waals proximity to Ser-278 and general base Lys-145 side-chain atoms. We propose that replacement of the hydrogen side chain of Gly-272 with a methyl group results in steric crowding, perturbation of the active site conformation, and specifically, disruption of the Ser-90/Lys-145 hydrogen bond. A refined model is proposed for the catalytic dyad mechanism of signal peptidase I in which the general base Lys-145 is positioned by Ser-278, which in turn is held in place by Asp-280.
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Affiliation(s)
- P A Klenotic
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
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Chen X, Van Valkenburgh C, Fang H, Green N. Signal peptides having standard and nonstandard cleavage sites can be processed by Imp1p of the mitochondrial inner membrane protease. J Biol Chem 1999; 274:37750-4. [PMID: 10608835 DOI: 10.1074/jbc.274.53.37750] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have performed a site-directed mutagenesis study showing that residues comprising the type I signal peptidase signature in the two catalytic subunits of the yeast inner membrane protease, Imp1p and Imp2p, are functionally important, consistent with the idea that these subunits contain a serine/lysine catalytic dyad. Previous studies have shown that Imp1p cleaves signal peptides having asparagine at the -1 position, which deviates from the typical signal peptide possessing a small uncharged amino acid at this position. To determine whether asparagine is responsible for the nonoverlapping substrate specificities exhibited by the inner membrane protease subunits, we have substituted asparagine with 19 amino acids in the Imp1p substrate i-cytochrome (cyt) b(2). The resulting signal peptides containing alanine, serine, cysteine, leucine, and methionine can be cleaved efficiently by Imp1p. The remaining mutant signal peptides are cleaved inefficiently or not at all. Surprisingly, none of the amino acid changes results in the recognition of i-cyt b(2) by Imp2p, whose natural substrate, i-cyt c(1), has alanine at the -1 position. The data demonstrate that (i) although the -1 residue is important in substrates recognized by Imp1p, signal peptides having standard and nonstandard cleavage sites can be processed by Imp1p, and (ii) a -1 asparagine does not govern the substrate specificity of the inner membrane protease subunits.
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Affiliation(s)
- X Chen
- Department of Microbiology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232-2363, USA
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Schacht S, Van Mellaert L, Lammertyn E, Tjalsma H, van Dijl JM, Bron S, Anné J. The Sip(Sli) gene of Streptomyces lividans TK24 specifies an unusual signal peptidase with a putative C-terminal transmembrane anchor. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 1999; 9:79-88. [PMID: 10520736 DOI: 10.3109/10425179809086432] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Type I signal peptidases (SPases) are a widespread family of enzymes which remove signal peptides from proteins translocated across cellular membranes. Here, we report the first isolation of a gene coding for type I signal peptidase of Streptomyces, denoted Sip(Sli). The sip(sli) gene specifies a protein of 291 amino acids. Thus Sip(Sli) is much larger (approximately 100 amino acids) than other known SPases of Gram-positive bacteria and resembles SPases of Gram-negative bacteria, showing the highest degree of similarity to an SPase of the cyanobacterium Phormidium laminosum. Sip(Sli) contains conserved serine and lysine residues, which are believed to be required for the catalytic activity. Similar to other known SPases from Gram-positive bacteria, Sip(Sli) seems to have only one N-terminal transmembrane anchor. In addition, Sip(Sli) seems to contain a second transmembrane anchor at the C-terminus, which is an unusual feature for type I signal peptidases.
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Affiliation(s)
- S Schacht
- Laboratory of Bacteriology, Rega Institute, Katholieke Universiteit Leuven, Belgium
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Parro V, Mellado RP. A new signal peptidase gene from Streptomyces lividans TK21. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 1999; 9:71-7. [PMID: 10520735 DOI: 10.3109/10425179809086431] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Using synthetic oligonucleotides derived from known signal peptidase genes and a multicopy plasmid as a vector, a signal peptidase gene (sipZ) from Streptomyces lividansTK21 has been cloned. The primary structure of the gene has been determined and the amino acid composition of the SipZ protein inferred. SipZ is 258 aa long and showed homology to other type I signal peptidases, containing like them an N-terminal transmembrane anchor. Alignment of SipZ with other known SPases allowed the identification of a conserved sequence of amino acids specific for Gram-positive bacteria.
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Affiliation(s)
- V Parro
- Centro Nacional de Biotecnología (CSIC), Madrid, Spain
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