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Kifayat S, Yele V, Ashames A, Sigalapalli DK, Bhandare RR, Shaik AB, Nasipireddy V, Sanapalli BKR. Filamentous temperature sensitive mutant Z: a putative target to combat antibacterial resistance. RSC Adv 2023; 13:11368-11384. [PMID: 37057268 PMCID: PMC10089256 DOI: 10.1039/d3ra00013c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/28/2023] [Indexed: 04/15/2023] Open
Abstract
In the pre-antibiotic era, common bacterial infections accounted for high mortality and morbidity. Moreover, the discovery of penicillin in 1928 marked the beginning of an antibiotic revolution, and this antibiotic era witnessed the discovery of many novel antibiotics, a golden era. However, the misuse or overuse of these antibiotics, natural resistance that existed even before the antibiotics were discovered, genetic variations in bacteria, natural selection, and acquisition of resistance from one species to another consistently increased the resistance to the existing antibacterial targets. Antibacterial resistance (ABR) is now becoming an ever-increasing concern jeopardizing global health. Henceforth, there is an urgent unmet need to discover novel compounds to combat ABR, which act through untapped pathways/mechanisms. Filamentous Temperature Sensitive mutant Z (FtsZ) is one such unique target, a tubulin homolog involved in developing a cytoskeletal framework for the cytokinetic ring. Additionally, its pivotal role in bacterial cell division and the lack of homologous structural protein in mammals makes it a potential antibacterial target for developing novel molecules. Approximately 2176 X-crystal structures of FtsZ were available, which initiated the research efforts to develop novel antibacterial agents. The literature has reported several natural, semisynthetic, peptides, and synthetic molecules as FtsZ inhibitors. This review provides valuable insights into the basic crystal structure of FtsZ, its inhibitors, and their inhibitory activities. This review also describes the available in vitro detection and quantification methods of FtsZ-drug complexes and the various approaches for determining drugs targeting FtsZ polymerization.
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Affiliation(s)
- Sumaiya Kifayat
- Department of Pharmacology, NIMS Institute of Pharmacy, NIMS University Rajasthan Jaipur 303121 India +91-9291661992
| | - Vidyasrilekha Yele
- Department of Pharmaceutical Chemistry, NIMS Institute of Pharmacy, NIMS University Rajasthan Jaipur 303121 India
| | - Akram Ashames
- College of Pharmacy & Health Sciences, Ajman University PO Box 340 Ajman United Arab Emirates
- Center of Medical and Bio-allied Health Sciences Research, Ajman University PO Box 340 Ajman United Arab Emirates +97167056240
| | - Dilep Kumar Sigalapalli
- Department of Pharmaceutical Chemistry, Vignan Pharmacy College, Jawaharlal Nehru Technological University Vadlamudi 522213 Andhra Pradesh India
| | - Richie R Bhandare
- College of Pharmacy & Health Sciences, Ajman University PO Box 340 Ajman United Arab Emirates
- Center of Medical and Bio-allied Health Sciences Research, Ajman University PO Box 340 Ajman United Arab Emirates +97167056240
| | - Afzal B Shaik
- St. Mary's College of Pharmacy, St. Mary's Group of Institutions Guntur, Affiliated to Jawaharlal Nehru Technological University Kakinada Chebrolu Guntur 522212 Andhra Pradesh India
| | | | - Bharat Kumar Reddy Sanapalli
- Department of Pharmacology, NIMS Institute of Pharmacy, NIMS University Rajasthan Jaipur 303121 India +91-9291661992
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Misal SA, Ovhal SD, Li S, Karty JA, Tang H, Radivojac P, Reilly JP. Non-Specific Signal Peptidase Processing of Extracellular Proteins in Staphylococcus aureus N315. Proteomes 2023; 11:proteomes11010008. [PMID: 36810564 PMCID: PMC9944065 DOI: 10.3390/proteomes11010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/05/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Staphylococcus aureus is one of the major community-acquired human pathogens, with growing multidrug-resistance, leading to a major threat of more prevalent infections to humans. A variety of virulence factors and toxic proteins are secreted during infection via the general secretory (Sec) pathway, which requires an N-terminal signal peptide to be cleaved from the N-terminus of the protein. This N-terminal signal peptide is recognized and processed by a type I signal peptidase (SPase). SPase-mediated signal peptide processing is the crucial step in the pathogenicity of S. aureus. In the present study, the SPase-mediated N-terminal protein processing and their cleavage specificity were evaluated using a combination of N-terminal amidination bottom-up and top-down proteomics-based mass spectrometry approaches. Secretory proteins were found to be cleaved by SPase, specifically and non-specifically, on both sides of the normal SPase cleavage site. The non-specific cleavages occur at the relatively smaller residues that are present next to the -1, +1, and +2 locations from the original SPase cleavage site to a lesser extent. Additional random cleavages at the middle and near the C-terminus of some protein sequences were also observed. This additional processing could be a part of some stress conditions and unknown signal peptidase mechanisms.
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Affiliation(s)
- Santosh A. Misal
- Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, IN 47405, USA
- Correspondence: ; Tel.: +1-301-761-7277
| | - Shital D. Ovhal
- Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Sujun Li
- Luddy School of Informatics, Computing, and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN 47408, USA
| | - Jonathan A. Karty
- Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Haixu Tang
- Luddy School of Informatics, Computing, and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN 47408, USA
| | - Predrag Radivojac
- Luddy School of Informatics, Computing, and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN 47408, USA
- Khoury College of Computer Sciences, Northeastern University, 177 Huntington Avenue, Boston, MA 02115, USA
| | - James P. Reilly
- Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, IN 47405, USA
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Gestaut D, Zhao Y, Park J, Ma B, Leitner A, Collier M, Pintilie G, Roh SH, Chiu W, Frydman J. Structural visualization of the tubulin folding pathway directed by human chaperonin TRiC/CCT. Cell 2022; 185:4770-4787.e20. [PMID: 36493755 PMCID: PMC9735246 DOI: 10.1016/j.cell.2022.11.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 09/01/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022]
Abstract
The ATP-dependent ring-shaped chaperonin TRiC/CCT is essential for cellular proteostasis. To uncover why some eukaryotic proteins can only fold with TRiC assistance, we reconstituted the folding of β-tubulin using human prefoldin and TRiC. We find unstructured β-tubulin is delivered by prefoldin to the open TRiC chamber followed by ATP-dependent chamber closure. Cryo-EM resolves four near-atomic-resolution structures containing progressively folded β-tubulin intermediates within the closed TRiC chamber, culminating in native tubulin. This substrate folding pathway appears closely guided by site-specific interactions with conserved regions in the TRiC chamber. Initial electrostatic interactions between the TRiC interior wall and both the folded tubulin N domain and its C-terminal E-hook tail establish the native substrate topology, thus enabling C-domain folding. Intrinsically disordered CCT C termini within the chamber promote subsequent folding of tubulin's core and middle domains and GTP-binding. Thus, TRiC's chamber provides chemical and topological directives that shape the folding landscape of its obligate substrates.
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Affiliation(s)
- Daniel Gestaut
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Yanyan Zhao
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Junsun Park
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Boxue Ma
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Dept of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Miranda Collier
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Grigore Pintilie
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Soung-Hun Roh
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea,Co-Corresponding authors: (lead contact), ,
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA,Co-Corresponding authors: (lead contact), ,
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA 94305, USA,Department of Genetics, Stanford University, Stanford, CA 94305, USA,Co-Corresponding authors: (lead contact), ,
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Andreu JM, Huecas S, Araújo-Bazán L, Vázquez-Villa H, Martín-Fontecha M. The Search for Antibacterial Inhibitors Targeting Cell Division Protein FtsZ at Its Nucleotide and Allosteric Binding Sites. Biomedicines 2022; 10:biomedicines10081825. [PMID: 36009372 PMCID: PMC9405007 DOI: 10.3390/biomedicines10081825] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
The global spread of bacterial antimicrobial resistance is associated to millions of deaths from bacterial infections per year, many of which were previously treatable. This, combined with slow antibiotic deployment, has created an urgent need for developing new antibiotics. A still clinically unexploited mode of action consists in suppressing bacterial cell division. FtsZ, an assembling GTPase, is the key protein organizing division in most bacteria and an attractive target for antibiotic discovery. Nevertheless, developing effective antibacterial inhibitors targeting FtsZ has proven challenging. Here we review our decade-long multidisciplinary research on small molecule inhibitors of bacterial division, in the context of global efforts to discover FtsZ-targeting antibiotics. We focus on methods to characterize synthetic inhibitors that either replace bound GTP from the FtsZ nucleotide binding pocket conserved across diverse bacteria or selectively bind into the allosteric site at the interdomain cleft of FtsZ from Bacillus subtilis and the pathogen Staphylococcus aureus. These approaches include phenotype screening combined with fluorescence polarization screens for ligands binding into each site, followed by detailed cytological profiling, and biochemical and structural studies. The results are analyzed to design an optimized workflow to identify effective FtsZ inhibitors, and new approaches for the discovery of FtsZ-targeting antibiotics are discussed.
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Affiliation(s)
- José M. Andreu
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (S.H.); (L.A.-B.)
- Correspondence: (J.M.A.); (M.M.-F.)
| | - Sonia Huecas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (S.H.); (L.A.-B.)
| | - Lidia Araújo-Bazán
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (S.H.); (L.A.-B.)
| | - Henar Vázquez-Villa
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040 Madrid, Spain;
| | - Mar Martín-Fontecha
- Departamento de Química Orgánica, Facultad de Óptica y Optometría, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040 Madrid, Spain
- Correspondence: (J.M.A.); (M.M.-F.)
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Ruiz FM, Huecas S, Santos-Aledo A, Prim EA, Andreu JM, Fernández-Tornero C. FtsZ filament structures in different nucleotide states reveal the mechanism of assembly dynamics. PLoS Biol 2022; 20:e3001497. [PMID: 35312677 PMCID: PMC8936486 DOI: 10.1371/journal.pbio.3001497] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/21/2022] [Indexed: 11/19/2022] Open
Abstract
Treadmilling protein filaments perform essential cellular functions by growing from one end while shrinking from the other, driven by nucleotide hydrolysis. Bacterial cell division relies on the primitive tubulin homolog FtsZ, a target for antibiotic discovery that assembles into single treadmilling filaments that hydrolyse GTP at an active site formed upon subunit association. We determined high-resolution filament structures of FtsZ from the pathogen Staphylococcus aureus in complex with different nucleotide analogs and cations, including mimetics of the ground and transition states of catalysis. Together with mutational and biochemical analyses, our structures reveal interactions made by the GTP γ-phosphate and Mg2+ at the subunit interface, a K+ ion stabilizing loop T7 for co-catalysis, new roles of key residues at the active site and a nearby crosstalk area, and rearrangements of a dynamic water shell bridging adjacent subunits upon GTP hydrolysis. We propose a mechanistic model that integrates nucleotide hydrolysis signaling with assembly-associated conformational changes and filament treadmilling. Equivalent assembly mechanisms may apply to more complex tubulin and actin cytomotive filaments that share analogous features with FtsZ. Bacterial cell division critically relies on the tubulin homolog FtsZ, which assembles into filaments that treadmill, fuelled by GTP hydrolysis. This structural and biochemical study of FtsZ from Staphylocuccus aureus reveals the mechanism of GTP hydrolysis and its connection with filament dynamics.
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Affiliation(s)
- Federico M. Ruiz
- Centro de Investigaciones Biológicas Margarita Salas CSIC, Madrid, Spain
| | - Sonia Huecas
- Centro de Investigaciones Biológicas Margarita Salas CSIC, Madrid, Spain
| | | | - Elena A. Prim
- Centro de Investigaciones Biológicas Margarita Salas CSIC, Madrid, Spain
| | - José M. Andreu
- Centro de Investigaciones Biológicas Margarita Salas CSIC, Madrid, Spain
- * E-mail: (JMA); (CFT)
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An overlooked UV spectroscopic tool for sensing coil-to-helix and helix-to-coil conformational transitions of proteins and peptides. Anal Biochem 2021; 639:114512. [PMID: 34875249 DOI: 10.1016/j.ab.2021.114512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 11/22/2022]
Abstract
A simple spectrophotometric approach is proposed for sensing coil-to-helix and helix-to-coil conformational transitions of intrinsically disordered and folded peptide/protein sequences. Helix formation induced by a variety of physico-chemical factors results in a substantial intensity reduction (hypochromism) of the intense far-UV absorption band associated with the π-π* transition of amide chromophores. Conversely, the same band exhibits intensity increase (hyperchromism) as the consequence of unfolding events. This method, faded into obscurity several decades ago, may obtain widespread applications in the field of protein science.
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Antistaphylococcal Activity of the FtsZ Inhibitor C109. Pathogens 2021; 10:pathogens10070886. [PMID: 34358036 PMCID: PMC8308607 DOI: 10.3390/pathogens10070886] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/08/2021] [Accepted: 07/10/2021] [Indexed: 01/22/2023] Open
Abstract
Staphylococcus aureus infections represent a great concern due to their versatility and involvement in different types of diseases. The shortage of available clinical options, especially to treat multiresistant strains, makes the discovery of new effective compounds essential. Here we describe the activity of the previously described cell division inhibitor C109 against methicillin-sensitive and -resistant S. aureus strains. Antibiofilm activity was assessed using microtiter plates, confocal microscopy, and in an in vitro biofilm wound model. The ability of C109 to block FtsZ GTPase activity and polymerization was tested in vitro. Altogether, the results show that the FtsZ inhibitor C109 has activity against a wide range of S. aureus strains and support its use as an antistaphylococcal compound.
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Huecas S, Araújo-Bazán L, Ruiz FM, Ruiz-Ávila LB, Martínez RF, Escobar-Peña A, Artola M, Vázquez-Villa H, Martín-Fontecha M, Fernández-Tornero C, López-Rodríguez ML, Andreu JM. Targeting the FtsZ Allosteric Binding Site with a Novel Fluorescence Polarization Screen, Cytological and Structural Approaches for Antibacterial Discovery. J Med Chem 2021; 64:5730-5745. [PMID: 33908781 PMCID: PMC8478281 DOI: 10.1021/acs.jmedchem.0c02207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Bacterial resistance to antibiotics makes previously manageable infections again disabling and lethal, highlighting the need for new antibacterial strategies. In this regard, inhibition of the bacterial division process by targeting key protein FtsZ has been recognized as an attractive approach for discovering new antibiotics. Binding of small molecules to the cleft between the N-terminal guanosine triphosphate (GTP)-binding and the C-terminal subdomains allosterically impairs the FtsZ function, eventually inhibiting bacterial division. Nonetheless, the lack of appropriate chemical tools to develop a binding screen against this site has hampered the discovery of FtsZ antibacterial inhibitors. Herein, we describe the first competitive binding assay to identify FtsZ allosteric ligands interacting with the interdomain cleft, based on the use of specific high-affinity fluorescent probes. This novel assay, together with phenotypic profiling and X-ray crystallographic insights, enables the identification and characterization of FtsZ inhibitors of bacterial division aiming at the discovery of more effective antibacterials.
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Affiliation(s)
- Sonia Huecas
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Lidia Araújo-Bazán
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Federico M Ruiz
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Laura B Ruiz-Ávila
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - R Fernando Martínez
- Dept. Química Orgánica, Facultad de Ciencias Químicas, UCM, Avda. Complutense s/n, 28040 Madrid, Spain
| | - Andrea Escobar-Peña
- Dept. Química Orgánica, Facultad de Ciencias Químicas, UCM, Avda. Complutense s/n, 28040 Madrid, Spain
| | - Marta Artola
- Dept. Química Orgánica, Facultad de Ciencias Químicas, UCM, Avda. Complutense s/n, 28040 Madrid, Spain
| | - Henar Vázquez-Villa
- Dept. Química Orgánica, Facultad de Ciencias Químicas, UCM, Avda. Complutense s/n, 28040 Madrid, Spain
| | - Mar Martín-Fontecha
- Dept. Química Orgánica, Facultad de Ciencias Químicas, UCM, Avda. Complutense s/n, 28040 Madrid, Spain
| | - Carlos Fernández-Tornero
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - María L López-Rodríguez
- Dept. Química Orgánica, Facultad de Ciencias Químicas, UCM, Avda. Complutense s/n, 28040 Madrid, Spain
| | - José M Andreu
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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Padhan B, Poddar K, Sarkar D, Sarkar A. Production, purification, and process optimization of intracellular pigment from novel psychrotolerant Paenibacillus sp. BPW19. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 29:e00592. [PMID: 33537212 PMCID: PMC7840853 DOI: 10.1016/j.btre.2021.e00592] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 12/16/2020] [Accepted: 01/10/2021] [Indexed: 01/01/2023]
Abstract
A pink pigment-producing bacterial strain was isolated from wastewater and identified as Paenibacillus sp. BPW19. The motile bacterial strain was Gram-positive, acid fermenting, glucose, sucrose utilizing and rod-shaped with an average cell length of 1.55 μm as studied under the Environmental Scanning Electron Microscope. Even though being psychrotolerant, the cell growth condition of BPW19 was optimized as 25 ºC along with pH 8, and 2.25% inoculum concentration considering the operational ease of the production. Sonication assisted solvent extraction produced 5.41% crude pigment which showed zones of exclusion against gram-negative strains Escherichia coli DH5α, Enterobacter sp. EtK3, and Klebsiella sp. SHC1. Gas Chromatography-Mass Spectrometry analysis of the crude pigment exhibited the dominant presence of major compounds as dotriacontane; 3,7 dimethyl 7 octanal; 1-eicosene and erucic acid. While column chromatography (ethanol:chloroform in 1:4 (v/v) ratio) purified pigment was identified as erucic acid using Nuclear Magnetic Resonance with a net yield of 3.06%.
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Affiliation(s)
- Bhagyashree Padhan
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Odisha, 769008, India
| | - Kasturi Poddar
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Odisha, 769008, India
| | - Debapriya Sarkar
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Odisha, 769008, India
| | - Angana Sarkar
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Odisha, 769008, India
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Cell Division Protein FtsZ Is Unfolded for N-Terminal Degradation by Antibiotic-Activated ClpP. mBio 2020; 11:mBio.01006-20. [PMID: 32605984 PMCID: PMC7327170 DOI: 10.1128/mbio.01006-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Acyldepsipeptide (ADEP) antibiotics effectively kill multidrug-resistant Gram-positive pathogens, including vancomycin-resistant enterococcus, penicillin-resistant Streptococcus pneumoniae (PRSP), and methicillin-resistant Staphylococcus aureus (MRSA). The antibacterial activity of ADEP depends on a new mechanism of action, i.e., the deregulation of bacterial protease ClpP that leads to bacterial self-digestion. Our data allow new insights into the mode of ADEP action by providing a molecular explanation for the distinct bacterial phenotypes observed at low versus high ADEP concentrations. In addition, we show that ClpP alone, in the absence of any unfoldase or energy-consuming system, and only activated by the small molecule antibiotic ADEP, leads to the unfolding of the cell division protein FtsZ. Antibiotic acyldepsipeptides (ADEPs) deregulate ClpP, the proteolytic core of the bacterial Clp protease, thereby inhibiting its native functions and concomitantly activating it for uncontrolled proteolysis of nonnative substrates. Importantly, although ADEP-activated ClpP is assumed to target multiple polypeptide and protein substrates in the bacterial cell, not all proteins seem equally susceptible. In Bacillus subtilis, the cell division protein FtsZ emerged to be particularly sensitive to degradation by ADEP-activated ClpP at low inhibitory ADEP concentrations. In fact, FtsZ is the only bacterial protein that has been confirmed to be degraded in vitro as well as within bacterial cells so far. However, the molecular reason for this preferred degradation remained elusive. Here, we report the unexpected finding that ADEP-activated ClpP alone, in the absence of any Clp-ATPase, leads to an unfolding and subsequent degradation of the N-terminal domain of FtsZ, which can be prevented by the stabilization of the FtsZ fold via nucleotide binding. At elevated antibiotic concentrations, importantly, the C terminus of FtsZ is notably targeted for degradation in addition to the N terminus. Our results show that different target structures are more or less accessible to ClpP, depending on the ADEP level present. Moreover, our data assign a Clp-ATPase-independent protein unfolding capability to the ClpP core of the bacterial Clp protease and suggest that the protein fold of FtsZ may be more flexible than previously anticipated.
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