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Jin M, Zhu S, Tang Y, Kong X, Wang X, Li Y, Jiang S, Wei L, Hu C, Wang B, Song W. Ayanin, a natural flavonoid inhibitor of Caseinolytic protease, is a promising therapeutic agent to combat methicillin-resistant Staphylococcus aureus infections. Biochem Pharmacol 2023; 217:115814. [PMID: 37769713 DOI: 10.1016/j.bcp.2023.115814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/16/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
Antimicrobial resistance (AMR) is a global health threat. The dramatic increase of Methicillin-resistant Staphylococcus aureus (MRSA) infections emphasizes the need to find new anti-infective agents with a novel mode of action. The Caseinolytic protease (ClpP) is a central virulence factor in stress survival, virulence, and antibiotic resistance of MRSA. Here, we found ayanin, a flavonoid isolated from Callicarpa nudiflora, was an inhibitor of MRSA ClpP with an IC50 of 19.63 μM. Using quantitative real-time PCR, ayanin reduced the virulence of Staphylococcus aureus (S. aureus) by down-regulating the level of some important virulence factors, including agrA, RNAⅢ, hla, pvl, psmα and spa. The results of cellular thermal shift assay and thermal shift assay revealed a binding between ayanin and ClpP. Molecular docking showed that ASP-168, ASN-173 and ARG-171 were the potential binding sites for ClpP binding to ayanin. ClpP mutagenesis study further indicated that ARG-171 and ASN-173 were the main active sites of ClpP. The affinity constant (KD) value of ayanin with ClpP was 3.15 × 10-5 M measured by surface plasmon resonance. In addition, ayanin exhibited a significant therapeutic effect on pneumonia infection induced by S. aureus in mice in vivo, especially in combination with vancomycin. This is the first report of ayanin with in vivo and in vitro efficacy against S. aureus infection. In conclusion, ayanin is a promising therapeutic agent to combat MRSA infections by targeting ClpP.
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Affiliation(s)
- Mengli Jin
- Changchun University of Chinese Medicine, Changchun 130117, China
| | - Shuyue Zhu
- Changchun University of Chinese Medicine, Changchun 130117, China
| | - Yating Tang
- Changchun University of Chinese Medicine, Changchun 130117, China
| | - Xiangri Kong
- Changchun University of Chinese Medicine, Changchun 130117, China
| | - Xingye Wang
- Changchun University of Chinese Medicine, Changchun 130117, China
| | - Yufen Li
- Changchun University of Chinese Medicine, Changchun 130117, China
| | - Shuang Jiang
- Changchun University of Chinese Medicine, Changchun 130117, China
| | - Lin Wei
- Changchun University of Chinese Medicine, Changchun 130117, China
| | - Chunjie Hu
- Changchun University of Chinese Medicine, Changchun 130117, China; Proctology Department, Affiliated Hospital of Changchun University of Chinese Medicine, Changchun 130021, China.
| | - Bingmei Wang
- Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Wu Song
- Changchun University of Chinese Medicine, Changchun 130117, China.
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2
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Ogbonna EC, Anderson HR, Beardslee PC, Bheemreddy P, Schmitz KR. Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1. Microbiol Spectr 2023; 11:e0454822. [PMID: 37341639 PMCID: PMC10433963 DOI: 10.1128/spectrum.04548-22] [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: 11/08/2022] [Accepted: 05/31/2023] [Indexed: 06/22/2023] Open
Abstract
The prevalence of drug-resistant Mycobacterium tuberculosis infections has prompted extensive efforts to exploit new drug targets in this globally important pathogen. ClpC1, the unfoldase component of the essential ClpC1P1P2 protease, has emerged as one particularly promising antibacterial target. However, efforts to identify and characterize compounds that impinge on ClpC1 activity are constrained by our limited knowledge of Clp protease function and regulation. To expand our understanding of ClpC1 physiology, we employed a coimmunoprecipitation and mass spectrometry workflow to identify proteins that interact with ClpC1 in Mycolicibacterium smegmatis, a surrogate for M. tuberculosis. We identify a diverse panel of interaction partners, many of which coimmunoprecipitate with both the regulatory N-terminal domain and the ATPase core of ClpC1. Notably, our interactome analysis establishes MSMEI_3879, a truncated gene product unique to M. smegmatis, as a novel proteolytic substrate. Degradation of MSMEI_3879 by ClpC1P1P2 in vitro requires exposure of its N-terminal sequence, reinforcing the idea that ClpC1 selectively recognizes disordered motifs on substrates. Fluorescent substrates incorporating MSMEI_3879 may be useful in screening for novel ClpC1-targeting antibiotics to help address the challenge of M. tuberculosis drug resistance. IMPORTANCE Drug-resistant tuberculosis infections are a major challenge to global public health. Much effort has been invested in identifying new drug targets in the causative pathogen, Mycobacterium tuberculosis. One such target is the ClpC1 unfoldase. Compounds have been identified that kill M. tuberculosis by disrupting ClpC1 activity, yet the physiological function of ClpC1 in cells has remained poorly defined. Here, we identify interaction partners of ClpC1 in a model mycobacterium. By building a broader understanding of the role of this prospective drug target, we can more effectively develop compounds that inhibit its essential cellular activities.
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Affiliation(s)
- Emmanuel C. Ogbonna
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Henry R. Anderson
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Patrick C. Beardslee
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Priyanka Bheemreddy
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Karl R. Schmitz
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
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3
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Schmitz KR, Handy EL, Compton CL, Gupta S, Bishai WR, Sauer RT, Sello JK. Acyldepsipeptide Antibiotics and a Bioactive Fragment Thereof Differentially Perturb Mycobacterium tuberculosis ClpXP1P2 Activity in Vitro. ACS Chem Biol 2023; 18:724-733. [PMID: 32083462 PMCID: PMC7842861 DOI: 10.1021/acschembio.9b00454] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Proteolytic complexes in Mycobacterium tuberculosis (Mtb), the deadliest bacterial pathogen, are major foci in tuberculosis drug development programs. The Clp proteases, which are essential for Mtb viability, are high-priority targets. These proteases function through the collaboration of ClpP1P2, a barrel-shaped heteromeric peptidase, with associated ATP-dependent chaperones like ClpX and ClpC1 that recognize and unfold specific substrates in an ATP-dependent fashion. The critical interaction of the peptidase and its unfoldase partners is blocked by the competitive binding of acyldepsipeptide antibiotics (ADEPs) to the interfaces of the ClpP2 subunits. The resulting inhibition of Clp protease activity is lethal to Mtb. Here, we report the surprising discovery that a fragment of the ADEPs retains anti-Mtb activity yet stimulates rather than inhibits the ClpXP1P2-catalyzed degradation of proteins. Our data further suggest that the fragment stabilizes the ClpXP1P2 complex and binds ClpP1P2 in a fashion distinct from that of the intact ADEPs. A structure-activity relationship study of the bioactive fragment defines the pharmacophore and points the way toward the development of new drug leads for the treatment of tuberculosis.
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Affiliation(s)
- Karl R. Schmitz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
- Department of Biological Sciences, University of Delaware, Newark, DE
| | - Emma L. Handy
- Department of Chemistry, Brown University, Providence, RI
| | | | - Shashank Gupta
- Department of Chemistry, Brown University, Providence, RI
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD
| | - William R. Bishai
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD
| | - Robert T. Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
| | - Jason K. Sello
- Department of Chemistry, Brown University, Providence, RI
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
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4
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Schwarz M, Hübner I, Sieber SA. Tailored phenyl esters inhibit ClpXP and attenuate Staphylococcus aureus α-hemolysin secretion. Chembiochem 2022; 23:e202200253. [PMID: 35713329 PMCID: PMC9544270 DOI: 10.1002/cbic.202200253] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/15/2022] [Indexed: 11/14/2022]
Abstract
Novel strategies against multidrug‐resistant bacteria are urgently needed in order to overcome the current silent pandemic. Manipulation of toxin production in pathogenic species serves as a promising approach to attenuate virulence and prevent infections. In many bacteria such as Staphylococcus aureus or Listeria monocyotgenes, serine protease ClpXP is a key contributor to virulence and thus represents a prime target for antimicrobial drug discovery. The limited stability of previous electrophilic warheads has prevented a sustained effect of virulence attenuation in bacterial culture. Here, we systematically tailor the stability and inhibitory potency of phenyl ester ClpXP inhibitors by steric shielding of the ester bond and fine‐tuning the phenol leaving group. Out of 17 derivatives, two (MAS‐19 and MAS‐30) inhibited S. aureus ClpP peptidase and ClpXP protease activities by >60 % at 1 μM. Furthermore, the novel inhibitors did not exhibit pronounced cytotoxicity against human and bacterial cells. Unlike the first generation phenylester AV170, these molecules attenuated S. aureus virulence markedly and displayed increased stability in aqueous buffer compared to the previous benchmark AV170.
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Affiliation(s)
- Markus Schwarz
- Technical University Munich: Technische Universitat Munchen, Chemistry, Ernst-Otto-Fischer-Straße 8, 85748, Garching bei München, GERMANY
| | - Ines Hübner
- Technical University of Munich: Technische Universitat Munchen, Chemistry, GERMANY
| | - Stephan Axel Sieber
- Technische Universitat Munchen, Department of Chemistry, Lichtenbergstr. 4, 85747, Garching, GERMANY
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Wang M, Buist G, van Dijl JM. Staphylococcus aureus cell wall maintenance - the multifaceted roles of peptidoglycan hydrolases in bacterial growth, fitness, and virulence. FEMS Microbiol Rev 2022; 46:6604383. [PMID: 35675307 PMCID: PMC9616470 DOI: 10.1093/femsre/fuac025] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/22/2022] [Accepted: 05/25/2022] [Indexed: 01/07/2023] Open
Abstract
Staphylococcus aureus is an important human and livestock pathogen that is well-protected against environmental insults by a thick cell wall. Accordingly, the wall is a major target of present-day antimicrobial therapy. Unfortunately, S. aureus has mastered the art of antimicrobial resistance, as underscored by the global spread of methicillin-resistant S. aureus (MRSA). The major cell wall component is peptidoglycan. Importantly, the peptidoglycan network is not only vital for cell wall function, but it also represents a bacterial Achilles' heel. In particular, this network is continuously opened by no less than 18 different peptidoglycan hydrolases (PGHs) encoded by the S. aureus core genome, which facilitate bacterial growth and division. This focuses attention on the specific functions executed by these enzymes, their subcellular localization, their control at the transcriptional and post-transcriptional levels, their contributions to staphylococcal virulence and their overall importance in bacterial homeostasis. As highlighted in the present review, our understanding of the different aspects of PGH function in S. aureus has been substantially increased over recent years. This is important because it opens up new possibilities to exploit PGHs as innovative targets for next-generation antimicrobials, passive or active immunization strategies, or even to engineer them into effective antimicrobial agents.
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Affiliation(s)
- Min Wang
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, PO Box 30001, 9700 RB Groningen, the Netherlands
| | | | - Jan Maarten van Dijl
- Corresponding author: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. box 30001, HPC EB80, 9700 RB Groningen, the Netherlands, Tel. +31-50-3615187; Fax. +31-50-3619105; E-mail:
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6
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Liao F, Gu W, Fu X, Yuan B, Zhang Y. Community-acquired methicillin-resistant Staphylococcus aureus provoked cytokine storm causing severe infection on BALB/c mice. Mol Immunol 2021; 140:167-174. [PMID: 34717146 DOI: 10.1016/j.molimm.2021.10.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/07/2021] [Accepted: 10/17/2021] [Indexed: 12/30/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has become the most important pathogen of hospital-acquired (HA) or community-acquired (CA) infections. However, it is unclear of the cytokines responsible for pathological hyper-inflammation in sepsis related cytokine storm for MRSA infection. In this study, we selected typical HA-MRSA strain (YNSA163: ST239-t030-SCCmecⅢ) and two CA-MRSA isolates (YNSA7: ST59-t439-SCCmecⅣa and YNSA53: ST59-t437-SCCmecⅤb) from our previous research, infected on BALB/c mice, and analyzed the cytokine storm patterns during infection process. The animal experiments revealed the most serious lethal effect on BALB/c mice caused by YNSA7 strain infection, followed by YNSA53, and no BALB/c mice died for YNSA163 infection. Histopathological analyses revealed that lung was the most seriously damaged organs, followed by spleen and kidney, especially for CA-MRSA infection. The severe inflammatory reactions, tissue destruction, and massive exudation of inflammatory mediators and cells could be identified in CA-MRSA strains infected mice. Interleukin-6 (IL-6) and IL-10 were both highly expressed in spleen and lung of YNSA7 and YNSA53 dead cases compared with YNSA53 survived and YNSA163 cases, which demonstrated cytokine storm pattern for CA-MRSA strains infection. The results of IL-6 intervention experiment verified that the enhanced IL-6 secretion was responsible for the host lethality of YNSA7 infection. RNA-sequencing results among three MRSA isolates indicated most of the differentially expressed genes referred to cellular process, metabolism and genetic information processing of bacteria. Specifically, clpP, chp chemotaxis inhibit, fnbB, pathogencity island protein and virulence associated protein E were highly expressed in YNSA7 strain. In general, CA-MRSA strains provoked cytokine storm on BALB/c mice led to severe infection and lethality, the up-regulated of some virulence genes might play important role in pathogenesis.
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Affiliation(s)
- Feng Liao
- Department of Respiratory Medicine, The First People's Hospital of Yunnan Province, 650022, Kunming, PR China; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, PR China; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650500, PR China
| | - Wenpeng Gu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, 650022, Kunming, PR China
| | - Xiaoqing Fu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, 650022, Kunming, PR China
| | - Bin Yuan
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650500, PR China
| | - Yunhui Zhang
- Department of Respiratory Medicine, The First People's Hospital of Yunnan Province, 650022, Kunming, PR China; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650500, PR China.
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7
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Identification of ClpP Dual Isoform Disruption as an Anti-sporulation Strategy for Clostridioides difficile. J Bacteriol 2021; 204:e0041121. [PMID: 34807726 DOI: 10.1128/jb.00411-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Gram-positive bacterium Clostridioides difficile is a primary cause of hospital-acquired diarrhea, threatening both immunocompromised and healthy individuals. An important aspect of defining mechanisms that drive C. difficile persistence and virulence relies on developing a more complete understanding of sporulation. C. difficile sporulation is the single determinant of transmission and complicates treatment and prevention due to the chemical and physical resilience of spores. By extension, the identification of druggable targets that significantly attenuate sporulation would have a significant impact on thwarting C. difficile infection. Using a new CRISPR-Cas9 nickase genome editing methodology, stop codons were inserted early in the coding sequence for clpP1 and clpP2 to generate C. difficile mutants that no longer produced the corresponding isoforms of caseinolytic protease P (ClpP). The data show that genetic ablation of ClpP isoforms leads to altered sporulation phenotypes with the clpP1/clpP2 double mutant exhibiting asporogenic behavior. A small screen of known ClpP inhibitors in a fluorescence-based biochemical assay identified bortezomib as an inhibitor of C. difficile ClpP that produces dose-dependent inhibition of purified ClpP. Incubation of C. difficile cultures in the presence of bortezomib reveals anti-sporulation effects approaching that observed in the clpP1/clpP2 double mutant. This work identifies ClpP as a key contributor to C. difficile sporulation and provides compelling support for the pursuit of small molecule ClpP inhibitors as C. difficile anti-sporulating agents. IMPORTANCE Due to diverse roles of ClpP and the reliance of pathogens upon this system for infection, it has emerged as a target for antimicrobial development. Biology regulated by ClpP is organism-dependent and has not been defined in C. difficile. This work identifies ClpP as a key contributor to C. difficile sporulation and provides compelling support for the pursuit of small molecule ClpP inhibitors as anti-sporulating agents. The identification of new approaches and/or drug targets that reduce C. difficile sporulation would be transformative and are expected to find high utility in prophylaxis, transmission attenuation, and relapse prevention. Discovery of the ClpP system as a major driver to sporulation also provides a new avenue of inquiry for advancing the understanding of sporulation.
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8
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Jing S, Wang L, Wang T, Fan L, Chen L, Xiang H, Shi Y, Wang D. Myricetin protects mice against MRSA-related lethal pneumonia by targeting ClpP. Biochem Pharmacol 2021; 192:114753. [PMID: 34474040 DOI: 10.1016/j.bcp.2021.114753] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 10/20/2022]
Abstract
Methicillin-resistant Staphylococcus aureus is one of the leading causes of community and nosocomial infections, which has created the urgent need for innovative anti-infective agents to control MRSA-associated infections. A conserved serine protease, caseinolytic peptidase P (ClpP) in Staphylococcus aureus is highly associated with pathogenicity and has been claimed to be a novel antimicrobial target. We aim to search suitable inhibitors of ClpP to attenuate the virulence of MRSA and combat their infections in vivo. Over 500 natural compounds were pre-screened via fluorescence resonance energy transfer using the Suc-LY-AMC substrate. The binding of myricetin to ClpP was determined and the mechanism of action was elucidated by thermal shift assay, surface plasmon resonance, and molecular dynamics simulations. The therapeutic effects of myricetin on S. aureus infection were further investigated using a S. aureus-induced pneumonia model. We revealed that myricetin could effectively block the activity of ClpP without disturbing the growth of the bacteria and the Gln-47 and Met-31 residues were necessary for myricetin binding to ClpP. Importantly, myricetin attenuated the pathogenicity of S. aureus in vivo, while improving the efficacy of the traditional antibiotic oxacillin against MRSA infection and protecting mice from fatal lung infections caused by MRSA. These findings indicate that myricetin has the potential to be applied in the pharmaceutical industry as a promising therapeutic agent.
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Affiliation(s)
- Shisong Jing
- Department of Pharmacology, School of Pharmaceutical Science, Jilin University, Changchun 130021, China; College of Animal Science, Jilin University, Changchun 130062, China
| | - Li Wang
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Tiedong Wang
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Lianghai Fan
- Department of Nutrition, the Fifth People's Hospital of Chongqing, Chongqing 400062, China
| | - Lin Chen
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Hua Xiang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yan Shi
- Department of Pharmacology, School of Pharmaceutical Science, Jilin University, Changchun 130021, China.
| | - Dacheng Wang
- College of Animal Science, Jilin University, Changchun 130062, China.
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Illigmann A, Thoma Y, Pan S, Reinhardt L, Brötz-Oesterhelt H. Contribution of the Clp Protease to Bacterial Survival and Mitochondrial Homoeostasis. Microb Physiol 2021; 31:260-279. [PMID: 34438398 DOI: 10.1159/000517718] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/07/2021] [Indexed: 11/19/2022]
Abstract
Fast adaptation to environmental changes ensures bacterial survival, and proteolysis represents a key cellular process in adaptation. The Clp protease system is a multi-component machinery responsible for protein homoeostasis, protein quality control, and targeted proteolysis of transcriptional regulators in prokaryotic cells and prokaryote-derived organelles of eukaryotic cells. A functional Clp protease complex consists of the tetradecameric proteolytic core ClpP and a hexameric ATP-consuming Clp-ATPase, several of which can associate with the same proteolytic core. Clp-ATPases confer substrate specificity by recognising specific degradation tags, and further selectivity is conferred by adaptor proteins, together allowing for a fine-tuned degradation process embedded in elaborate regulatory networks. This review focuses on the contribution of the Clp protease system to prokaryotic survival and summarises the current state of knowledge for exemplary bacteria in an increasing degree of interaction with eukaryotic cells. Starting from free-living bacteria as exemplified by a non-pathogenic and a pathogenic member of the Firmicutes, i.e., Bacillus subtilis and Staphylococcus aureus, respectively, we turn our attention to facultative and obligate intracellular bacterial pathogens, i.e., Mycobacterium tuberculosis, Listeria monocytogenes, and Chlamydia trachomatis, and conclude with mitochondria. Under stress conditions, the Clp protease system exerts its pivotal role in the degradation of damaged proteins and controls the timing and extent of the heat-shock response by regulatory proteolysis. Key regulators of developmental programmes like natural competence, motility, and sporulation are also under Clp proteolytic control. In many pathogenic species, the Clp system is required for the expression of virulence factors and essential for colonising the host. In accordance with its evolutionary origin, the human mitochondrial Clp protease strongly resembles its bacterial counterparts, taking a central role in protein quality control and homoeostasis, energy metabolism, and apoptosis in eukaryotic cells, and several cancer cell types depend on it for proliferation.
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Affiliation(s)
- Astrid Illigmann
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Yvonne Thoma
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Stefan Pan
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Laura Reinhardt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.,Cluster of Excellence Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
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10
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Yang T, Zhang T, Zhou X, Wang P, Gan J, Song B, Yang S, Yang CG. Dysregulation of ClpP by Small-Molecule Activators Used Against Xanthomonas oryzae pv. oryzae Infections. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:7545-7553. [PMID: 34218658 DOI: 10.1021/acs.jafc.1c01470] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Rice bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is considered a destructive plant bacterial disease. The looming crisis of antibiotic resistance necessitates the discovery of antibiotics with new modes of action. Activated caseinolytic protease P (ClpP) can degrade bacterial FtsZ proteins that are essential for cell division; thus, we hypothesized that small-molecule-induced dysregulation of XooClpP may result in degradation of XooFtsZ to treat leaf blight diseases. In this work, we have determined the crystal structures of XooClpP, and its mutant bound with ADEP4, which revealed the action modes of XooClpP assemblies and XooFtsZ degradation by dysregulated XooClpP in the presence of small-molecule activators, such as ONC212 and ADEP4. Additionally, an antibacterial assessment demonstrated that ONC212 displays excellent activity against Xoo and prevents rice bacterial leaf blight in vivo. Thus, these unique antibacterial effects of small-molecule activators of XooClpP represent a potential strategy for the development of agricultural antibiotics by targeting bacterial ClpP.
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Affiliation(s)
- Teng Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China
- The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tao Zhang
- The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiang Zhou
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Pengyu Wang
- The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhua Gan
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Baoan Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Cai-Guang Yang
- The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
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11
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Ju Y, An Q, Zhang Y, Sun K, Bai L, Luo Y. Recent advances in Clp protease modulation to address virulence, resistance and persistence of MRSA infection. Drug Discov Today 2021; 26:2190-2197. [PMID: 34048895 DOI: 10.1016/j.drudis.2021.05.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/17/2021] [Accepted: 05/20/2021] [Indexed: 02/05/2023]
Abstract
The Clp protease is an AAA+ protease that executes abnormally folded or malfunctioning proteins, and has an important role in producing virulence factors, forming biofilms or persisters and developing methicillin-resistant Staphylococcus aureus (MRSA). Recent studies showed that Clp protease controls virulence via agr signaling and degrades antitoxins of the toxin-antitoxin system to modulate the formation of persisters and biofilms. In this review, we focus on recent developments concerning the virulence and persistence regulatory pathways and resistance-related mechanism of Clp protease in S. aureus, with an overview of the Clp modulators developed to treat MRSA infection.
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Affiliation(s)
- Yuan Ju
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China; Sichuan University Library, Sichuan University, Chengdu 610041, China
| | - Qi An
- Public Health Clinical Center of Chengdu, Chengdu 610041, China
| | - Yiwen Zhang
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Ke Sun
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Lang Bai
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
| | - Youfu Luo
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
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12
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Kirsch VC, Fetzer C, Sieber SA. Global Inventory of ClpP- and ClpX-Regulated Proteins in Staphylococcus aureus. J Proteome Res 2020; 20:867-879. [PMID: 33210542 DOI: 10.1021/acs.jproteome.0c00668] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Staphylococcus aureus represents an opportunistic pathogen, which utilizes elaborate quorum sensing mechanisms to precisely control the expression and secretion of virulence factors. Previous studies indicated a role of the ClpXP proteolytic system in controlling pathogenesis. While detailed transcriptome data for S. aureus ClpP and ClpX knockout mutants is available, corresponding studies on the proteome and secretome level are largely lacking. To globally decipher the functional roles of ClpP and ClpX, we utilized S. aureus genomic deletion mutants of the corresponding genes for in-depth proteomic liquid chromatography-mass spectrometry (LC-MS)/MS analysis. These studies were complemented by an inactive ClpP active-site mutant strain to monitor changes solely depending on the activity and not the presence of the protein. A comparison of these strains with the wildtype revealed, e.g., downregulation of virulence, purine/pyrimidine biosynthesis, iron uptake, and stress response. Correspondingly, the integration of metabolomics data showed a reduction in the subset of purine and pyrimidine metabolite levels. Interestingly, a comparison between the ClpP knockout and ClpP S98A active-site mutant strains revealed characteristic differences. These results are not only of fundamental importance to understand the cellular role of ClpXP but also have implications for the development of novel virulence inhibitor classes.
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Affiliation(s)
- Volker C Kirsch
- Department of Chemistry, Chair of Organic Chemistry II, Center for Protein Assemblies (CPA), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Christian Fetzer
- Department of Chemistry, Chair of Organic Chemistry II, Center for Protein Assemblies (CPA), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Protein Assemblies (CPA), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
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13
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Schelin J, Cohn MT, Frisk B, Frees D. A Functional ClpXP Protease is Required for Induction of the Accessory Toxin Genes, tst, sed, and sec. Toxins (Basel) 2020; 12:E553. [PMID: 32872362 PMCID: PMC7551677 DOI: 10.3390/toxins12090553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 01/09/2023] Open
Abstract
Staphylococcal toxic shock syndrome is a potentially lethal illness attributed to superantigens produced by Staphylococcus aureus, in particular toxic shock syndrome toxin 1 (TSST-1), but staphylococcal enterotoxins (SEs) are also implicated. The genes encoding these important toxins are carried on mobile genetic elements, and the regulatory networks controlling expression of these toxins remain relatively unexplored. We show here that the highly conserved ClpXP protease stimulates transcription of tst (TSST-1), sec (SEC), and sed (SED) genes in the prototypical strains, SA564 and RN4282. In the wild-type cells, the post-exponential upregulation of toxin gene transcription was proposed to occur via RNAIII-mediated downregulation of the Rot repressor. Contradictive to this model, we showed that the post-exponential induction of tst, sed, and sec transcription did not occur in cells devoid of ClpXP activity, despite the Rot level being diminished. To identify transcriptional regulators with a changed expression in cells devoid of ClpXP activity, RNA sequencing was performed. The RNAseq analysis revealed a number of global virulence regulators that might act downstream of ClpXP, to control expression of tst and other virulence genes. Collectively, the results extend our understanding of the complex transcriptional regulation of the tst, sed, and sec genes.
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Affiliation(s)
- Jenny Schelin
- Division of Applied Microbiology, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden; (J.S.); (B.F.)
| | - Marianne Thorup Cohn
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederikberg C, Denmark;
| | - Barbro Frisk
- Division of Applied Microbiology, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden; (J.S.); (B.F.)
| | - Dorte Frees
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederikberg C, Denmark;
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14
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Ju Y, He L, Zhou Y, Yang T, Sun K, Song R, Yang Y, Li C, Sang Z, Bao R, Luo Y. Discovery of Novel Peptidomimetic Boronate ClpP Inhibitors with Noncanonical Enzyme Mechanism as Potent Virulence Blockers in Vitro and in Vivo. J Med Chem 2020; 63:3104-3119. [PMID: 32031798 DOI: 10.1021/acs.jmedchem.9b01746] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Caseinolytic protease P (ClpP) is considered as a promising target for the treatment of Staphylococcus aureus infections. In an unbiased screen of 2632 molecules, a peptidomimetic boronate, MLN9708, was found to be a potent suppressor of SaClpP function. A time-saving and cost-efficient strategy integrating in silico position scanning, multistep miniaturized synthesis, and bioactivity testing was deployed for optimization of this hit compound and led to fast exploration of structure-activity relationships. Five of 150 compounds from the miniaturized synthesis exhibited improved inhibitory activity. Compound 43Hf was the most active inhibitor and showed reversible covalent binding to SaClpP while did not destabilize the tetradecameric structure of SaClpP. The crystal structure of 43Hf-SaClpP complex provided mechanistic insight into the covalent binding mode of peptidomimetic boronate and SaClpP. Furthermore, 43Hf could bind endogenous ClpP in S. aureus cells and exhibited significant efficacy in attenuating S. aureus virulence in vitro and in vivo.
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Affiliation(s)
- Yuan Ju
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lihui He
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yuanzheng Zhou
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.,Laboratory of Human Disease and Immunotherapies, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ke Sun
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Rao Song
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yang Yang
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Chengwei Li
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.,Suzhou Zelgen Biopharmaceuticals Co., Ltd., Kunshan, Jiangsu 215301, China
| | - Zitai Sang
- Institute of Life Science, Luoyang Normal University, Luoyang, Henan 471934, China
| | - Rui Bao
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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15
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Staphylococcus aureus ClpX localizes at the division septum and impacts transcription of genes involved in cell division, T7-secretion, and SaPI5-excision. Sci Rep 2019; 9:16456. [PMID: 31712583 PMCID: PMC6848492 DOI: 10.1038/s41598-019-52823-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/12/2019] [Indexed: 11/25/2022] Open
Abstract
In all living cells, molecular chaperones are essential for facilitating folding and unfolding of proteins. ClpX is a highly conserved ATP-dependent chaperone that besides functioning as a classical chaperone can associate with ClpP to form the ClpXP protease. To investigate the relative impact of the ClpXP protease and the ClpX chaperone in cell physiology of the important pathogenic bacterium Staphylococcus aureus, we assessed the transcriptional changes induced by inactivating only ClpXP, or by completely deleting ClpX. This analysis revealed that ClpX has a profound impact on S. aureus cell physiology that is mediated primarily via ClpXP-dependent pathways. As an example, ClpX impacts expression of virulence genes entirely via ClpXP-dependent mechanisms. Furthermore, ClpX controls a high number of genes and sRNAs via pathways involving both ClpXP protease and ClpX chaperone activities; an interesting example being genes promoting excision and replication of the pathogenicity island SaPI5. Independently of ClpP, ClpX, impacts transcription of only a restricted number of genes involved in peptidoglycan synthesis, cell division, and type seven secretion. Finally, we demonstrate that ClpX localizes in single foci in close proximity to the division septum lending support to the idea that ClpX plays a role in S. aureus cell division.
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16
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Moreno-Cinos C, Sassetti E, Salado IG, Witt G, Benramdane S, Reinhardt L, Cruz CD, Joossens J, Van der Veken P, Brötz-Oesterhelt H, Tammela P, Winterhalter M, Gribbon P, Windshügel B, Augustyns K. α-Amino Diphenyl Phosphonates as Novel Inhibitors of Escherichia coli ClpP Protease. J Med Chem 2019; 62:774-797. [PMID: 30571121 DOI: 10.1021/acs.jmedchem.8b01466] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Increased Gram-negative bacteria resistance to antibiotics is becoming a global problem, and new classes of antibiotics with novel mechanisms of action are required. The caseinolytic protease subunit P (ClpP) is a serine protease conserved among bacteria that is considered as an interesting drug target. ClpP function is involved in protein turnover and homeostasis, stress response, and virulence among other processes. The focus of this study was to identify new inhibitors of Escherichia coli ClpP and to understand their mode of action. A focused library of serine protease inhibitors based on diaryl phosphonate warheads was tested for ClpP inhibition, and a chemical exploration around the hit compounds was conducted. Altogether, 14 new potent inhibitors of E. coli ClpP were identified. Compounds 85 and 92 emerged as most interesting compounds from this study due to their potency and, respectively, to its moderate but consistent antibacterial properties as well as the favorable cytotoxicity profile.
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Affiliation(s)
- Carlos Moreno-Cinos
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Elisa Sassetti
- Fraunhofer Institute for Molecular Biology and Applied Ecology, ScreeningPort , Schnackenburgallee 114 , 22525 Hamburg , Germany.,Department of Life Sciences and Chemistry , Jacobs University Bremen gGmbH , Campus Ring 1 , 28759 Bremen , Germany
| | - Irene G Salado
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Gesa Witt
- Fraunhofer Institute for Molecular Biology and Applied Ecology, ScreeningPort , Schnackenburgallee 114 , 22525 Hamburg , Germany
| | - Siham Benramdane
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Laura Reinhardt
- Interfaculty Institute for Microbiology and Infection Medicine , University of Tübingen , Auf der Morgenstelle 28 , 72076 Tübingen , Germany
| | - Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences , University of Helsinki , Viikinkaari 5E , FI-00014 Helsinki , Finland
| | - Jurgen Joossens
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Pieter Van der Veken
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute for Microbiology and Infection Medicine , University of Tübingen , Auf der Morgenstelle 28 , 72076 Tübingen , Germany
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences , University of Helsinki , Viikinkaari 5E , FI-00014 Helsinki , Finland
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry , Jacobs University Bremen gGmbH , Campus Ring 1 , 28759 Bremen , Germany
| | - Philip Gribbon
- Fraunhofer Institute for Molecular Biology and Applied Ecology, ScreeningPort , Schnackenburgallee 114 , 22525 Hamburg , Germany
| | - Björn Windshügel
- Fraunhofer Institute for Molecular Biology and Applied Ecology, ScreeningPort , Schnackenburgallee 114 , 22525 Hamburg , Germany
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , B-2610 Antwerp , Belgium
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17
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Fetzer C, Korotkov VS, Sieber SA. Hydantoin analogs inhibit the fully assembled ClpXP protease without affecting the individual peptidase and chaperone domains. Org Biomol Chem 2019; 17:7124-7127. [DOI: 10.1039/c9ob01339c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new class of non-covalent inhibitors attenuates ClpXP turnover, neither impairing chaperone nor peptidase activity.
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Affiliation(s)
- Christian Fetzer
- Technische Universität München
- Center for Integrated Protein Science Munich (CIPSM)
- 85748 Garching
- Germany
| | - Vadim S. Korotkov
- Technische Universität München
- Center for Integrated Protein Science Munich (CIPSM)
- 85748 Garching
- Germany
| | - Stephan A. Sieber
- Technische Universität München
- Center for Integrated Protein Science Munich (CIPSM)
- 85748 Garching
- Germany
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18
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Thinking Outside the Box-Novel Antibacterials To Tackle the Resistance Crisis. Angew Chem Int Ed Engl 2018; 57:14440-14475. [PMID: 29939462 DOI: 10.1002/anie.201804971] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Indexed: 12/13/2022]
Abstract
The public view on antibiotics as reliable medicines changed when reports about "resistant superbugs" appeared in the news. While reasons for this resistance development are easily spotted, solutions for re-establishing effective antibiotics are still in their infancy. This Review encompasses several aspects of the antibiotic development pipeline from very early strategies to mature drugs. An interdisciplinary overview is given of methods suitable for mining novel antibiotics and strategies discussed to unravel their modes of action. Select examples of antibiotics recently identified by using these platforms not only illustrate the efficiency of these measures, but also highlight promising clinical candidates with therapeutic potential. Furthermore, the concept of molecules that disarm pathogens by addressing gatekeepers of virulence will be covered. The Review concludes with an evaluation of antibacterials currently in clinical development. Overall, this Review aims to connect select innovative antimicrobial approaches to stimulate interdisciplinary partnerships between chemists from academia and industry.
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Affiliation(s)
- Markus Lakemeyer
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Weining Zhao
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Franziska A Mandl
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases, Sanofi-Aventis (Deutschland) GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
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19
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Über bisherige Denkweisen hinaus - neue Wirkstoffe zur Überwindung der Antibiotika-Krise. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804971] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Markus Lakemeyer
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Weining Zhao
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Franziska A. Mandl
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases; Sanofi-Aventis (Deutschland) GmbH; Industriepark Höchst 65926 Frankfurt am Main Deutschland
| | - Stephan A. Sieber
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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20
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Suppression of Staphylococcus aureus virulence by a small-molecule compound. Proc Natl Acad Sci U S A 2018; 115:8003-8008. [PMID: 30012613 DOI: 10.1073/pnas.1720520115] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Emerging antibiotic resistance among bacterial pathogens has necessitated the development of alternative approaches to combat drug-resistance-associated infection. The abolition of Staphylococcus aureus virulence by targeting multiple-virulence gene products represents a promising strategy for exploration. A multiplex promoter reporter platform using gfp-luxABCDE dual-reporter plasmids with selected promoters from S. aureus-virulence-associated genes was used to identify compounds that modulate the expression of virulence factors. One small-molecule compound, M21, was identified from a chemical library to reverse virulent S. aureus into its nonvirulent state. M21 is a noncompetitive inhibitor of ClpP and alters α-toxin expression in a ClpP-dependent manner. A mouse model of infection indicated that M21 could attenuate S. aureus virulence. This nonantibiotic compound has been shown to suppress the expression of multiple unrelated virulence factors in S. aureus, suggesting that targeting a master regulator of virulence is an effective way to control virulence. Our results illustrate the power of chemical genetics in the modulation of virulence gene expression in pathogenic bacteria.
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21
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Hofbauer B, Vomacka J, Stahl M, Korotkov VS, Jennings MC, Wuest WM, Sieber SA. Dual Inhibitor of Staphylococcus aureus Virulence and Biofilm Attenuates Expression of Major Toxins and Adhesins. Biochemistry 2018; 57:1814-1820. [PMID: 29451388 DOI: 10.1021/acs.biochem.7b01271] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Staphylococcus aureus is a major bacterial pathogen that invades and damages host tissue by the expression of devastating toxins. We here performed a phenotypic screen of 35 molecules that were structurally inspired by previous hydroxyamide-based S. aureus virulence inhibitors compiled from commercial sources or designed and synthesized de novo. One of the most potent compounds, AV73, not only reduced hemolytic alpha-hemolysin production in S. aureus but also impeded in vitro biofilm formation. The effect of AV73 on bacterial proteomes and extracellular protein levels was analyzed by quantitative proteomics and revealed a significant down-regulation of major virulence and biofilm promoting proteins. To elucidate the mode of action of AV73, target identification was performed using affinity-based protein profiling (AfBPP), where among others YidC was identified as a target.
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Affiliation(s)
- Barbara Hofbauer
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Institute of Advanced Studies (IAS) , Technische Universität München (TUM) , Lichtenbergstraße 4 , D-85747 Garching , Germany
| | - Jan Vomacka
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Institute of Advanced Studies (IAS) , Technische Universität München (TUM) , Lichtenbergstraße 4 , D-85747 Garching , Germany
| | - Matthias Stahl
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Institute of Advanced Studies (IAS) , Technische Universität München (TUM) , Lichtenbergstraße 4 , D-85747 Garching , Germany
| | - Vadim S Korotkov
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Institute of Advanced Studies (IAS) , Technische Universität München (TUM) , Lichtenbergstraße 4 , D-85747 Garching , Germany
| | - Megan C Jennings
- Department of Chemistry , Temple University , 1910 North 13th Street , Philadelphia , Pennsylvania 19122 , United States
| | - William M Wuest
- Department of Chemistry , Temple University , 1910 North 13th Street , Philadelphia , Pennsylvania 19122 , United States
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Institute of Advanced Studies (IAS) , Technische Universität München (TUM) , Lichtenbergstraße 4 , D-85747 Garching , Germany
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22
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Horn J, Stelzner K, Rudel T, Fraunholz M. Inside job: Staphylococcus aureus host-pathogen interactions. Int J Med Microbiol 2017; 308:607-624. [PMID: 29217333 DOI: 10.1016/j.ijmm.2017.11.009] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/17/2017] [Accepted: 11/21/2017] [Indexed: 12/21/2022] Open
Abstract
Staphylococcus aureus is a notorious opportunistic pathogen causing a plethora of diseases. Recent research established that once phagocytosed by neutrophils and macrophages, a certain percentage of S. aureus is able to survive within these phagocytes which thereby even may contribute to dissemination of the pathogen. S. aureus further induces its uptake by otherwise non-phagocytic cells and the ensuing intracellular cytotoxicity is suggested to lead to tissue destruction, whereas bacterial persistence within cells is thought to lead to immune evasion and chronicity of infections. We here review recent work on the S. aureus host pathogen interactions with a focus on the intracellular survival of the pathogen.
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Affiliation(s)
- Jessica Horn
- Chair of Microbiology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Kathrin Stelzner
- Chair of Microbiology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Thomas Rudel
- Chair of Microbiology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Martin Fraunholz
- Chair of Microbiology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
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23
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Fetzer C, Korotkov VS, Thänert R, Lee KM, Neuenschwander M, von Kries JP, Medina E, Sieber SA. Verringerung der Virulenz von multiresistentem Staphylococcus aureus
mithilfe eines chemischen Disruptors des ClpX-Chaperon-Komplexes. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Christian Fetzer
- Center for Integrated Protein Science am Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Vadim S. Korotkov
- Center for Integrated Protein Science am Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Robert Thänert
- Infektionsimmunologie, Helmholtz-Zentrum für Infektionsforschung; Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Kyu Myung Lee
- Center for Integrated Protein Science am Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Martin Neuenschwander
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Robert-Roessle-Straße 10 13125 Berlin Deutschland
| | - Jens Peter von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Robert-Roessle-Straße 10 13125 Berlin Deutschland
| | - Eva Medina
- Infektionsimmunologie, Helmholtz-Zentrum für Infektionsforschung; Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Stephan A. Sieber
- Center for Integrated Protein Science am Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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24
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Fetzer C, Korotkov VS, Thänert R, Lee KM, Neuenschwander M, von Kries JP, Medina E, Sieber SA. A Chemical Disruptor of the ClpX Chaperone Complex Attenuates the Virulence of Multidrug-Resistant Staphylococcus aureus. Angew Chem Int Ed Engl 2017; 56:15746-15750. [DOI: 10.1002/anie.201708454] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/08/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Christian Fetzer
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
| | - Vadim S. Korotkov
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
| | - Robert Thänert
- Infection Immunology Research Group; Helmholtz Centre for Infection Research; Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Kyu Myung Lee
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
| | - Martin Neuenschwander
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - Jens Peter von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - Eva Medina
- Infection Immunology Research Group; Helmholtz Centre for Infection Research; Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Stephan A. Sieber
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
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Juhlin A, Svensson S, Thomsen P, Trobos M. Staphylococcal biofilm gene expression on biomaterials - A methodological study. J Biomed Mater Res A 2017; 105:3400-3412. [PMID: 28782178 DOI: 10.1002/jbm.a.36171] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/01/2017] [Indexed: 01/02/2023]
Abstract
The combination of increased healthcare access, universal aging, and infallible therapy demands, synergistically drive the need for the development of biomaterial technologies that mitigate the challenge of biomaterial-associated infections (BAI). Staphylococcus epidermidis and Staphylococcus aureus account for the majority of BAI due to their ability to accumulate in adherent multilayered biofilm. This investigation details the development of gene expression assays to evaluate the genetic processes of attachment, accumulation, maturation, and dispersal phases of biofilms on biomaterials in vitro, while abiding by the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines. The biofilm formation of S. epidermidis on polyurethane (PU) central venous catheters and S. aureus on machined titanium (Ti) was examined in terms of gene expression at early and late time points. The results provided insight into how each stage of biofilm formation is orchestrated over time on these biomaterials in vitro. Furthermore, the results suggested that mechanical RNA extraction, organic solvents, elimination of genomic DNA, and preamplification are advisable strategies to implement for biofilm gene expression analysis. It is concluded that this method can be employed for the assessment of biofilm-biomaterial interactions at the molecular level. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 3400-3412, 2017.
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Affiliation(s)
- Annika Juhlin
- Department of Biomaterials, Sahlgrenska Academy, University of Gothenburg, P.O. Box 412, 40530, Gothenburg, Sweden.,BIOMATCELL VINN Excellence Center of Biomaterials and Cell Therapy, University of Gothenburg, P.O. Box 412, 40530, Gothenburg, Sweden
| | - Sara Svensson
- Department of Biomaterials, Sahlgrenska Academy, University of Gothenburg, P.O. Box 412, 40530, Gothenburg, Sweden.,BIOMATCELL VINN Excellence Center of Biomaterials and Cell Therapy, University of Gothenburg, P.O. Box 412, 40530, Gothenburg, Sweden
| | - Peter Thomsen
- Department of Biomaterials, Sahlgrenska Academy, University of Gothenburg, P.O. Box 412, 40530, Gothenburg, Sweden.,BIOMATCELL VINN Excellence Center of Biomaterials and Cell Therapy, University of Gothenburg, P.O. Box 412, 40530, Gothenburg, Sweden
| | - Margarita Trobos
- Department of Biomaterials, Sahlgrenska Academy, University of Gothenburg, P.O. Box 412, 40530, Gothenburg, Sweden.,BIOMATCELL VINN Excellence Center of Biomaterials and Cell Therapy, University of Gothenburg, P.O. Box 412, 40530, Gothenburg, Sweden
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Lehmann J, Richers J, Pöthig A, Sieber SA. Synthesis of ramariolide natural products and discovery of their targets in mycobacteria. Chem Commun (Camb) 2017; 53:107-110. [PMID: 27847948 PMCID: PMC5322466 DOI: 10.1039/c6cc08365j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The total synthesis of ramariolides A–D and ABPP (photoprobe) derivatives have been synthesized for target identification in mycobacterial strains.
Ramariolides A–D are natural products with antibacterial activity. To exploit their cellular mechanism, we here devise the first total synthesis and prepare a photoprobe for target identification. Antibacterial testing against several pathogenic strains including Mycobacterium tuberculosis revealed the highest potency for ramariolide A. Chemical proteomics unraveled binding to essential proteins for amino acid anabolism.
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Affiliation(s)
- Johannes Lehmann
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany.
| | - Johannes Richers
- Catalysis Research Center (CRC), Technische Universität München, Ernst-Otto-Fischer Straße 1, 85747 Garching, Germany
| | - Alexander Pöthig
- Catalysis Research Center (CRC), Technische Universität München, Ernst-Otto-Fischer Straße 1, 85747 Garching, Germany
| | - Stephan A Sieber
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany.
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27
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Srisuwan S, Voravuthikunchai SP. Rhodomyrtus tomentosa Leaf Extract Inhibits Methicillin-Resistant Staphylococcus aureus Adhesion, Invasion, and Intracellular Survival in Human HaCaT Keratinocytes. Microb Drug Resist 2017; 23:1002-1012. [PMID: 28475464 DOI: 10.1089/mdr.2016.0284] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has an ability to invade nonprofessional phagocytic cells, resulting in persistent infections and most likely host cell death. Series of our studies have claimed pronounced antibacterial efficacy of Rhodomyrtus tomentosa leaf extract. This study was to further investigate potency of the extract in intracellular killing of human HaCaT keratinocytes. Pretreatment of MRSA with the extract resulted in a remarkable reduction in the bacterial adhesion to HaCaT keratinocytes, compared with untreated control (p < 0.001). In addition, at least 60% inhibition of the bacterial invasion into HaCaT cells was observed. Intracellular killing assay demonstrated that the extract exhibited strong antibacterial activity against intracellular MRSA at nontoxic concentrations (128 mg/L), which may have resulted from the increase in bactericidal activity under phagolysosomal pH. Transmission electron microscopy displayed the effects of the extract on alterations in the bacterial cell morphology with cell lysis. Fluorescence microscopy revealed that the extract decreased MRSA-induced apoptosis in HaCaT cells. In addition, cytotoxicity of HaCaT cells caused by MRSA supernatant was reduced at least 50% by the extract. The potential activities of R. tomentosa extract may be useful in an alternative treatment of MRSA infections in slight acidic compartments, particularly skin infections.
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Affiliation(s)
- Sutthirat Srisuwan
- Excellence Research Laboratory on Natural Products and Department of Microbiology, Faculty of Science and Natural Products Research Center of Excellence, Prince of Songkla University , Songkhla, Thailand
| | - Supayang Piyawan Voravuthikunchai
- Excellence Research Laboratory on Natural Products and Department of Microbiology, Faculty of Science and Natural Products Research Center of Excellence, Prince of Songkla University , Songkhla, Thailand
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Krysiak J, Stahl M, Vomacka J, Fetzer C, Lakemeyer M, Fux A, Sieber SA. Quantitative Map of β-Lactone-Induced Virulence Regulation. J Proteome Res 2017; 16:1180-1192. [DOI: 10.1021/acs.jproteome.6b00705] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Joanna Krysiak
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Matthias Stahl
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Jan Vomacka
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Christian Fetzer
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Markus Lakemeyer
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Anja Fux
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Stephan A. Sieber
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
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Malik IT, Brötz-Oesterhelt H. Conformational control of the bacterial Clp protease by natural product antibiotics. Nat Prod Rep 2017; 34:815-831. [DOI: 10.1039/c6np00125d] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Natural products targeting the bacterial Clp protease unravel key interfaces for protein–protein–interaction and long-distance conformational control.
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Affiliation(s)
- I. T. Malik
- Department of Microbial Bioactive Compounds
- Interfaculty Institute of Microbiology and Infection Medicine
- University of Tuebingen
- Germany
| | - H. Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds
- Interfaculty Institute of Microbiology and Infection Medicine
- University of Tuebingen
- Germany
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Gil F, Paredes-Sabja D. Acyldepsipeptide antibiotics as a potential therapeutic agent against Clostridium difficile recurrent infections. Future Microbiol 2016; 11:1179-89. [DOI: 10.2217/fmb-2016-0064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Alternative antimicrobial therapies based on acyldepsipeptides may hold promising results, based on the fact that they have shown to efficiently eradicate persister cells, stationary cells and cell in biofilm structures of several pathogenic bacteria from the infected host. Clostridium difficile infection is considered the result of extensive hospital use of expanded-spectrum antibiotics, which cause dysbiosis of the intestinal microbiota, enhancing susceptibility to infection and persistence. Considering the urgent need for the development of novel and efficient antimicrobial strategies against C. difficile, we review the potential application to treat C. difficile infections of acyldepsipeptides family of antibiotics, its mechanism of action and current developmental stages.
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Affiliation(s)
- Fernando Gil
- Microbiota–Host Interactions & Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Daniel Paredes-Sabja
- Microbiota–Host Interactions & Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
- Center for Bioinformatic & Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
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The Cell Wall Polymer Lipoteichoic Acid Becomes Nonessential in Staphylococcus aureus Cells Lacking the ClpX Chaperone. mBio 2016; 7:mBio.01228-16. [PMID: 27507828 PMCID: PMC4981727 DOI: 10.1128/mbio.01228-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED Lipoteichoic acid (LTA) is an important cell wall component of Gram-positive bacteria and a promising target for the development of vaccines and antimicrobial compounds against Staphylococcus aureus Here we demonstrate that mutations in the conditionally essential ltaS (LTA synthase) gene arise spontaneously in an S. aureus mutant lacking the ClpX chaperone. A wide variety of ltaS mutations were selected, and among these, a substantial portion resulted in premature stop codons and other changes predicted to abolish LtaS synthesis. Consistent with this assumption, the clpX ltaS double mutants did not produce LTA, and genetic analyses confirmed that LTA becomes nonessential in the absence of the ClpX chaperone. In fact, inactivation of ltaS alleviated the severe growth defect conferred by the clpX deletion. Microscopic analyses showed that the absence of ClpX partly alleviates the septum placement defects of an LTA-depleted strain, while other phenotypes typical of LTA-negative S. aureus mutants, including increased cell size and decreased autolytic activity, are retained. In conclusion, our results indicate that LTA has an essential role in septum placement that can be bypassed by inactivating the ClpX chaperone. IMPORTANCE Lipoteichoic acid is an essential component of the Staphylococcus aureus cell envelope and an attractive target for the development of vaccines and antimicrobials directed against antibiotic-resistant Gram-positive bacteria such as methicillin-resistant S. aureus and vancomycin-resistant enterococci. In this study, we showed that the lipoteichoic acid polymer is essential for growth of S. aureus only as long as the ClpX chaperone is present in the cell. Our results indicate that lipoteichoic acid and ClpX play opposite roles in a pathway that controls two key cell division processes in S. aureus, namely, septum formation and autolytic activity. The discovery of a novel functional connection in the genetic network that controls cell division in S. aureus may expand the repertoire of possible strategies to identify compounds or compound combinations that kill antibiotic-resistant S. aureus.
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Springer MT, Singh VK, Cheung AL, Donegan NP, Chamberlain NR. Effect of clpP and clpC deletion on persister cell number in Staphylococcus aureus. J Med Microbiol 2016; 65:848-857. [PMID: 27375177 DOI: 10.1099/jmm.0.000304] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Staphylococcus aureus is responsible for a wide variety of infections that include superficial skin and soft tissue infections, septicaemia, central nervous system infections, endocarditis, osteomyelitis and pneumonia. Others have demonstrated the importance of toxin-antitoxin (TA) modules in the formation of persisters and the role of the Clp proteolytic system in the regulation of these TA modules. This study was conducted to determine the effect of clpP and clpC deletion on S. aureus persister cell numbers following antibiotic treatment. Deletion of clpP resulted in a significant decrease in persister cells following treatment with oxacillin and erythromycin but not with levofloxacin and daptomycin. Deletion of clpC resulted in a decrease in persister cells following treatment with oxacillin. These differences were dependent on the antibiotic class and the CFU ml-1 in which the cells were treated. Persister revival assays for all the bacterial strains in these studies demonstrated a significant delay in resumption of growth characteristic of persister cells, indicating that the surviving organisms in this study were not likely due to spontaneous antibiotic resistance. Based on our results, ClpP and possibly ClpC play a role in persister cell formation or maintenance, and this effect is dependent on antibiotic class and the CFU ml-1 or the growth phase of the cells.
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Affiliation(s)
- Matthew T Springer
- Department of Microbiology/Immunology, A.T. Still University of Health Sciences, Kirksville College of Osteopathic Medicine, Kirksville, MO, USA
| | - Vineet K Singh
- Department of Microbiology/Immunology, A.T. Still University of Health Sciences, Kirksville College of Osteopathic Medicine, Kirksville, MO, USA
| | - Ambrose L Cheung
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Niles P Donegan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Neal R Chamberlain
- Department of Microbiology/Immunology, A.T. Still University of Health Sciences, Kirksville College of Osteopathic Medicine, Kirksville, MO, USA
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Positive Regulation of Staphylococcal Enterotoxin H by Rot (Repressor of Toxin) Protein and Its Importance in Clonal Complex 81 Subtype 1 Lineage-Related Food Poisoning. Appl Environ Microbiol 2015; 81:7782-90. [PMID: 26341202 DOI: 10.1128/aem.01936-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/22/2015] [Indexed: 11/20/2022] Open
Abstract
We previously demonstrated the clonal complex 81 (CC81) subtype 1 lineage is the major staphylococcal food poisoning (SFP)-associated lineage in Japan (Y. Sato'o et al., J Clin Microbiol 52:2637-2640, 2014, http://dx.doi.org/10.1128/JCM.00661-14). Strains of this lineage produce staphylococcal enterotoxin H (SEH) in addition to SEA. However, an evaluation of the risk for the recently reported SEH has not been sufficiently conducted. We first searched for staphylococcal enterotoxin (SE) genes and SE proteins in milk samples that caused a large SFP outbreak in Japan. Only SEA and SEH were detected, while there were several SE genes detected in the samples. We next designed an experimental model using a meat product to assess the productivity of SEs and found that only SEA and SEH were detectably produced in situ. Therefore, we investigated the regulation of SEH production using a CC81 subtype 1 isolate. Through mutant analysis of global regulators, we found the repressor of toxin (Rot) functioned oppositely as a stimulator of SEH production. SEA production was not affected by Rot. seh mRNA expression correlated with rot both in media and on the meat product, and the Rot protein was shown to directly bind to the seh promoter. The seh promoter sequence was predicted to form a loop structure and to hide the RNA polymerase binding sequences. We propose Rot binds to the promoter sequence of seh and unfolds the secondary structure that may lead the RNA polymerase to bind the promoter, and then seh mRNA transcription begins. This alternative Rot regulation for SEH may contribute to sufficient toxin production by the CC81 subtype 1 lineage in foods to induce SFP.
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Stepwise decrease in daptomycin susceptibility in clinical Staphylococcus aureus isolates associated with an initial mutation in rpoB and a compensatory inactivation of the clpX gene. Antimicrob Agents Chemother 2015; 59:6983-91. [PMID: 26324273 DOI: 10.1128/aac.01303-15] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/25/2015] [Indexed: 12/16/2022] Open
Abstract
Daptomycin is a lipopeptide antibiotic used clinically for the treatment of methicillin-resistant Staphylococcus aureus (MRSA) infections. The emergence of daptomycin-nonsusceptible S. aureus isolates during therapy is often associated with multiple genetic changes; however, the relative contributions of these changes to resistance and other phenotypic changes usually remain unclear. The present study was undertaken to investigate this issue using a genetically characterized series of four isogenic clinical MRSA strains derived from a patient with bacteremia before and during daptomycin treatment. The first strain obtained after daptomycin therapy carried a single-nucleotide polymorphism (SNP) in rpoB (RpoB A477D) that decreased susceptibility not only to daptomycin but also to vancomycin, β-lactams, and rifampin. Furthermore, the rpoB mutant exhibited pleiotropic phenotypes, including increased cell wall thickness, reduced expression of virulence traits, induced expression of the stress-associated transcriptional regulator Spx, and slow growth. A subsequently acquired loss-of-function mutation in clpX partly alleviated the growth defect conferred by the rpoB mutation without changing antibiotic susceptibility. The final isolate acquired three additional mutations, including an SNP in mprF (MprF S295L) known to confer daptomycin nonsusceptibility, and accordingly, this isolate was the only daptomycin-nonsusceptible strain of this series. Interestingly, in this isolate, the cell wall had regained the same thickness as that of the parental strain, while the level of transcription of the vraSR (cell wall stress regulator) was increased. In conclusion, this study illustrates how serial genetic changes selected in vivo contribute to daptomycin nonsusceptibility, growth fitness, and virulence traits.
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Hackl MW, Lakemeyer M, Dahmen M, Glaser M, Pahl A, Lorenz-Baath K, Menzel T, Sievers S, Böttcher T, Antes I, Waldmann H, Sieber SA. Phenyl Esters Are Potent Inhibitors of Caseinolytic Protease P and Reveal a Stereogenic Switch for Deoligomerization. J Am Chem Soc 2015; 137:8475-83. [PMID: 26083639 DOI: 10.1021/jacs.5b03084] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Caseinolytic protease P (ClpP) represents a central bacterial degradation machinery that is involved in cell homeostasis and pathogenicity. The functional role of ClpP has been studied by genetic knockouts and through the use of beta-lactones, which remain the only specific inhibitors of ClpP discovered to date. Beta-lactones have served as chemical tools to manipulate ClpP in several organisms; however, their potency, selectivity and stability is limited. Despite detailed structural insights into the composition and conformational flexibility of the ClpP active site, no rational efforts to design specific non-beta-lactone inhibitors have been reported to date. In this work, an unbiased screen of more than 137 000 compounds was used to identify five phenyl ester compounds as highly potent ClpP inhibitors that were selective for bacterial, but not human ClpP. The potency of phenyl esters largely exceeded that of beta-lactones in ClpP peptidase and protease inhibition assays and displayed unique target selectivity in living S. aureus cells. Analytical studies revealed that while phenyl esters are cleaved like native peptide substrates, they remain covalently trapped as acyl-enzyme intermediates in the active site. The synthesis of 36 derivatives and subsequent structure-activity relationship (SAR) studies provided insights into conserved structural elements that are important for inhibition potency and acylation reactivity. Moreover, the stereochemistry of a methyl-substituent at the alpha position to the ester, resembling amino acid side chains in peptide substrates, impacted ClpP complex stability, causing either dissociation into heptamers or retention of the tetradecameric state. Mechanistic insights into this intriguing stereo switch and the phenyl ester binding mode were obtained by molecular docking experiments.
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Affiliation(s)
- Mathias W Hackl
- †Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, Garching, D-85747, Germany
| | - Markus Lakemeyer
- †Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, Garching, D-85747, Germany
| | - Maria Dahmen
- †Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, Garching, D-85747, Germany
| | - Manuel Glaser
- ‡Center for Integrated Protein Science at the Department of Life Sciences, Technische Universität München, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany
| | - Axel Pahl
- †Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, Garching, D-85747, Germany
| | - Katrin Lorenz-Baath
- †Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, Garching, D-85747, Germany
| | - Thomas Menzel
- †Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, Garching, D-85747, Germany
| | - Sonja Sievers
- §Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
| | - Thomas Böttcher
- ⊥Department of Chemistry, Universität Konstanz, Universitätsstrasse 10, D-78457 Konstanz, Germany
| | - Iris Antes
- ‡Center for Integrated Protein Science at the Department of Life Sciences, Technische Universität München, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany
| | - Herbert Waldmann
- §Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.,∥Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany
| | - Stephan A Sieber
- †Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, Garching, D-85747, Germany
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Carney DW, Compton CL, Schmitz KR, Stevens JP, Sauer RT, Sello JK. A simple fragment of cyclic acyldepsipeptides is necessary and sufficient for ClpP activation and antibacterial activity. Chembiochem 2014; 15:2216-20. [PMID: 25212124 PMCID: PMC4343535 DOI: 10.1002/cbic.201402358] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Indexed: 12/30/2022]
Abstract
The development of new antibacterial agents, particularly those with unique biological targets, is essential to keep pace with the inevitable emergence of drug resistance in pathogenic bacteria. We identified the minimal structural component of the cyclic acyldepsipeptide (ADEP) antibiotics that exhibits antibacterial activity. We found that N-acyldifluorophenylalanine fragments function via the same mechanism of action as ADEPs, as evidenced by the requirement of ClpP for the fragments' antibacterial activity, the ability of fragments to activate Bacillus subtilis ClpP in vitro, and the capacity of an N-acyldifluorophenylalanine affinity matrix to capture ClpP from B. subtilis cell lysates. N-acyldifluorophenylalanine fragments are much simpler in structure than the full ADEPs and are also highly amenable to structural diversification. Thus, the stage has been set for the development of non-peptide activators of ClpP that can be used as antibacterial agents.
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Affiliation(s)
- Daniel W. Carney
- Department of Chemistry, Brown University, 324 Brook Street, Providence, RI 02912
| | - Corey L. Compton
- Department of Chemistry, Brown University, 324 Brook Street, Providence, RI 02912
| | - Karl R. Schmitz
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - Julia P. Stevens
- Department of Chemistry, Brown University, 324 Brook Street, Providence, RI 02912
| | - Robert T. Sauer
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - Jason K. Sello
- Department of Chemistry, Brown University, 324 Brook Street, Providence, RI 02912
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Knudsen GM, Nielsen MB, Thomsen LE, Aabo S, Rychlik I, Olsen JE. The role of ClpP, RpoS and CsrA in growth and filament formation of Salmonella enterica serovar Typhimurium at low temperature. BMC Microbiol 2014; 14:208. [PMID: 25123657 PMCID: PMC4236599 DOI: 10.1186/s12866-014-0208-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 07/21/2014] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Salmonellae are food-borne pathogens of great health and economic importance. To pose a threat to humans, Salmonellae normally have to cope with a series of stressful conditions in the food chain, including low temperature. In the current study, we evaluated the importance of the Clp proteolytic complex and the carbon starvation protein, CsrA, for the ability of Salmonella Typhimurium to grow at low temperature. RESULTS A clpP mutant was severely affected in growth and formed pin point colonies at 10°C. Contrary to this, rpoS and clpP/rpoS mutants were only slightly affected. The clpP mutant formed cold resistant suppressor mutants at a frequency of 2.5 × 10(-3) and these were found not to express RpoS. Together these results indicated that the impaired growth of the clpP mutant was caused by high level of RpoS. Evaluation by microscopy of the clpP mutant revealed that it formed filamentous cells when grown at 10°C, and this phenotype too, disappered when rpoS was mutated in parallel indicating a RpoS-dependency. A csrA (sup) mutant was also growth attenuated a low temperature. An rpoS/csrA (sup) double mutant was also growth attenuated, indicating that the phenotype of the csrA mutant was independent from RpoS. CONCLUSIONS The cold sensitivity of clpP mutant was associated with increased levels of RpoS and probably caused by toxic levels of RpoS. Although a csrA mutant also accumulated high level of RpoS, growth impairment caused by lack of csrA was not related to RpoS levels in a similar way.
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Affiliation(s)
| | | | | | | | | | - John Elmerdahl Olsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, Frederiksberg C 1870, Denmark.
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Weinandy F, Lorenz-Baath K, Korotkov VS, Böttcher T, Sethi S, Chakraborty T, Sieber SA. A β-Lactone-Based Antivirulence Drug AmelioratesStaphylococcus aureusSkin Infections in Mice. ChemMedChem 2014; 9:710-3. [DOI: 10.1002/cmdc.201300325] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 01/24/2014] [Indexed: 11/07/2022]
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Carney D, Schmitz KR, Truong J, Sauer RT, Sello JK. Restriction of the conformational dynamics of the cyclic acyldepsipeptide antibiotics improves their antibacterial activity. J Am Chem Soc 2014; 136:1922-9. [PMID: 24422534 PMCID: PMC4004210 DOI: 10.1021/ja410385c] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Indexed: 02/07/2023]
Abstract
The cyclic acyldepsipeptide (ADEP) antibiotics are a new class of antibacterial agents that kill bacteria via a mechanism that is distinct from all clinically used drugs. These molecules bind and dysregulate the activity of the ClpP peptidase. The potential of these antibiotics as antibacterial drugs has been enhanced by the elimination of pharmacological liabilities through medicinal chemistry efforts. Here, we demonstrate that the ADEP conformation observed in the ADEP-ClpP crystal structure is fortified by transannular hydrogen bonding and can be further stabilized by judicious replacement of constituent amino acids within the peptidolactone core structure with more conformationally constrained counterparts. Evidence supporting constraint of the molecule into the bioactive conformer was obtained by measurements of deuterium-exchange kinetics of hydrogens that were proposed to be engaged in transannular hydrogen bonds. We show that the rigidified ADEP analogs bind and activate ClpP at lower concentrations in vitro. Remarkably, these compounds have up to 1200-fold enhanced antibacterial activity when compared to those with the peptidolactone core structure common to two ADEP natural products. This study compellingly demonstrates how rational modulation of conformational dynamics may be used to improve the bioactivities of natural products.
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Affiliation(s)
- Daniel
W. Carney
- Department
of Chemistry, Brown University, 324 Brook Street, Providence, Rhode Island 02912, United States
| | - Karl R. Schmitz
- Department
of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jonathan
V. Truong
- Department
of Chemistry, Brown University, 324 Brook Street, Providence, Rhode Island 02912, United States
| | - Robert T. Sauer
- Department
of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jason K. Sello
- Department
of Chemistry, Brown University, 324 Brook Street, Providence, Rhode Island 02912, United States
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40
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Kunzmann MH, Bach NC, Bauer B, Sieber SA. α-Methylene-γ-butyrolactones attenuate Staphylococcus aureus virulence by inhibition of transcriptional regulation. Chem Sci 2014. [DOI: 10.1039/c3sc52228h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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41
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Clp chaperones and proteases are central in stress survival, virulence and antibiotic resistance of Staphylococcus aureus. Int J Med Microbiol 2013; 304:142-9. [PMID: 24457183 DOI: 10.1016/j.ijmm.2013.11.009] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Intracellular proteolysis carried out by energy-dependent proteases is one of the most conserved biological processes. In all cells proteolysis maintains and shapes the cellular proteome by ridding the cell of damaged proteins and by regulating abundance of functional proteins such as regulatory proteins. The ATP-dependent ClpP protease is highly conserved among eubacteria and in the chloroplasts and mitochondria of eukaryotic cells. In the serious human pathogen, Staphylococcus aureus inactivation of clpP rendered the bacterium avirulent emphasizing the central role of proteolysis in virulence. The contribution of the Clp proteins to virulence is likely to occur at multiple levels. First of all, both Clp ATPases and the Clp protease are central players in stress responses required to cope with the adverse conditions met in the host. The ClpP protease has a dual role herein, as it both eliminates stress-damaged proteins as well as ensures the timely degradation of major stress regulators such as Spx, LexA and CtsR. Additionally, as we will summarize in this review, Clp proteases and Clp chaperones impact on such central processes as virulence gene expression, cell wall metabolism, survival in stationary phase, and cell division. These observations together with recent findings that Clp proteins contribute to adaptation to antibiotics highlights the importance of this interesting proteolytic machinery both for understanding pathogenicity of the organism and for treating staphylococcal infections.
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42
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Gersch M, Kolb R, Alte F, Groll M, Sieber SA. Disruption of oligomerization and dehydroalanine formation as mechanisms for ClpP protease inhibition. J Am Chem Soc 2013; 136:1360-6. [PMID: 24106749 DOI: 10.1021/ja4082793] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over 100 protease inhibitors are currently used in the clinics, and most of them use blockage of the active site for their mode of inhibition. Among the protease drug targets are several enzymes for which the correct multimeric assembly is crucial to their activity, such as the proteasome and the HIV protease. Here, we present a novel mechanism of protease inhibition that relies on active-site-directed small molecules that disassemble the protease complex. We show the applicability of this mechanism within the ClpP protease family, whose members are tetradecameric serine proteases and serve as regulators of several cellular processes, including homeostasis and virulence. Compound binding to ClpP in a substoichiometric fashion triggers the formation of completely inactive heptamers. Moreover, we report the selective β-sultam-induced dehydroalanine formation of the active site serine. This reaction proceeds through sulfonylation and subsequent elimination, thereby obliterating the catalytic charge relay system. The identity of the dehydroalanine was confirmed by mass spectrometry and crystallography. Activity-based protein profiling experiments suggest the formation of a dehydroalanine moiety in living S. aureus cells upon β-sultam treatment. Collectively, these findings extend our view on multicomponent protease inhibition that until now has mainly relied on blockage of the active site or occupation of a regulatory allosteric site.
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Affiliation(s)
- Malte Gersch
- Center for Integrated Protein Science at the Department of Chemistry, Institute of Advanced Studies IAS and ‡Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München , Lichtenbergstrasse 4, Garching D-85747, Germany
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43
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Genetic variation in the Staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing. PLoS One 2013; 8:e77122. [PMID: 24098817 PMCID: PMC3786944 DOI: 10.1371/journal.pone.0077122] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 09/05/2013] [Indexed: 01/05/2023] Open
Abstract
Staphylococcus aureus strains of the 8325 lineage, especially 8325-4 and derivatives lacking prophage, have been used extensively for decades of research. We report herein the results of our deep sequence analysis of strain 8325-4. Assignment of sequence variants compared with the reference strain 8325 (NRS77/PS47) required correction of errors in the 8325 reference genome, and reassessment of variation previously attributed to chemical mutagenesis of the restriction-defective RN4220. Using an extensive strain pedigree analysis, we discovered that 8325-4 contains 16 single nucleotide polymorphisms (SNP) arising prior to the construction of RN4220. We identified 5 indels in 8325-4 compared with 8325. Three indels correspond to expected Φ11, 12, 13 excisions, one indel is explained by a sequence assembly artifact, and the final indel (Δ63bp) in the spa-sarS intergenic region is common to only a sub-lineage of 8325-4 strains including SH1000. This deletion was found to significantly decrease (75%) steady state sarS but not spa transcript levels in post-exponential phase. The sub-lineage 8325-4 was also found to harbor 4 additional SNPs. We also found large sequence variation between 8325, 8325-4 and RN4220 in a cluster of repetitive hypothetical proteins (SA0282 homologs) near the Ess secretion cluster. The overall 8325-4 SNP set results in 17 alterations within coding sequences. Remarkably, we discovered that all tested strains of the 8325-4 lineage lack phenol soluble modulin α3 (PSMα3), a virulence determinant implicated in neutrophil chemotaxis, biofilm architecture and surface spreading. Collectively, our results clarify and define the 8325-4 pedigree and reveal clear evidence that mutations existing throughout all branches of this lineage, including the widely used RN6390 and SH1000 strains, could conceivably impact virulence regulation.
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44
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Regulation of host hemoglobin binding by the Staphylococcus aureus Clp proteolytic system. J Bacteriol 2013; 195:5041-50. [PMID: 23995637 DOI: 10.1128/jb.00505-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Protein turnover is a key process for bacterial survival mediated by intracellular proteases. Proteolytic degradation reduces the levels of unfolded and misfolded peptides that accumulate in the cell during stress conditions. Three intracellular proteases, ClpP, HslV, and FtsH, have been identified in the Gram-positive bacterium Staphylococcus aureus, a pathogen responsible for significant morbidity and mortality worldwide. Consistent with their crucial role in protein turnover, ClpP, HslV, and FtsH affect a number of cellular processes, including metabolism, stress responses, and virulence. The ClpP protease is believed to be the principal degradation machinery in S. aureus. This study sought to identify the effect of the Clp protease on the iron-regulated surface determinant (Isd) system, which extracts heme-iron from host hemoglobin during infection and is critical to S. aureus pathogenesis. Inactivation of components of the Clp protease alters abundance of several Isd proteins, including the hemoglobin receptor IsdB. Furthermore, the observed changes in IsdB abundance are the result of transcriptional regulation, since transcription of isdB is decreased by clpP or clpX inactivation. In contrast, inactivation of clpC enhances isdB transcription and protein abundance. Loss of clpP or clpX impairs host hemoglobin binding and utilization and results in severe virulence defects in a systemic mouse model of infection. These findings suggest that the Clp proteolytic system is important for regulating nutrient iron acquisition in S. aureus. The Clp protease and Isd complex are widely conserved in bacteria; therefore, these data reveal a novel Clp-dependent regulation pathway that may be present in other bacterial pathogens.
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45
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Trapping and identification of cellular substrates of the Staphylococcus aureus ClpC chaperone. J Bacteriol 2013; 195:4506-16. [PMID: 23913326 DOI: 10.1128/jb.00758-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
ClpC is an ATP-dependent Hsp100/Clp chaperone involved in protein quality control in low-GC Gram-positive bacteria. Previously, we found that ClpC affected the expression of a large number of genes, including capsule genes in Staphylococcus aureus. Here we constructed a His-tagged ClpC variant (ClpC(trap)) with mutations within the Walker B motifs to identify the direct substrates of ClpC by copurification with ClpC(trap) followed by gel electrophoresis combined with liquid chromatography-tandem mass spectrometry proteomics. We identified a total of 103 proteins that are potential substrates of ClpC in strain Newman. The direct protein-protein interaction of ClpC with a subset of the captured proteins was verified in a bacterial two-hybrid system. The captured proteins could be grouped into various functional categories, but most were related to proteins involved in the stress response. Several known ClpC substrates were captured, including ClpP, TrfA/MecA, ClpB, DnaK, DnaJ, GroL, RecA, and CodY, supporting the validity of our approach. Our results also revealed many new ClpC substrates, including AgrA, CcpA, RsbW, MurG, FtsA, SrtA, Rex, Atl, ClfA, and SbcC. Analysis of capsule production showed that three of the captured proteins, which were not previously known to be transcriptional regulators, did affect capsule production.
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46
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ClpP deletion causes attenuation of Salmonella Typhimurium virulence through mis-regulation of RpoS and indirect control of CsrA and the SPI genes. Microbiology (Reading) 2013; 159:1497-1509. [DOI: 10.1099/mic.0.065797-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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47
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Structural and functional insights into caseinolytic proteases reveal an unprecedented regulation principle of their catalytic triad. Proc Natl Acad Sci U S A 2013; 110:11302-7. [PMID: 23798410 DOI: 10.1073/pnas.1219125110] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Caseinolytic proteases (ClpPs) are large oligomeric protein complexes that contribute to cell homeostasis as well as virulence regulation in bacteria. Although most organisms possess a single ClpP protein, some organisms encode two or more ClpP isoforms. Here, we elucidated the crystal structures of ClpP1 and ClpP2 from pathogenic Listeria monocytogenes and observe an unprecedented regulation principle by the catalytic triad. Whereas L. monocytogenes (Lm)ClpP2 is both structurally and functionally similar to previously studied tetradecameric ClpP proteins from Escherichia coli and Staphylococcus aureus, heptameric LmClpP1 features an asparagine in its catalytic triad. Mutation of this asparagine to aspartate increased the reactivity of the active site and led to the assembly of a tetradecameric complex. We analyzed the heterooligomeric complex of LmClpP1 and LmClpP2 via coexpression and subsequent labeling studies with natural product-derived probes. Notably, the LmClpP1 peptidase activity is stimulated 75-fold in the complex providing insights into heterooligomerization as a regulatory mechanism. Collectively, our data point toward different preferences for substrates and inhibitors of the two ClpP enzymes and highlight their structural and functional characteristics.
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48
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Gersch M, Gut F, Korotkov VS, Lehmann J, Böttcher T, Rusch M, Hedberg C, Waldmann H, Klebe G, Sieber SA. The mechanism of caseinolytic protease (ClpP) inhibition. Angew Chem Int Ed Engl 2013; 52:3009-14. [PMID: 23361916 DOI: 10.1002/anie.201204690] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 10/29/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Malte Gersch
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Institute of Advanced Studies, Lichtenbergstrasse 4, 85747 Garching, Germany
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49
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Gersch M, Gut F, Korotkov VS, Lehmann J, Böttcher T, Rusch M, Hedberg C, Waldmann H, Klebe G, Sieber SA. Der Inhibitionsmechanismus der caseinolytischen Protease (ClpP). Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201204690] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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50
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Feng J, Michalik S, Varming AN, Andersen JH, Albrecht D, Jelsbak L, Krieger S, Ohlsen K, Hecker M, Gerth U, Ingmer H, Frees D. Trapping and Proteomic Identification of Cellular Substrates of the ClpP Protease in Staphylococcus aureus. J Proteome Res 2013; 12:547-58. [DOI: 10.1021/pr300394r] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jingyuan Feng
- Faculty of
Life Sciences, Department
of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - Stephan Michalik
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, 17487 Greifswald,
Germany
| | - Anders N. Varming
- Faculty of
Life Sciences, Department
of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - Julie H. Andersen
- Faculty of
Life Sciences, Department
of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - Dirk Albrecht
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, 17487 Greifswald,
Germany
| | - Lotte Jelsbak
- Faculty of
Life Sciences, Department
of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - Stefanie Krieger
- Institute for Molecular
Infectionsbiology, Würzburg University, Würzburg, Germany
| | - Knut Ohlsen
- Institute for Molecular
Infectionsbiology, Würzburg University, Würzburg, Germany
| | - Michael Hecker
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, 17487 Greifswald,
Germany
| | - Ulf Gerth
- Institut für Mikrobiologie, Ernst-Moritz-Arndt-Universität, 17487 Greifswald,
Germany
| | - Hanne Ingmer
- Faculty of
Life Sciences, Department
of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - Dorte Frees
- Faculty of
Life Sciences, Department
of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
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