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Grunfeld N, Levine E, Libby E. Experimental measurement and computational prediction of bacterial Hanks-type Ser/Thr signaling system regulatory targets. Mol Microbiol 2024; 122:152-164. [PMID: 38167835 PMCID: PMC11219531 DOI: 10.1111/mmi.15220] [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: 10/19/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024]
Abstract
Bacteria possess diverse classes of signaling systems that they use to sense and respond to their environments and execute properly timed developmental transitions. One widespread and evolutionarily ancient class of signaling systems are the Hanks-type Ser/Thr kinases, also sometimes termed "eukaryotic-like" due to their homology with eukaryotic kinases. In diverse bacterial species, these signaling systems function as critical regulators of general cellular processes such as metabolism, growth and division, developmental transitions such as sporulation, biofilm formation, and virulence, as well as antibiotic tolerance. This multifaceted regulation is due to the ability of a single Hanks-type Ser/Thr kinase to post-translationally modify the activity of multiple proteins, resulting in the coordinated regulation of diverse cellular pathways. However, in part due to their deep integration with cellular physiology, to date, we have a relatively limited understanding of the timing, regulatory hierarchy, the complete list of targets of a given kinase, as well as the potential regulatory overlap between the often multiple kinases present in a single organism. In this review, we discuss experimental methods and curated datasets aimed at elucidating the targets of these signaling pathways and approaches for using these datasets to develop computational models for quantitative predictions of target motifs. We emphasize novel approaches and opportunities for collecting data suitable for the creation of new predictive computational models applicable to diverse species.
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Affiliation(s)
- Noam Grunfeld
- Department of Bioengineering, Northeastern University, Boston MA USA
| | - Erel Levine
- Department of Bioengineering, Northeastern University, Boston MA USA
- Department of Chemical Engineering, Northeastern University, Boston MA USA
| | - Elizabeth Libby
- Department of Bioengineering, Northeastern University, Boston MA USA
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Hoffmann A, Steffens U, Maček B, Franz-Wachtel M, Nieselt K, Harbig TA, Scherlach K, Hertweck C, Sahl HG, Bierbaum G. The unusual mode of action of the polyketide glycoside antibiotic cervimycin C. mSphere 2024; 9:e0076423. [PMID: 38722162 PMCID: PMC11237698 DOI: 10.1128/msphere.00764-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/28/2024] [Indexed: 05/30/2024] Open
Abstract
Cervimycins A-D are bis-glycosylated polyketide antibiotics produced by Streptomyces tendae HKI 0179 with bactericidal activity against Gram-positive bacteria. In this study, cervimycin C (CmC) treatment caused a spaghetti-like phenotype in Bacillus subtilis 168, with elongated curved cells, which stayed joined after cell division, and exhibited a chromosome segregation defect, resulting in ghost cells without DNA. Electron microscopy of CmC-treated Staphylococcus aureus (3 × MIC) revealed swollen cells, misshapen septa, cell wall thickening, and a rough cell wall surface. Incorporation tests in B. subtilis indicated an effect on DNA biosynthesis at high cervimycin concentrations. Indeed, artificial downregulation of the DNA gyrase subunit B gene (gyrB) increased the activity of cervimycin in agar diffusion tests, and, in high concentrations (starting at 62.5 × MIC), the antibiotic inhibited S. aureus DNA gyrase supercoiling activity in vitro. To obtain a more global view on the mode of action of CmC, transcriptomics and proteomics of cervimycin treated versus untreated S. aureus cells were performed. Interestingly, 3 × MIC of cervimycin did not induce characteristic responses, which would indicate disturbance of the DNA gyrase activity in vivo. Instead, cervimycin induced the expression of the CtsR/HrcA heat shock operon and the expression of autolysins, exhibiting similarity to the ribosome-targeting antibiotic gentamicin. In summary, we identified the DNA gyrase as a target, but at low concentrations, electron microscopy and omics data revealed a more complex mode of action of cervimycin, which comprised induction of the heat shock response, indicating protein stress in the cell.IMPORTANCEAntibiotic resistance of Gram-positive bacteria is an emerging problem in modern medicine, and new antibiotics with novel modes of action are urgently needed. Secondary metabolites from Streptomyces species are an important source of antibiotics, like the cervimycin complex produced by Streptomyces tendae HKI 0179. The phenotypic response of Bacillus subtilis and Staphylococcus aureus toward cervimycin C indicated a chromosome segregation and septum formation defect. This effect was at first attributed to an interaction between cervimycin C and the DNA gyrase. However, omics data of cervimycin treated versus untreated S. aureus cells indicated a different mode of action, because the stress response did not include the SOS response but resembled the response toward antibiotics that induce mistranslation or premature chain termination and cause protein stress. In summary, these results point toward a possibly novel mechanism that generates protein stress in the cells and subsequently leads to defects in cell and chromosome segregation.
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Affiliation(s)
- Alina Hoffmann
- University Hospital Bonn, Institute of Medical Microbiology, Immunology and Parasitology, Bonn, Germany
| | - Ursula Steffens
- University Hospital Bonn, Institute of Medical Microbiology, Immunology and Parasitology, Bonn, Germany
| | - Boris Maček
- University of Tübingen, Proteome Center Tübingen, Tübingen, Germany
| | | | - Kay Nieselt
- University of Tübingen, Interfaculty Institute for Bioinformatics and Medical Informatics, Tübingen, Germany
| | - Theresa Anisja Harbig
- University of Tübingen, Interfaculty Institute for Bioinformatics and Medical Informatics, Tübingen, Germany
| | - Kirstin Scherlach
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
- Friedrich Schiller University Jena, Institute of Microbiology, Faculty of Biological Sciences, Jena, Germany
| | - Hans-Georg Sahl
- University of Bonn, Institute for Pharmaceutical Microbiology, Bonn, Germany
| | - Gabriele Bierbaum
- University Hospital Bonn, Institute of Medical Microbiology, Immunology and Parasitology, Bonn, Germany
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Ahator SD, Hegstad K, Lentz CS, Johannessen M. Deciphering Staphylococcus aureus-host dynamics using dual activity-based protein profiling of ATP-interacting proteins. mSystems 2024; 9:e0017924. [PMID: 38656122 PMCID: PMC11097646 DOI: 10.1128/msystems.00179-24] [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: 02/06/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
The utilization of ATP within cells plays a fundamental role in cellular processes that are essential for the regulation of host-pathogen dynamics and the subsequent immune response. This study focuses on ATP-binding proteins to dissect the complex interplay between Staphylococcus aureus and human cells, particularly macrophages (THP-1) and keratinocytes (HaCaT), during an intracellular infection. A snapshot of the various protein activity and function is provided using a desthiobiotin-ATP probe, which targets ATP-interacting proteins. In S. aureus, we observe enrichment in pathways required for nutrient acquisition, biosynthesis and metabolism of amino acids, and energy metabolism when located inside human cells. Additionally, the direct profiling of the protein activity revealed specific adaptations of S. aureus to the keratinocytes and macrophages. Mapping the differentially activated proteins to biochemical pathways in the human cells with intracellular bacteria revealed cell-type-specific adaptations to bacterial challenges where THP-1 cells prioritized immune defenses, autophagic cell death, and inflammation. In contrast, HaCaT cells emphasized barrier integrity and immune activation. We also observe bacterial modulation of host processes and metabolic shifts. These findings offer valuable insights into the dynamics of S. aureus-host cell interactions, shedding light on modulating host immune responses to S. aureus, which could involve developing immunomodulatory therapies. IMPORTANCE This study uses a chemoproteomic approach to target active ATP-interacting proteins and examines the dynamic proteomic interactions between Staphylococcus aureus and human cell lines THP-1 and HaCaT. It uncovers the distinct responses of macrophages and keratinocytes during bacterial infection. S. aureus demonstrated a tailored response to the intracellular environment of each cell type and adaptation during exposure to professional and non-professional phagocytes. It also highlights strategies employed by S. aureus to persist within host cells. This study offers significant insights into the human cell response to S. aureus infection, illuminating the complex proteomic shifts that underlie the defense mechanisms of macrophages and keratinocytes. Notably, the study underscores the nuanced interplay between the host's metabolic reprogramming and immune strategy, suggesting potential therapeutic targets for enhancing host defense and inhibiting bacterial survival. The findings enhance our understanding of host-pathogen interactions and can inform the development of targeted therapies against S. aureus infections.
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Affiliation(s)
- Stephen Dela Ahator
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
| | - Kristin Hegstad
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Christian S. Lentz
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
| | - Mona Johannessen
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
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Viering B, Balogh H, Cox CF, Kirpekar OK, Akers AL, Federico VA, Valenzano GZ, Stempel R, Pickett HL, Lundin PM, Blackledge MS, Miller HB. Loratadine Combats Methicillin-Resistant Staphylococcus aureus by Modulating Virulence, Antibiotic Resistance, and Biofilm Genes. ACS Infect Dis 2024; 10:232-250. [PMID: 38153409 PMCID: PMC10788911 DOI: 10.1021/acsinfecdis.3c00616] [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: 11/13/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 12/29/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has evolved to become resistant to multiple classes of antibiotics. New antibiotics are costly to develop and deploy, and they have a limited effective lifespan. Antibiotic adjuvants are molecules that potentiate existing antibiotics through nontoxic mechanisms. We previously reported that loratadine, the active ingredient in Claritin, potentiates multiple cell-wall active antibiotics in vitro and disrupts biofilm formation through a hypothesized inhibition of the master regulatory kinase Stk1. Loratadine and oxacillin combined repressed the expression of key antibiotic resistance genes in the bla and mec operons. We hypothesized that additional genes involved in antibiotic resistance, biofilm formation, and other cellular pathways would be modulated when looking transcriptome-wide. To test this, we used RNA-seq to quantify transcript levels and found significant effects in gene expression, including genes controlling virulence, antibiotic resistance, metabolism, transcription (core RNA polymerase subunits and sigma factors), and translation (a plethora of genes encoding ribosomal proteins and elongation factor Tu). We further demonstrated the impacts of these transcriptional effects by investigating loratadine treatment on intracellular ATP levels, persister formation, and biofilm formation and morphology. Loratadine minimized biofilm formation in vitro and enhanced the survival of infected Caenorhabditis elegans. These pleiotropic effects and their demonstrated outcomes on MRSA virulence and survival phenotypes position loratadine as an attractive anti-infective against MRSA.
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Affiliation(s)
- Brianna
L. Viering
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Halie Balogh
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Chloe F. Cox
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Owee K. Kirpekar
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - A. Luke Akers
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Victoria A. Federico
- Department
of Biology, High Point University, High Point, North Carolina 27268, United States
| | - Gabriel Z. Valenzano
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Robin Stempel
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Hannah L. Pickett
- Department
of Biology, High Point University, High Point, North Carolina 27268, United States
| | - Pamela M. Lundin
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Meghan S. Blackledge
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Heather B. Miller
- Department
of Chemistry, High Point University, High Point, North Carolina 27268, United States
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Hou Z, Liu L, Wei J, Xu B. Progress in the Prevalence, Classification and Drug Resistance Mechanisms of Methicillin-Resistant Staphylococcus aureus. Infect Drug Resist 2023; 16:3271-3292. [PMID: 37255882 PMCID: PMC10226514 DOI: 10.2147/idr.s412308] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/12/2023] [Indexed: 06/01/2023] Open
Abstract
Staphylococcus aureus is a common human pathogen with a variety of virulence factors, which can cause multiple infectious diseases. In recent decades, due to the constant evolution and the abuse of antibiotics, Staphylococcus aureus was becoming more resistant, the infection rate of MRSA remained high, and clinical treatment of MRSA became more difficult. The genetic diversity of MRSA was mainly represented by the continuous emergence of epidemic strains, resulting in the constant changes of epidemic clones. Different classes of MRSA resulted in different epidemics and resistance characteristics, which could affect the clinical symptoms and treatments. MRSA had also spread from traditional hospitals to community and livestock environments, and the new clones established a relationship between animals and humans, promoting further evolution of MRSA. Since the resistance mechanism of MRSA is very complex, it is important to clarify these resistance mechanisms at the molecular level for the treatment of infectious diseases. We firstly described the diversity of SCCmec elements, and discussed the types of SCCmec, its drug resistance mechanisms and expression regulations. Then, we described how the vanA operon makes Staphylococcus aureus resistant to vancomycin and its expression regulation. Finally, a brief introduction was given to the drug resistance mechanisms of biofilms and efflux pump systems. Analyzing the resistance mechanism of MRSA can help study new anti-infective drugs and alleviate the evolution of MRSA. At the end of the review, we summarized the treatment strategies for MRSA infection, including antibiotics, anti-biofilm agents and efflux pump inhibitors. To sum up, here we reviewed the epidemic characteristics of Staphylococcus aureus, summarized its classifications, drug resistance mechanisms of MRSA (SCCmec element, vanA operon, biofilm and active efflux pump system) and novel therapy strategies, so as to provide a theoretical basis for the treatment of MRSA infection.
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Affiliation(s)
- Zhuru Hou
- Department of Basic Medicine, Fenyang College of Shanxi Medical University, Fenyang, People’s Republic of China
- Key Laboratory of Lvliang for Clinical Molecular Diagnostics, Fenyang, People’s Republic of China
| | - Ling Liu
- Key Laboratory of Lvliang for Clinical Molecular Diagnostics, Fenyang, People’s Republic of China
- Department of Medical Laboratory Science, Fenyang College of Shanxi Medical University, Fenyang, People’s Republic of China
- Department of Clinical Laboratory, Fenyang Hospital of Shanxi Province, Fenyang, People’s Republic of China
| | - Jianhong Wei
- Department of Basic Medicine, Fenyang College of Shanxi Medical University, Fenyang, People’s Republic of China
| | - Benjin Xu
- Key Laboratory of Lvliang for Clinical Molecular Diagnostics, Fenyang, People’s Republic of China
- Department of Medical Laboratory Science, Fenyang College of Shanxi Medical University, Fenyang, People’s Republic of China
- Department of Clinical Laboratory, Fenyang Hospital of Shanxi Province, Fenyang, People’s Republic of China
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