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O'Boyle B, Yeung W, Lu JD, Katiyar S, Yaron-Barir TM, Johnson JL, Cantley LC, Kannan N. An atlas of bacterial serine-threonine kinases reveals functional diversity and key distinctions from eukaryotic kinases. Sci Signal 2025; 18:eadt8686. [PMID: 40327749 DOI: 10.1126/scisignal.adt8686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Accepted: 04/11/2025] [Indexed: 05/08/2025]
Abstract
Bacterial serine-threonine kinases (STKs) regulate diverse cellular processes associated with cell growth, virulence, and pathogenicity and are evolutionarily related to the druggable eukaryotic STKs. A deeper understanding of how bacterial STKs differ from their eukaryotic counterparts and how they have evolved to regulate diverse bacterial signaling functions is crucial for advancing the discovery and development of new antibiotic therapies. Here, we classified more than 300,000 bacterial STK sequences from the NCBI RefSeq nonredundant and UniProt protein databases into 35 canonical and seven pseudokinase families on the basis of the patterns of evolutionary constraints in the conserved catalytic domain and flanking regulatory domains. Through statistical comparisons, we identified features distinguishing bacterial STKs from eukaryotic STKs, including an arginine residue in a regulatory helix (C helix) that dynamically couples the ATP- and substrate-binding lobes of the kinase domain. Biochemical and peptide library screens demonstrated that evolutionarily constrained residues contributed to substrate specificity and kinase activation in the Mycobacterium tuberculosis kinase PknB. Together, these findings open previously unidentified avenues for investigating bacterial STK functions in cellular signaling and for developing selective bacterial STK inhibitors.
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Affiliation(s)
- Brady O'Boyle
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Jason D Lu
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Samiksha Katiyar
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Tomer M Yaron-Barir
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Natarajan Kannan
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
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Gao Y, Li X, Yang Y, Wang H, Niu X. CMCS-PVA@CA hydrogel dressing: A promoter of wound healing with MRSA virulence attenuation function. Int J Biol Macromol 2025; 295:139614. [PMID: 39793835 DOI: 10.1016/j.ijbiomac.2025.139614] [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: 08/17/2024] [Revised: 12/07/2024] [Accepted: 01/06/2025] [Indexed: 01/13/2025]
Abstract
Traditional wound dressings, primarily centered on antimicrobial or bactericidal strategies, have inadvertently contributed to the rise of drug-resistant bacterial colonies at wound sites, thus prolonging the healing process. In this study, we developed an innovative hydrogel dressing, CMCS-PVA@CA, incorporating carboxymethyl chitosan (CMCS), polyvinyl alcohol (PVA), and cichoric acid (CA), specifically designed to treat skin wounds infected with methicillin-resistant Staphylococcus aureus (MRSA). Computational biology analyses reveal that CA exerts substantial anti-virulence activity by targeting serine/threonine phosphatase (Stp1), achieving an IC50 of 3.912 μM, thereby mitigating MRSA pathogenicity. Notably, CA lacks intrinsic antibacterial properties, minimizing the risk of fostering drug resistance. Furthermore, CMCS-PVA@CA demonstrates effective wound healing acceleration and meets clinical application standards, with its robust mechanical properties enhancing patient comfort. In essence, this study presents CMCS-PVA@CA as a promising hydrogel dressing offering a viable solution for treating drug-resistant bacterial infections in skin wounds.
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Affiliation(s)
- Yawen Gao
- College of Food Science and Engineering, Jilin University, Changchun 130062, PR China; School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, PR China
| | - Xuening Li
- College of Food Science and Engineering, Jilin University, Changchun 130062, PR China
| | - Yanan Yang
- College of Food Science and Engineering, Jilin University, Changchun 130062, PR China; Faculty of Food Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou 215008, PR China
| | - Hongsu Wang
- College of Food Science and Engineering, Jilin University, Changchun 130062, PR China
| | - Xiaodi Niu
- College of Food Science and Engineering, Jilin University, Changchun 130062, PR China.
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Zorina AA, Los DA, Klychnikov OI. Serine-Threonine Protein Kinases of Cyanobacteria. BIOCHEMISTRY. BIOKHIMIIA 2025; 90:S287-S311. [PMID: 40164163 DOI: 10.1134/s0006297924604507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 09/18/2024] [Accepted: 09/25/2024] [Indexed: 04/02/2025]
Abstract
Protein phosphorylation is a pivotal mechanism for signal transduction, regulation of biochemical processes essential for reproduction, growth, and adaptation of organisms to changing conditions. Bacteria, which emerged more than 3.5 billion years ago, faced the need to adapt to a variety of ecological niches from the very beginning of their existence. It is not surprising that they developed a wide range of different types of kinases and target amino acid residues for phosphorylation. To date, many examples of phosphorylation of serine, threonine, tyrosine, histidine, arginine, lysine, aspartate, and cysteine have been discovered. Bacterial histidine kinases as part of two-component systems have been studied in most detail. More recently eukaryotic type serine-threonine and tyrosine kinases based on the conserved catalytic domain have been described in the genomes of many bacteria. The term "eukaryotic" is misleading, since evolutionary origin of these enzymes goes back to the last common universal ancestor - LUCA. Bioinformatics, molecular genetics, omics, and biochemical strategies combined provide new tools for researchers to establish relationship between the kinase abundance/activity and proteome changes, including studying of the kinase signaling network (kinome) within the cell. This manuscript presents several approaches to investigation of the serine-threonine protein kinases of cyanobacteria, as well as their combination, which allow to suggest new hypotheses and strategies for researchers.
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Affiliation(s)
- Anna A Zorina
- Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia.
| | - Dmitry A Los
- Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - Oleg I Klychnikov
- Department of Biochemistry, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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Gao Y, Wang H, Niu X. A hydrogen-bonded curdlan-chitosan/polyvinyl alcohol edible dual functional hydrogel bandage against MRSA promotes wound healing. Int J Biol Macromol 2024; 259:129351. [PMID: 38216019 DOI: 10.1016/j.ijbiomac.2024.129351] [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: 09/06/2023] [Revised: 12/23/2023] [Accepted: 01/07/2024] [Indexed: 01/14/2024]
Abstract
The most prevalent complication arising from skin injuries is bacterial infection, where pathogenic bacteria proliferate significantly at the wound site, leading to subsequent complications like septic shock and sepsis. Although antibiotics presently effectively manage wound infections caused by common bacteria, the escalating prevalence of antibiotic-resistant strains necessitates urgent novel approaches for addressing such infections. Here, we present CS9P1-RA, a dual functional hydrogel dressing, based on polyvinyl alcohol (PVA) matrix crosslinked through hydrogen bonding. CS9P1-RA combines chitosan (CS), a food-derived antibacterial agent, with the natural compound rosmarinic acid (RA) to specifically target skin injuries caused by MRSA. Computational and molecular biology assays illustrate RA's ability to selectively inhibit the activity of Staphylococcus aureus (S. aureus) serine/threonine phosphatase (Stp1), reducing the S. aureus pathogenicity. CS9P1-RA showcases exceptional antibacterial efficacy (MIC = 1 mg/mL) and demonstrates potency in reducing virulence (IC50 = 7.424 μM on Stp1). Notably, it effectively curbs bacterial growth and accelerates wound healing in the mice model, thereby fulfilling the practical requirements for clinical applications. Moreover, the mechanical properties of CS9P1-RA ensure user comfort during treatment. This work introduces a fresh design paradigm for dressing materials, offering a promising solution for treating skin injuries inflicted by antibiotic-resistant bacterial infections.
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Affiliation(s)
- Yawen Gao
- College of Food Science and Engineering, Jilin University, Changchun 130062, PR China
| | - Hongsu Wang
- College of Food Science and Engineering, Jilin University, Changchun 130062, PR China
| | - Xiaodi Niu
- College of Food Science and Engineering, Jilin University, Changchun 130062, PR China.
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Huemer M, Mairpady Shambat S, Hertegonne S, Bergada-Pijuan J, Chang CC, Pereira S, Gómez-Mejia A, Van Gestel L, Bär J, Vulin C, Pfammatter S, Stinear TP, Monk IR, Dworkin J, Zinkernagel AS. Serine-threonine phosphoregulation by PknB and Stp contributes to quiescence and antibiotic tolerance in Staphylococcus aureus. Sci Signal 2023; 16:eabj8194. [PMID: 36595572 DOI: 10.1126/scisignal.abj8194] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 12/06/2022] [Indexed: 01/05/2023]
Abstract
Staphylococcus aureus can cause infections that are often chronic and difficult to treat, even when the bacteria are not antibiotic resistant because most antibiotics act only on metabolically active cells. Subpopulations of persister cells are metabolically quiescent, a state associated with delayed growth, reduced protein synthesis, and increased tolerance to antibiotics. Serine-threonine kinases and phosphatases similar to those found in eukaryotes can fine-tune essential bacterial cellular processes, such as metabolism and stress signaling. We found that acid stress-mimicking conditions that S. aureus experiences in host tissues delayed growth, globally altered the serine and threonine phosphoproteome, and increased threonine phosphorylation of the activation loop of the serine-threonine protein kinase B (PknB). The deletion of stp, which encodes the only annotated functional serine-threonine phosphatase in S. aureus, increased the growth delay and phenotypic heterogeneity under different stress challenges, including growth in acidic conditions, the intracellular milieu of human cells, and abscesses in mice. This growth delay was associated with reduced protein translation and intracellular ATP concentrations and increased antibiotic tolerance. Using phosphopeptide enrichment and mass spectrometry-based proteomics, we identified targets of serine-threonine phosphorylation that may regulate bacterial growth and metabolism. Together, our findings highlight the importance of phosphoregulation in mediating bacterial quiescence and antibiotic tolerance and suggest that targeting PknB or Stp might offer a future therapeutic strategy to prevent persister formation during S. aureus infections.
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Affiliation(s)
- Markus Huemer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sanne Hertegonne
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Judith Bergada-Pijuan
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Chun-Chi Chang
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sandro Pereira
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Alejandro Gómez-Mejia
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Lies Van Gestel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Julian Bär
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Clément Vulin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sibylle Pfammatter
- Functional Genomics Center Zurich, ETH/University of Zurich, Zurich, Switzerland
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Ian R Monk
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jonathan Dworkin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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Identification of serine/threonine kinases that regulate metabolism and sporulation in Clostridium beijerinckii. Appl Microbiol Biotechnol 2022; 106:7563-7575. [DOI: 10.1007/s00253-022-12234-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 09/17/2022] [Accepted: 10/07/2022] [Indexed: 11/02/2022]
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PeSTK db a comprehensive data repository of Probiotic Serine Threonine kinases. Sci Data 2022; 9:282. [PMID: 35676297 PMCID: PMC9178022 DOI: 10.1038/s41597-022-01379-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
The signal transduction pathway of prokaryotes involves a peptidoglycan synthesis cluster (PG) to sense external stimuli. One of the major components of the PG synthesis cluster is protein kinases (pknA - G). The sequence data of probiotic eSTKs (Eukaryotic like Serine, Threonine kinases) are obscure, scarce and essentially required to understand the role of probiotic microbes in combating infectious diseases. The most essential need to understand and develop certain therapeutic drugs against pathogens is the eSTK sequence data. Hence, we developed a comprehensive user-friendly data repository of probiotic eSTK’s (PeSTK), which holds 830 STK sequences. Therefore, the data resource of PeSTK developed is unique, an open-access very summative containing various probiotic eSTK’s in a single locality. The sequence datasets of the eSTK developed with easy-to-operate browsing as well as searching. Therefore, eSTK data resources should be useful for sequence-based studies and drug development. The sequence datasets are available at Figshare Digital Object Identifier/DOI of the sequences is 10.6084/m9.figshare.146606. Measurement(s) | Serine threonine protein sequences of probiotic microbes | Technology Type(s) | Softwares uploading and downloading of sequences from various public sources | Factor Type(s) | Serine threonine kinases of Probiotic microbes | Sample Characteristic - Organism | Bifidobacteria spp • Lactocobacillus spp • Enterococcus spp • Streptococcus spp • Leuconostoc spp • Pediococcus spp | Sample Characteristic - Location | India |
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Ren L, Shen D, Liu C, Ding Y. Protein Tyrosine and Serine/Threonine Phosphorylation in Oral Bacterial Dysbiosis and Bacteria-Host Interaction. Front Cell Infect Microbiol 2022; 11:814659. [PMID: 35087767 PMCID: PMC8787120 DOI: 10.3389/fcimb.2021.814659] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/13/2021] [Indexed: 02/05/2023] Open
Abstract
The human oral cavity harbors approximately 1,000 microbial species, and dysbiosis of the microflora and imbalanced microbiota-host interactions drive many oral diseases, such as dental caries and periodontal disease. Oral microbiota homeostasis is critical for systemic health. Over the last two decades, bacterial protein phosphorylation systems have been extensively studied, providing mounting evidence of the pivotal role of tyrosine and serine/threonine phosphorylation in oral bacterial dysbiosis and bacteria-host interactions. Ongoing investigations aim to discover novel kinases and phosphatases and to understand the mechanism by which these phosphorylation events regulate the pathogenicity of oral bacteria. Here, we summarize the structures of bacterial tyrosine and serine/threonine kinases and phosphatases and discuss the roles of tyrosine and serine/threonine phosphorylation systems in Porphyromonas gingivalis and Streptococcus mutans, emphasizing their involvement in bacterial metabolism and virulence, community development, and bacteria-host interactions.
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Affiliation(s)
- Liang Ren
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Daonan Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chengcheng Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yi Ding
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Ulrych A, Fabrik I, Kupčík R, Vajrychová M, Doubravová L, Branny P. Cell Wall Stress Stimulates the Activity of the Protein Kinase StkP of Streptococcus pneumoniae, Leading to Multiple Phosphorylation. J Mol Biol 2021; 433:167319. [PMID: 34688688 DOI: 10.1016/j.jmb.2021.167319] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/06/2021] [Accepted: 10/15/2021] [Indexed: 12/28/2022]
Abstract
Streptococcus pneumoniae is an opportunistic human pathogen that encodes a single eukaryotic-type Ser/Thr protein kinase StkP and its functional counterpart, the protein phosphatase PhpP. These signaling enzymes play critical roles in coordinating cell division and growth in pneumococci. In this study, we determined the proteome and phosphoproteome profiles of relevant mutants. Comparison of those with the wild-type provided a representative dataset of novel phosphoacceptor sites and StkP-dependent substrates. StkP phosphorylates key proteins involved in cell division and cell wall biosynthesis in both the unencapsulated laboratory strain Rx1 and the encapsulated virulent strain D39. Furthermore, we show that StkP plays an important role in triggering an adaptive response induced by a cell wall-directed antibiotic. Phosphorylation of the sensor histidine kinase WalK and downregulation of proteins of the WalRK core regulon suggest crosstalk between StkP and the WalRK two-component system. Analysis of proteomic profiles led to the identification of gene clusters regulated by catabolite control mechanisms, indicating a tight coupling of carbon metabolism and cell wall homeostasis. The imbalance of steady-state protein phosphorylation in the mutants as well as after antibiotic treatment is accompanied by an accumulation of the global Spx regulator, indicating a Spx-mediated envelope stress response. In summary, StkP relays the perceived signal of cell wall status to key cell division and regulatory proteins, controlling the cell cycle and cell wall homeostasis.
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Affiliation(s)
- Aleš Ulrych
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Ivo Fabrik
- Biomedical Research Center, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic.
| | - Rudolf Kupčík
- Biomedical Research Center, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic.
| | - Marie Vajrychová
- Biomedical Research Center, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic.
| | - Linda Doubravová
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Pavel Branny
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
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Yang Y, Wang X, Gao Y, Wang H, Niu X. Insight into the Dual inhibitory Mechanism of verbascoside targeting serine/threonine phosphatase Stp1 against Staphylococcus aureus. Eur J Pharm Sci 2021; 157:105628. [PMID: 33115673 DOI: 10.1016/j.ejps.2020.105628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 12/19/2022]
Abstract
The eukaryotic-like serine/threonine phosphatase (Stp1) is an enzyme-dependent protein phosphatase involved in regulating various virulence factors of Staphylococcus aureus. Owing to its role in S. aureus infections, Stp1 has become a potential target for antibiotic development. Unfortunately, there are very few reports describing Stp1 inhibitors. Using virtual screening, we have identified a potent and effective Stp1 inhibitor, verbascoside (VBS). Interestingly, the kinetics of the enzymatic reaction revealed that this natural inhibitor acts via both competitive and allosteric mechanisms. To explore the mechanism of interaction between VBS and Stp1, standard molecular dynamics (MD) simulations were performed for the Stp1-VBS complex. Consistent with the experimental results, competitive and allosteric binding sites for VBS were identified in Stp1. Met39, Gly41, His42, Arg161, and Asn162 residues were involved in the competitive binding of VBS, while Arg122, Ser136, Asp137, Asn142, and Val145 residues were associated with the allosteric binding of VBS. The contributions of these residues were confirmed by amino acid site-directed mutagenesis and fluorescence quenching experiments. This work demonstrates that VBS is a potent anti-virulence compound against S. aureus infection, laying the foundation for the further development of novel anti-virulence agents.
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Affiliation(s)
- Yanan Yang
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Xiyan Wang
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Yawen Gao
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Hongsu Wang
- College of Food Science and Engineering, Jilin University, Changchun, China.
| | - Xiaodi Niu
- College of Food Science and Engineering, Jilin University, Changchun, China.
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Are antibacterial effects of non-antibiotic drugs random or purposeful because of a common evolutionary origin of bacterial and mammalian targets? Infection 2020; 49:569-589. [PMID: 33325009 PMCID: PMC7737717 DOI: 10.1007/s15010-020-01547-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/28/2020] [Indexed: 01/09/2023]
Abstract
Purpose Advances in structural biology, genetics, bioinformatics, etc. resulted in the availability of an enormous pool of information enabling the analysis of the ancestry of pro- and eukaryotic genes and proteins. Methods This review summarizes findings of structural and/or functional homologies of pro- and eukaryotic enzymes catalysing analogous biological reactions because of their highly conserved active centres so that non-antibiotics interacted with bacterial targets. Results Protease inhibitors such as staurosporine or camostat inhibited bacterial serine/threonine or serine/tyrosine protein kinases, serine/threonine phosphatases, and serine/threonine kinases, to which penicillin-binding-proteins are linked, so that these drugs synergized with β-lactams, reverted aminoglycoside-resistance and attenuated bacterial virulence. Calcium antagonists such as nitrendipine or verapamil blocked not only prokaryotic ion channels but interacted with negatively charged bacterial cell membranes thus disrupting membrane energetics and inducing membrane stress response resulting in inhibition of P-glycoprotein such as bacterial pumps thus improving anti-mycobacterial activities of rifampicin, tetracycline, fluoroquinolones, bedaquilin and imipenem-activity against Acinetobacter spp. Ciclosporine and tacrolimus attenuated bacterial virulence. ACE-inhibitors like captopril interacted with metallo-β-lactamases thus reverting carbapenem-resistance; prokaryotic carbonic anhydrases were inhibited as well resulting in growth impairment. In general, non-antibiotics exerted weak antibacterial activities on their own but synergized with antibiotics, and/or reverted resistance and/or attenuated virulence. Conclusions Data summarized in this review support the theory that prokaryotic proteins represent targets for non-antibiotics because of a common evolutionary origin of bacterial- and mammalian targets resulting in highly conserved active centres of both, pro- and eukaryotic proteins with which the non-antibiotics interact and exert antibacterial actions.
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Kordafshari S, Shil P, Marenda MS, Olaogun OM, Konsak-Ilievski B, Disint J, Noormohammadi AH. Preliminary comparative analysis of the genomes of selected field reisolates of the Mycoplasma synoviae vaccine strain MS-H reveals both stable and unstable mutations after passage in vivo. BMC Genomics 2020; 21:598. [PMID: 32859151 PMCID: PMC7456371 DOI: 10.1186/s12864-020-06995-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023] Open
Abstract
Background Genomic comparison of Mycoplasma synoviae vaccine strain MS-H and the MS-H parental strain 86,079/7NS established a preliminary profile of genes related to attenuation of MS-H. In this study we aimed to identify the stability of mutations found in MS-H after passage in experimental or field chickens, and to evaluate if any reverse mutation may be associated with changes in characteristics of MS-H in vitro or in vivo. Results Whole genome sequence analysis of 5 selected MS-H field reisolates revealed that out of 32 mutations reported previously in MS-H, 28 remained stable, while four found to be reversible to the wild-type. Each isolate possessed mutations in one to three of the genes obg, oppF1 and gap and/or a non-coding region. Examination of the 4 reversible mutations by protein modeling predicted that only two of them (in obg and oppF1 genes) could potentially restore the function of the respective protein to that of the wild-type. Conclusions These results suggest that the majority of the MS-H mutations are stable after passage in vaccinated chickens. Characterisation of stable mutations found in MS-H could be utilised to develop rapid diagnostic techniques for differentiation of vaccine from field strains or ts- MS-H reisolates.
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Affiliation(s)
- Somayeh Kordafshari
- Asia Pacific Centre for Animal Health, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Victoria, 3030, Australia.
| | - Pollob Shil
- Asia Pacific Centre for Animal Health, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Victoria, 3030, Australia
| | - Marc S Marenda
- Asia Pacific Centre for Animal Health, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Victoria, 3030, Australia
| | - Olusola M Olaogun
- Asia Pacific Centre for Animal Health, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Victoria, 3030, Australia
| | - Barbara Konsak-Ilievski
- Asia Pacific Centre for Animal Health, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Victoria, 3030, Australia
| | - Jillian Disint
- Asia Pacific Centre for Animal Health, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Victoria, 3030, Australia
| | - Amir H Noormohammadi
- Asia Pacific Centre for Animal Health, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Victoria, 3030, Australia
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13
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Gao Y, Wang G, Wang X, Yang Y, Niu X. Structure-Activity relationship of MDSA and its derivatives against Staphylococcus aureus Ser/Thr phosphatase Stp1. Comput Biol Chem 2020; 85:107230. [DOI: 10.1016/j.compbiolchem.2020.107230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 02/03/2020] [Accepted: 02/06/2020] [Indexed: 01/23/2023]
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Marie-Joelle Virolle. Antibiotics (Basel) 2020; 9:antibiotics9020083. [PMID: 32069930 PMCID: PMC7168255 DOI: 10.3390/antibiotics9020083] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 12/15/2022] Open
Abstract
Antibiotics are often considered as weapons conferring a competitive advantage to their producers in their ecological niche. However, since these molecules are produced in specific environmental conditions, notably phosphate limitation that triggers a specific metabolic state, they are likely to play important roles in the physiology of the producing bacteria that have been overlooked. Our recent experimental data as well as careful analysis of the scientific literature led us to propose that, in conditions of moderate to severe phosphate limitation—conditions known to generate energetic stress—antibiotics play crucial roles in the regulation of the energetic metabolism of the producing bacteria. A novel classification of antibiotics into types I, II, and III, based on the nature of the targets of these molecules and on their impact on the cellular physiology, is proposed. Type I antibiotics are known to target cellular membranes, inducing energy spilling and cell lysis of a fraction of the population to provide nutrients, and especially phosphate, to the surviving population. Type II antibiotics inhibit respiration through different strategies, to reduce ATP generation in conditions of low phosphate availability. Lastly, Type III antibiotics that are known to inhibit ATP consuming anabolic processes contribute to ATP saving in conditions of phosphate starvation.
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15
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Hu L, Kong W, Yang D, Han Q, Guo L, Shi Y. Threonine Phosphorylation Fine-Tunes the Regulatory Activity of Histone-Like Nucleoid Structuring Protein in Salmonella Transcription. Front Microbiol 2019; 10:1515. [PMID: 31333620 PMCID: PMC6616471 DOI: 10.3389/fmicb.2019.01515] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 06/18/2019] [Indexed: 12/30/2022] Open
Abstract
Histone-like nucleoid structuring protein (H-NS) in enterobacteria plays an important role in facilitating chromosome organization and functions as a crucial transcriptional regulator for global gene regulation. Here, we presented an observation that H-NS of Salmonella enterica serovar Typhimurium could undergo protein phosphorylation at threonine 13 residue (T13). Analysis of the H-NS wild-type protein and its T13E phosphomimetic substitute suggested that T13 phosphorylation lead to alterations of H-NS structure, thus reducing its dimerization to weaken its DNA binding affinity. Proteomic analysis revealed that H-NS phosphorylation exerts regulatory effects on a wide range of genetic loci including the PhoP/PhoQ-regulated genes. In this study, we investigated an effect of T13 phosphorylation of H-NS that rendered transcription upregulation of the PhoP/PhoQ-activated genes. A lower promoter binding of the T13 phosphorylated H-NS protein was correlated with a stronger interaction of the PhoP protein, i.e., a transcription activator and also a competitor of H-NS, to the PhoP/PhoQ-dependent promoters. Unlike depletion of H-NS which dramatically activated the PhoP/PhoQ-dependent transcription even in a PhoP/PhoQ-repressing condition, mimicking of H-NS phosphorylation caused a moderate upregulation. Wild-type H-NS protein produced heterogeneously could rescue the phenotype of T13E mutant and fully restored the PhoP/PhoQ-dependent transcription enhanced by T13 phosphorylation of H-NS to wild-type levels. Therefore, our findings uncover a strategy in S. typhimurium to fine-tune the regulatory activity of H-NS through specific protein phosphorylation and highlight a regulatory mechanism for the PhoP/PhoQ-dependent transcription via this post-translational modification.
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Affiliation(s)
- Lizhi Hu
- The State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China.,School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Wei Kong
- The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Dezhi Yang
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Qiangqiang Han
- The State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lin Guo
- The State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yixin Shi
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,The Biodesign Institute, Arizona State University, Tempe, AZ, United States
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16
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Besbes F, Franz-Oberdorf K, Schwab W. Phosphorylation-dependent ribonuclease activity of Fra a 1 proteins. JOURNAL OF PLANT PHYSIOLOGY 2019; 233:1-11. [PMID: 30572279 DOI: 10.1016/j.jplph.2018.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 12/06/2018] [Accepted: 12/06/2018] [Indexed: 05/24/2023]
Abstract
Abiotic and biotic stress situations cause the upregulation of the transcription of a number of plant defence genes. They code for so-called pathogenesis-related (PR) proteins such as PR proteins of class-10 (PR-10), whose biological functions are still unclear. PR10 proteins are members of the Bet v 1 (major birch pollen allergen) superfamily including related proteins from the cultivated strawberry Fragaria × ananassa (Fra a 1 proteins). Here, we analyzed the expression of 21 Fra a 1 genes in different tissues of the strawberry plant by quantitative real-time PCR. Thirteen members were mainly expressed in roots, three in stems, two in red fruits and leaves, and one in flowers. Five genes (Fra a 1.04-1.08) were selected based on their expression profiles, heterologously expressed in Escherichia coli, and their recombinant proteins functionally characterized. Ribonuclease activity, demonstrated by in-solution and in-gel RNA degradation assays, indicated complete hydrolysis of RNA only by Fra a 1.06. Moreover, phosphorylation assays showed that except for Fra a 1.06, the remaining four recombinant proteins were phosphorylated. Consequently, we investigated whether the phosphorylation status of the proteins affects their ribonuclease activity. Using an in-solution as well as an in-gel RNase activity assay, results demonstrated that the four recombinant proteins, dephosphorylated with phosphatases, exhibited ribonucleolytic activity against total RNA. Thus, the PR10 related proteins characterized in this study harbour a phosphorylation-dependent RNase activity. The results shed new light on the assumed function of PR10 proteins in plant defence.
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Affiliation(s)
- Fatma Besbes
- Biotechnology of Natural Products, Technische Universität München, 85354 Freising, Germany
| | - Katrin Franz-Oberdorf
- Biotechnology of Natural Products, Technische Universität München, 85354 Freising, Germany
| | - Wilfried Schwab
- Biotechnology of Natural Products, Technische Universität München, 85354 Freising, Germany.
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17
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Gómez L, Alvarez F, Betancur D, Oñate A. Brucellosis vaccines based on the open reading frames from genomic island 3 of Brucella abortus. Vaccine 2018; 36:2928-2936. [PMID: 29685597 DOI: 10.1016/j.vaccine.2018.04.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/02/2018] [Accepted: 04/04/2018] [Indexed: 01/18/2023]
Abstract
Brucella abortus is the etiological agent of brucellosis, a zoonotic disease affecting cattle and humans. This disease has been partially controlled in cattle by immunization with live attenuated B. abortus S19 and RB51 strains. However, use of these vaccine strains has been associated with safety issues in animals and humans. New vaccines have since emerged in the prevention of brucellosis, particularly DNA vaccines, which have shown effectiveness and a good safety profile. Their protection efficacy in mice is associated with the induction of Th1 type and cytotoxic T cell mediated immune response against structural antigens and virulence factors expressed during B. abortus infection. Some antigenic candidate for vaccine design against brucellosis (mainly DNA vaccines) have been obtained from genomic island 3 (GI-3) of B. abortus, which encodes several open reading frames (ORFs) involved in the intracellular survival and virulence of this pathogen. The immunogenicity and protection conferred by these DNA vaccines in a murine model is reviewed in this article, suggesting that some of them could be safe and effective vaccine candidates against to prevent B. abortus infection.
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Affiliation(s)
- Leonardo Gómez
- Laboratory of Molecular Immunology, Faculty of Biological Sciences, Department of Microbiology, University of Concepción, Concepción, Chile
| | - Francisco Alvarez
- Laboratory of Molecular Immunology, Faculty of Biological Sciences, Department of Microbiology, University of Concepción, Concepción, Chile
| | - Daniel Betancur
- Laboratory of Molecular Immunology, Faculty of Biological Sciences, Department of Microbiology, University of Concepción, Concepción, Chile
| | - Angel Oñate
- Laboratory of Molecular Immunology, Faculty of Biological Sciences, Department of Microbiology, University of Concepción, Concepción, Chile.
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18
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Bruchhagen C, Jarick M, Mewis C, Hertlein T, Niemann S, Ohlsen K, Peters G, Planz O, Ludwig S, Ehrhardt C. Metabolic conversion of CI-1040 turns a cellular MEK-inhibitor into an antibacterial compound. Sci Rep 2018; 8:9114. [PMID: 29904167 PMCID: PMC6002397 DOI: 10.1038/s41598-018-27445-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/04/2018] [Indexed: 12/17/2022] Open
Abstract
Influenza virus (IV) infections cause severe respiratory illnesses that can be complicated by bacterial super-infections. Previously, we identified the cellular Raf-MEK-ERK cascade as a promising antiviral target. Inhibitors of MEK, such as CI-1040, showed potent antiviral activity. However, it remained unclear if this inhibitor and its active form, ATR-002, might sensitize host cells to either IV or secondary bacterial infections. To address these questions, we studied the anti-pathogen activity of ATR-002 in comparison to CI-1040, particularly, its impact on Staphylococcus aureus (S. aureus), which is a major cause of IV super-infections. We analysed IV and S. aureus titres in vitro during super-infection in the presence and absence of the drugs and characterized the direct impact of ATR-002 on bacterial growth and phenotypic changes. Importantly, neither CI-1040 nor ATR-002 treatment led to increased bacterial titres during super-infection, indicating that the drug does not sensitize cells for bacterial infection. In contrast, we rather observed reduced bacterial titres in presence of ATR-002. Surprisingly, ATR-002 also led to reduced bacterial growth in suspension cultures, reduced stress- and antibiotic tolerance without resistance induction. Our data identified for the first time that a particular MEK-inhibitor metabolite exhibits direct antibacterial activity, which is likely due to interference with the bacterial PknB kinase/Stp phosphatase signalling system.
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Affiliation(s)
- Christin Bruchhagen
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Von-Esmarch-Str. 56, D-48149, Muenster, Germany
| | - Marcel Jarick
- Institute for Molecular Infection Biology (IMIB), University of Wuerzburg, Josef-Schneider-Str. 2/D15, D-97080, Wuerzburg, Germany
| | - Carolin Mewis
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Von-Esmarch-Str. 56, D-48149, Muenster, Germany
| | - Tobias Hertlein
- Institute for Molecular Infection Biology (IMIB), University of Wuerzburg, Josef-Schneider-Str. 2/D15, D-97080, Wuerzburg, Germany
| | - Silke Niemann
- Institute of Medical Microbiology, University Hospital of Muenster, Domagkstr. 10, D-48149, Muenster, Germany
| | - Knut Ohlsen
- Institute for Molecular Infection Biology (IMIB), University of Wuerzburg, Josef-Schneider-Str. 2/D15, D-97080, Wuerzburg, Germany
| | - Georg Peters
- Institute of Medical Microbiology, University Hospital of Muenster, Domagkstr. 10, D-48149, Muenster, Germany
| | - Oliver Planz
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tuebingen, Auf der Morgenstelle 15, D-72076, Tuebingen, Germany
| | - Stephan Ludwig
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Von-Esmarch-Str. 56, D-48149, Muenster, Germany
| | - Christina Ehrhardt
- Institute of Virology Muenster (IVM), Westfaelische Wilhelms-University Muenster, Von-Esmarch-Str. 56, D-48149, Muenster, Germany.
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19
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Global proteome and phosphoproteome dynamics indicate novel mechanisms of vitamin C induced dormancy in Mycobacterium smegmatis. J Proteomics 2018; 180:1-10. [DOI: 10.1016/j.jprot.2017.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 09/20/2017] [Accepted: 10/10/2017] [Indexed: 01/30/2023]
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20
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Misra HS, Maurya GK, Chaudhary R, Misra CS. Interdependence of bacterial cell division and genome segregation and its potential in drug development. Microbiol Res 2018; 208:12-24. [DOI: 10.1016/j.micres.2017.12.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 12/05/2017] [Accepted: 12/31/2017] [Indexed: 11/28/2022]
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21
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Structure function relations in PDZ-domain-containing proteins: Implications for protein networks in cellular signalling. J Biosci 2017. [DOI: 10.1007/s12038-017-9727-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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22
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Righino B, Galisson F, Pirolli D, Vitale S, Réty S, Gouet P, De Rosa MC. Structural model of the full-length Ser/Thr protein kinase StkP from S. pneumoniae and its recognition of peptidoglycan fragments. J Biomol Struct Dyn 2017; 36:3666-3679. [PMID: 29057709 DOI: 10.1080/07391102.2017.1395767] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The unique eukaryotic-like Ser/Thr protein kinases of Streptococcus pneumoniae, StkP, plays a primary role in the cell division process. It is composed of an intracellular kinase domain, a transmembrane helix and four extracellular PASTA subunits. PASTA domains were shown to interact with cell wall fragments but the key questions related to the molecular mechanism governing ligand recognition remain unclear. To address this issue, the full-length structural model of StkP was generated by combining small-angle X-ray scattering data with the results of computer simulations. Docking and molecular dynamics studies on the generated three-dimensional model structure reveal the possibility of peptidoglycan fragment binding at the hinge regions between PASTA subunits with a preference for a bent hinge between PASTA3 and PASTA4.
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Affiliation(s)
- Benedetta Righino
- a Istituto di Biochimica e Biochimica Clinica , Università Cattolica del Sacro Cuore , L.go F. Vito 1, Rome 00168 , Italy
| | - Frédéric Galisson
- b Molecular Microbiology and Structural Biochemistry Institute , UMR5086 CNRS Univ-Lyon , Cedex 7, Lyon F-69367 , France
| | - Davide Pirolli
- a Istituto di Biochimica e Biochimica Clinica , Università Cattolica del Sacro Cuore , L.go F. Vito 1, Rome 00168 , Italy.,c Istituto di Chimica del Riconoscimento Molecolare (ICRM) , CNR c/o Università Cattolica del Sacro Cuore L.go F , Vito 1, Rome 00168 , Italy
| | - Serena Vitale
- a Istituto di Biochimica e Biochimica Clinica , Università Cattolica del Sacro Cuore , L.go F. Vito 1, Rome 00168 , Italy
| | - Stéphane Réty
- b Molecular Microbiology and Structural Biochemistry Institute , UMR5086 CNRS Univ-Lyon , Cedex 7, Lyon F-69367 , France
| | - Patrice Gouet
- b Molecular Microbiology and Structural Biochemistry Institute , UMR5086 CNRS Univ-Lyon , Cedex 7, Lyon F-69367 , France
| | - Maria Cristina De Rosa
- c Istituto di Chimica del Riconoscimento Molecolare (ICRM) , CNR c/o Università Cattolica del Sacro Cuore L.go F , Vito 1, Rome 00168 , Italy
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23
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Koo H, Hakim JA, Morrow CD, Eipers PG, Davila A, Andersen DT, Bej AK. Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica. J Microbiol Methods 2017; 140:15-22. [PMID: 28655556 PMCID: PMC6108183 DOI: 10.1016/j.mimet.2017.06.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 01/01/2023]
Abstract
In this study, using NextGen sequencing of the collective 16S rRNA genes obtained from two sets of samples collected from Lake Obersee, Antarctica, we compared and contrasted two bioinformatics tools, PICRUSt and Tax4Fun. We then developed an R script to assess the taxonomic and predictive functional profiles of the microbial communities within the samples. Taxa such as Pseudoxanthomonas, Planctomycetaceae, Cyanobacteria Subsection III, Nitrosomonadaceae, Leptothrix, and Rhodobacter were exclusively identified by Tax4Fun that uses SILVA database; whereas PICRUSt that uses Greengenes database uniquely identified Pirellulaceae, Gemmatimonadetes A1-B1, Pseudanabaena, Salinibacterium and Sinobacteraceae. Predictive functional profiling of the microbial communities using Tax4Fun and PICRUSt separately revealed common metabolic capabilities, while also showing specific functional IDs not shared between the two approaches. Combining these functional predictions using a customized R script revealed a more inclusive metabolic profile, such as hydrolases, oxidoreductases, transferases; enzymes involved in carbohydrate and amino acid metabolisms; and membrane transport proteins known for nutrient uptake from the surrounding environment. Our results present the first molecular-phylogenetic characterization and predictive functional profiles of the microbial mat communities in Lake Obersee, while demonstrating the efficacy of combining both the taxonomic assignment information and functional IDs using the R script created in this study for a more streamlined evaluation of predictive functional profiles of microbial communities.
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Affiliation(s)
- Hyunmin Koo
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Joseph A Hakim
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Casey D Morrow
- Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Peter G Eipers
- Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alfonso Davila
- NASA Ames Research Center, MS 245-3, Moffett Field, CA, USA
| | | | - Asim K Bej
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
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24
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Gómez LA, Alvarez FI, Fernández PA, Flores MR, Molina RE, Coloma RF, Oñate AA. Immunogenicity and Protective Response Induced by Recombinant Plasmids Based on the BAB1_0267 and BAB1_0270 Open Reading Frames of Brucella abortus 2308 in BALB/c Mice. Front Cell Infect Microbiol 2016; 6:117. [PMID: 27747197 PMCID: PMC5041321 DOI: 10.3389/fcimb.2016.00117] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/16/2016] [Indexed: 01/05/2023] Open
Abstract
Immunogenicity induced by recombinant plasmids based on the BAB1_0267 and BAB1_0270 open reading frames (ORFs) of Brucella abortus 2308 was evaluated. Bioinformatics analyses indicate that the BAB1_0267 and BAB1_0270 ORFs encode a protein with a SH3 domain and a Zn-dependent metalloproteinase, respectively. Both ORFs have important effects on intracellular survival and replication of B. abortus 2308, mediated via professional and non-professional phagocytic cells. Our results show that immunization with the recombinant plasmid based on the BAB1_0267 ORF significantly increases the production of IgG1, levels of IFN-γ and the lymphoproliferative response of splenocytes. However, BAB1_0267 did not provide significant levels of protection. The plasmid based on the BAB1_0270 significantly increased IgG2a production, levels of IFN-γ and TNF-α, and the lymphoproliferative response of splenocytes. These results demonstrate that immunization with the BAB1_0270 derived recombinant plasmid induce a Th1-type immune response, correlated with a heightened resistance to B. abortus 2308 infection in mice. It is concluded that the Th1-type immune response against bacterial Zn-dependent metalloproteinase induces a protective response in mice, and that pV270 recombinant plasmid is an effective candidate microbicide against brucellosis.
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Affiliation(s)
- Leonardo A Gómez
- Laboratory of Molecular Immunology, Department of Immunology, Faculty of Biological Sciences, Universidad de Concepción Concepción, Chile
| | - Francisco I Alvarez
- Laboratory of Molecular Immunology, Department of Immunology, Faculty of Biological Sciences, Universidad de Concepción Concepción, Chile
| | - Pablo A Fernández
- Laboratory of Molecular Immunology, Department of Immunology, Faculty of Biological Sciences, Universidad de Concepción Concepción, Chile
| | - Manuel R Flores
- Laboratory of Molecular Immunology, Department of Immunology, Faculty of Biological Sciences, Universidad de Concepción Concepción, Chile
| | - Raúl E Molina
- Laboratory of Molecular Immunology, Department of Immunology, Faculty of Biological Sciences, Universidad de Concepción Concepción, Chile
| | - Roberto F Coloma
- Laboratory of Molecular Immunology, Department of Immunology, Faculty of Biological Sciences, Universidad de Concepción Concepción, Chile
| | - Angel A Oñate
- Laboratory of Molecular Immunology, Department of Immunology, Faculty of Biological Sciences, Universidad de Concepción Concepción, Chile
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25
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Calder B, Albeldas C, Blackburn JM, Soares NC. Mass Spectrometry Offers Insight into the Role of Ser/Thr/Tyr Phosphorylation in the Mycobacteria. Front Microbiol 2016; 7:141. [PMID: 26904014 PMCID: PMC4751927 DOI: 10.3389/fmicb.2016.00141] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 01/25/2016] [Indexed: 12/23/2022] Open
Abstract
Phosphorylation is a post translational modification which can rapidly regulate biochemical pathways by altering protein function, and has been associated with pathogenicity in bacteria. Once engulfed by host macrophages, pathogenic bacteria are exposed to harsh conditions and must respond rapidly in order to survive. The causative agent of TB, Mycobacterium tuberculosis, is unusual amongst the bacteria because it can survive within the host macrophage for decades in a latent state, demonstrating a remarkable capacity to successfully evade the host immune response. This ability may be mediated in part by regulatory mechanisms such as ser/thr/tyr phosphorylation. Mass spectrometry-based proteomics has afforded us the capacity to identify hundreds of phosphorylation sites in the bacterial proteome, allowing for comparative phosphoproteomic studies in the mycobacteria. There remains an urgent need to validate the reported phosphosites, and to elucidate their biological function in the context of pathogenicity. However, given the sheer number of putative phosphorylation events in the mycobacterial proteome, and the technical difficulty of assigning biological function to a phosphorylation event, it will not be trivial to do so. There are currently six published phosphoproteomic investigations of a member of mycobacteria. Here, we combine the datasets from these studies in order to identify commonly detected phosphopeptides and phosphosites in order to present high confidence candidates for further validation. By applying modern mass spectrometry-based techniques to improve our understanding of phosphorylation and other PTMs in pathogenic bacteria, we may identify candidates for therapeutic intervention.
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Affiliation(s)
- Bridget Calder
- Applied and Chemical Proteomics Group, Medical Biochemistry Division, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Claudia Albeldas
- Applied and Chemical Proteomics Group, Medical Biochemistry Division, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Jonathan M Blackburn
- Applied and Chemical Proteomics Group, Medical Biochemistry Division, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Nelson C Soares
- Applied and Chemical Proteomics Group, Medical Biochemistry Division, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
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26
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Design strategies, structure activity relationship and mechanistic insights for purines as kinase inhibitors. Eur J Med Chem 2016; 112:298-346. [PMID: 26907156 DOI: 10.1016/j.ejmech.2016.02.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 12/22/2022]
Abstract
Kinases control a diverse set of cellular processes comprising of reversible phosphorylation of proteins. Protein kinases play a pivotal role in human tumor cell proliferation, migration and survival of neoplasia. In the recent past, purine based molecules have emerged as significantly potent kinase inhibitors. In view of their promising potential for the inhibition of kinases, this review article focuses on purines which have progressed as kinase inhibitors during the last five years. A detailed account of the design strategies employed for the synthesis of purine analogs exerting inhibitory effects on diverse kinases has been presented. Apart from presenting the design strategies, the article also highlights the structure activity relationship along with mechanistic insights revealed during the biological evaluation of the purine analogs for kinase inhibition. The interactions with the amino acid residues responsible for kinase inhibitory potential of purine based molecules have also been discussed. In this assemblage, purine based protein kinase inhibitors patented in the past have also been summarized in the tabular form. This compilation will be of great interest for the researchers working in the area of protein kinase inhibitors.
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27
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Wieland T, Attwood PV. Alterations in reversible protein histidine phosphorylation as intracellular signals in cardiovascular disease. Front Pharmacol 2015; 6:173. [PMID: 26347652 PMCID: PMC4543942 DOI: 10.3389/fphar.2015.00173] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 08/03/2015] [Indexed: 01/27/2023] Open
Abstract
Reversible phosphorylation of amino acid side chains in proteins is a frequently used mechanism in cellular signal transduction and alterations of such phosphorylation patterns are very common in cardiovascular diseases. They reflect changes in the activities of the protein kinases and phosphatases involving signaling pathways. Phosphorylation of serine, threonine, and tyrosine residues has been extensively investigated in vertebrates, whereas reversible histidine phosphorylation, a well-known regulatory signal in lower organisms, has been largely neglected as it has been generally assumed that histidine phosphorylation is of minor importance in vertebrates. More recently, it has become evident that the nucleoside diphosphate kinase isoform B (NDPK-B), an ubiquitously expressed enzyme involved in nucleotide metabolism, and a highly specific phosphohistidine phosphatase (PHP) form a regulatory histidine protein kinase/phosphatase system in mammals. At least three well defined substrates of NDPK-B are known: The β-subunit of heterotrimeric G-proteins (Gβ), the intermediate conductance potassium channel SK4 and the Ca(2+) conducting TRP channel family member, TRPV5. In each of these proteins the phosphorylation of a specific histidine residue regulates cellular signal transduction or channel activity. This article will therefore summarize our current knowledge on protein histidine phosphorylation and highlight its relevance for cardiovascular physiology and pathophysiology.
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Affiliation(s)
- Thomas Wieland
- Institute for Experimental and Clinical Pharmacology and Toxicology, Mannheim Medical Faculty, Heidelberg University , Mannheim, Germany
| | - Paul V Attwood
- School of Chemistry and Biochemistry, The University of Western Australia , Crawley, Australia
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28
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Yingping F, Lemeille S, González A, Risoul V, Denis Y, Richaud P, Lamrabet O, Fillat MF, Zhang CC, Latifi A. The Pkn22 Ser/Thr kinase in Nostoc PCC 7120: role of FurA and NtcA regulators and transcript profiling under nitrogen starvation and oxidative stress. BMC Genomics 2015. [PMID: 26220092 PMCID: PMC4518582 DOI: 10.1186/s12864-015-1703-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background The filamentous cyanobacterium Nostoc sp. strain PCC 7120 can fix N2 when combined nitrogen is not available. Furthermore, it has to cope with reactive oxygen species generated as byproducts of photosynthesis and respiration. We have previously demonstrated the synthesis of Ser/Thr kinase Pkn22 as an important survival response of Nostoc to oxidative damage. In this study we wished to investigate the possible involvement of this kinase in signalling peroxide stress and nitrogen deprivation. Results Quantitative RT-PCR experiments revealed that the pkn22 gene is induced in response to peroxide stress and to combined nitrogen starvation. Electrophoretic motility assays indicated that the pkn22 promoter is recognized by the global transcriptional regulators FurA and NtcA. Transcriptomic analysis comparing a pkn22-insertion mutant and the wild type strain indicated that this kinase regulates genes involved in important cellular functions such as photosynthesis, carbon metabolism and iron acquisition. Since metabolic changes may lead to oxidative stress, we investigated whether this is the case with nitrogen starvation. Our results rather invalidate this hypothesis thereby suggesting that the function of Pkn22 under nitrogen starvation is independent of its role in response to peroxide stress. Conclusions Our analyses have permitted a more complete functional description of Ser/Thr kinase in Nostoc. We have decrypted the transcriptional regulation of the pkn22 gene, and analysed the whole set of genes under the control of this kinase in response to the two environmental changes often encountered by cyanobacteria in their natural habitat: oxidative stress and nitrogen deprivation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1703-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fan Yingping
- Aix-Marseille University and CNRS, Laboratoire de Chimie Bactérienne - UMR7283, IMM, 31 Chemin Joseph Aiguier, 13402, Marseille cedex 20, France.
| | - Sylvain Lemeille
- Department of Microbiology and Molecular Medicine, CMU, Medical Faculty, University of Geneva, Genève, 1211, Switzerland.
| | - Andrés González
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009, Zaragoza, Spain.
| | - Véronique Risoul
- Aix-Marseille University and CNRS, Laboratoire de Chimie Bactérienne - UMR7283, IMM, 31 Chemin Joseph Aiguier, 13402, Marseille cedex 20, France.
| | - Yann Denis
- Plate-forme Transcriptome FR3479, IMM-CNRS, Marseille, France.
| | - Pierre Richaud
- CEA, DSV, IBEB, SBVME, Saint-Paul-lez-Durance, F-13108, France. .,CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France. .,Aix Marseille Université, BVME UMR7265, Marseille, F-13284, France.
| | - Otmane Lamrabet
- Aix-Marseille University and CNRS, Laboratoire de Chimie Bactérienne - UMR7283, IMM, 31 Chemin Joseph Aiguier, 13402, Marseille cedex 20, France.
| | - Maria F Fillat
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009, Zaragoza, Spain.
| | - Cheng-Cai Zhang
- Aix-Marseille University and CNRS, Laboratoire de Chimie Bactérienne - UMR7283, IMM, 31 Chemin Joseph Aiguier, 13402, Marseille cedex 20, France.
| | - Amel Latifi
- Aix-Marseille University and CNRS, Laboratoire de Chimie Bactérienne - UMR7283, IMM, 31 Chemin Joseph Aiguier, 13402, Marseille cedex 20, France.
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Yan J, Zou W, Fang J, Huang X, Gao F, He Z, Zhang K, Zhao N. Eukaryote-like Ser/Thr protein kinase PrkA modulates sporulation via regulating the transcriptional factor σ(K) in Bacillus subtilis. Front Microbiol 2015; 6:382. [PMID: 25983726 PMCID: PMC4415436 DOI: 10.3389/fmicb.2015.00382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/14/2015] [Indexed: 12/31/2022] Open
Abstract
Protein kinase A (PrkA), also known as AMP-activated protein kinase, functions as a serine/threonine protein kinase (STPK), has been shown to be involved in a variety of important biologic processes, including pathogenesis of many important diseases in mammals. However, the biological functions of PrkA are less known in prokaryote cells. Here, we explored the function of PrkA as well as its underlying molecular mechanisms using the model bacterium Bacillus subtilis168. When PrkA is inhibited by 9-β-D-arabinofuranosyladenine (ara-A) in the wild type strain or deleted in the ΔprkA mutant strain, we observed sporulation defects in B. subtilis 168, suggesting that PrkA functions as a sporulation-related protein. Transcriptional analysis using the lacZ reporter gene demonstrated that deletion of prkA significantly reduced the expression of the transcriptional factor σ(K) and its downstream genes. Complementation of sigK gene in prkA knockout mutant partially rescued the phenotype of ΔprkA, further supporting the hypothesis that the decreased σ(K) expression should be one of the reasons for the sporulation defect resulting from prkA disruption. Finally, our data confirmed that Hpr (ScoC) negatively controlled the expression of transcriptional factor σ(K), and thus PrkA accelerated sporulation and the expression of σ(K) by suppression of Hpr (ScoC). Taken together, our study discovered a novel function of the eukaryotic-like STPK PrkA in spore development as well as its underlying molecular mechanism in B. subtilis.
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Affiliation(s)
- Jinyuan Yan
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University Kunming, China
| | - Wei Zou
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University Kunming, China
| | - Juan Fang
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University Kunming, China
| | - Xiaowei Huang
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University Kunming, China
| | - Feng Gao
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University Kunming, China
| | - Zeying He
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University Kunming, China
| | - Keqin Zhang
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University Kunming, China
| | - Ninghui Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical College Kunming, China
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Zheng W, Liang Y, Zhao H, Zhang J, Li Z. 5,5'-Methylenedisalicylic Acid (MDSA) Modulates SarA/MgrA Phosphorylation by Targeting Ser/Thr Phosphatase Stp1. Chembiochem 2015; 16:1035-40. [PMID: 25810089 DOI: 10.1002/cbic.201500003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Indexed: 11/07/2022]
Abstract
SarA (staphylococcal accessory protein A), MgrA (MarR family of global transcriptional regulator A), and SarZ (a paralogue of SarA) play critical roles in modulating the virulence, drug resistance and autolysis of Staphylococcus aureus. Recently, eukaryotic-like Ser/Thr kinase/phosphatases (Stk1/Stp1) were found to modulate phosphorylation of these transcriptional regulators as well as staphylococcal virulence. Importantly, an stp1-deficient strain showed significant virulence reduction in mice, indicative of Stp1 as a potential drug target. Here, we report that MDSA, an inhibitor of MgrA, enhances phosphorylation of SarA/MgrA by inhibiting Stp1 in S. aureus. MDSA is a more-potent inhibitor (IC50 =9.68 ± 0.52 μM) of Stp1 than commonly used phosphatase inhibitors. We anticipate that MDSA could be a lead compound to develop new approaches for reducing staph virulence by targeting Stp1.
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Affiliation(s)
- Weihao Zheng
- Key Lab of Chemical Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen 518055 (China)
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Nagarajan SN, Upadhyay S, Chawla Y, Khan S, Naz S, Subramanian J, Gandotra S, Nandicoori VK. Protein kinase A (PknA) of Mycobacterium tuberculosis is independently activated and is critical for growth in vitro and survival of the pathogen in the host. J Biol Chem 2015; 290:9626-45. [PMID: 25713147 DOI: 10.1074/jbc.m114.611822] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Indexed: 01/09/2023] Open
Abstract
The essential mycobacterial protein kinases PknA and PknB play crucial roles in modulating cell shape and division. However, the precise in vivo functional aspects of PknA have not been investigated. This study aims to dissect the role of PknA in mediating cell survival in vitro as well as in vivo. We observed aberrant cell shape and severe growth defects when PknA was depleted. Using the mouse infection model, we observe that PknA is essential for survival of the pathogen in the host. Complementation studies affirm the importance of the kinase, juxtamembrane, and transmembrane domains of PknA. Surprisingly, the extracytoplasmic domain is dispensable for cell growth and survival in vitro. We find that phosphorylation of the activation loop at Thr(172) of PknA is critical for bacterial growth. PknB has been previously suggested to be the receptor kinase, which activates multiple kinases, including PknA, by trans-phosphorylating their activation loop residues. Using phospho-specific PknA antibodies and conditional pknB mutant, we find that PknA autophosphorylates its activation loop independent of PknB. Fluorescently tagged PknA and PknB show distinctive distribution patterns within the cell, suggesting that although both kinases are known to modulate cell shape and division, their modes of action are likely to be different. This is supported by our findings that expression of kinase-dead PknA versus kinase-dead PknB in mycobacterial cells leads to different cellular phenotypes. Data indicate that although PknA and PknB are expressed as part of the same operon, they appear to be regulating cellular processes through divergent signaling pathways.
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Affiliation(s)
- Sathya Narayanan Nagarajan
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India, the Department of Biotechnology, Nehru Arts and Science College, Coimbatore 641105, India, and
| | - Sandeep Upadhyay
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Yogesh Chawla
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shazia Khan
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saba Naz
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jayashree Subramanian
- the Department of Biotechnology, Nehru Arts and Science College, Coimbatore 641105, India, and
| | - Sheetal Gandotra
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Vinay Kumar Nandicoori
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India,
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Schillinger T, Zingler N. The low incidence of diversity-generating retroelements in sequenced genomes. Mob Genet Elements 2014; 2:287-291. [PMID: 23481467 PMCID: PMC3575424 DOI: 10.4161/mge.23244] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The insertion of a retrotransposable element is usually associated with adverse or, at best, neutral effects on the host. Diversity-generating retroelements (DGRs) are the first elements that seem to offer a direct selective advantage to their phage or prokaryote host by exact replacement of a short, defined region of a host gene with a hypermutated variant. In a previous study, we presented the software DiGReF for identification of DGRs in genome sequences, and compiled the first comprehensive set of diversity-generating retroelements in public databases. We identified 155 elements in more than 6000 prokaryotic and phage genomes, which was a surprisingly low number. In this commentary, we will discuss the low incidence of these elements and speculate about the biological role of bacterial DGRs.
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Affiliation(s)
- Thomas Schillinger
- Department of Molecular Genetics; University of Kaiserslautern; Kaiserslautern, Germany
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Ortiz-Román L, Riquelme-Neira R, RobertoVidal, Oñate A. Roles of genomic island 3 (GI-3) BAB1_0267 and BAB1_0270 open reading frames (ORFs) in the virulence of Brucella abortus 2308. Vet Microbiol 2014; 172:279-84. [DOI: 10.1016/j.vetmic.2014.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 04/29/2014] [Accepted: 05/04/2014] [Indexed: 12/25/2022]
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Selective pharmacologic inhibition of a PASTA kinase increases Listeria monocytogenes susceptibility to β-lactam antibiotics. Antimicrob Agents Chemother 2014; 58:4486-94. [PMID: 24867981 DOI: 10.1128/aac.02396-14] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
While β-lactam antibiotics are a critical part of the antimicrobial arsenal, they are frequently compromised by various resistance mechanisms, including changes in penicillin binding proteins of the bacterial cell wall. Genetic deletion of the penicillin binding protein and serine/threonine kinase-associated protein (PASTA) kinase in methicillin-resistant Staphylococcus aureus (MRSA) has been shown to restore β-lactam susceptibility. However, the mechanism remains unclear, and whether pharmacologic inhibition would have the same effect is unknown. In this study, we found that deletion or pharmacologic inhibition of the PASTA kinase in Listeria monocytogenes by the nonselective kinase inhibitor staurosporine results in enhanced susceptibility to both aminopenicillin and cephalosporin antibiotics. Resistance to vancomycin, another class of cell wall synthesis inhibitors, or antibiotics that inhibit protein synthesis was unaffected by staurosporine treatment. Phosphorylation assays with purified kinases revealed that staurosporine selectively inhibited the PASTA kinase of L. monocytogenes (PrkA). Importantly, staurosporine did not inhibit a L. monocytogenes kinase without a PASTA domain (Lmo0618) or the PASTA kinase from MRSA (Stk1). Finally, inhibition of PrkA with a more selective kinase inhibitor, AZD5438, similarly led to sensitization of L. monocytogenes to β-lactam antibiotics. Overall, these results suggest that pharmacologic targeting of PASTA kinases can increase the efficacy of β-lactam antibiotics.
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Abstract
Bakal studies the signaling networks that control cell shape.
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36
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Ruggiero A, De Simone P, Smaldone G, Squeglia F, Berisio R. Bacterial cell division regulation by Ser/Thr kinases: a structural perspective. Curr Protein Pept Sci 2013; 13:756-66. [PMID: 23305362 PMCID: PMC3601408 DOI: 10.2174/138920312804871201] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 07/16/2012] [Accepted: 08/03/2012] [Indexed: 12/17/2022]
Abstract
Recent genetic, biochemical and structural studies have established that eukaryotic-like Ser/Thr protein-kinases are critical mediators of developmental changes and host pathogen interactions in bacteria. Although with lower abundance compared to their homologues from eukaryotes, Ser/Thr protein-kinases are widespread in gram-positive bacteria. These data underline a key role of reversible Ser/Thr phosphorylation in bacterial physiology and virulence. Numerous studies have revealed how phosphorylation/dephosphorylation of Ser/Thr protein-kinases governs cell division and cell wall biosynthesis and that Ser/Thr protein kinases are responsible for distinct phenotypes, dependent on different environmental signals. In this review we discuss the current understandings of Ser/Thr protein-kinases functional processes based on structural data.
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Affiliation(s)
- Alessia Ruggiero
- Institute of Biostructure and Bioimaging, CNR, Via Mezzocannone, 16. I-80134, Napoli, Italy.
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Paredi G, Sentandreu MA, Mozzarelli A, Fadda S, Hollung K, de Almeida AM. Muscle and meat: New horizons and applications for proteomics on a farm to fork perspective. J Proteomics 2013; 88:58-82. [DOI: 10.1016/j.jprot.2013.01.029] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 01/31/2013] [Indexed: 11/16/2022]
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Weiling H, Xiaowen Y, Chunmei L, Jianping X. Function and evolution of ubiquitous bacterial signaling adapter phosphopeptide recognition domain FHA. Cell Signal 2013. [DOI: 10.1016/j.cellsig.2012.11.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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39
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Jin J, Pawson T. Modular evolution of phosphorylation-based signalling systems. Philos Trans R Soc Lond B Biol Sci 2012; 367:2540-55. [PMID: 22889906 DOI: 10.1098/rstb.2012.0106] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Phosphorylation sites are formed by protein kinases ('writers'), frequently exert their effects following recognition by phospho-binding proteins ('readers') and are removed by protein phosphatases ('erasers'). This writer-reader-eraser toolkit allows phosphorylation events to control a broad range of regulatory processes, and has been pivotal in the evolution of new functions required for the development of multi-cellular animals. The proteins that comprise this system of protein kinases, phospho-binding targets and phosphatases are typically modular in organization, in the sense that they are composed of multiple globular domains and smaller peptide motifs with binding or catalytic properties. The linkage of these binding and catalytic modules in new ways through genetic recombination, and the selection of particular domain combinations, has promoted the evolution of novel, biologically useful processes. Conversely, the joining of domains in aberrant combinations can subvert cell signalling and be causative in diseases such as cancer. Major inventions such as phosphotyrosine (pTyr)-mediated signalling that flourished in the first multi-cellular animals and their immediate predecessors resulted from stepwise evolutionary progression. This involved changes in the binding properties of interaction domains such as SH2 and their linkage to new domain types, and alterations in the catalytic specificities of kinases and phosphatases. This review will focus on the modular aspects of signalling networks and the mechanism by which they may have evolved.
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Affiliation(s)
- Jing Jin
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada.
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40
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Protein cysteine phosphorylation of SarA/MgrA family transcriptional regulators mediates bacterial virulence and antibiotic resistance. Proc Natl Acad Sci U S A 2012; 109:15461-6. [PMID: 22927394 DOI: 10.1073/pnas.1205952109] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein posttranslational modifications (PTMs), particularly phosphorylation, dramatically expand the complexity of cellular regulatory networks. Although cysteine (Cys) in various proteins can be subject to multiple PTMs, its phosphorylation was previously considered a rare PTM with almost no regulatory role assigned. We report here that phosphorylation occurs to a reactive cysteine residue conserved in the staphylococcal accessary regulator A (SarA)/MarR family global transcriptional regulator A (MgrA) family of proteins, and is mediated by the eukaryotic-like kinase-phosphatase pair Stk1-Stp1 in Staphylococcus aureus. Cys-phosphorylation is crucial in regulating virulence determinant production and bacterial resistance to vancomycin. Cell wall-targeting antibiotics, such as vancomycin and ceftriaxone, inhibit the kinase activity of Stk1 and lead to decreased Cys-phosphorylation of SarA and MgrA. An in vivo mouse model of infection established that the absence of stp1, which results in elevated protein Cys-phosphorylation, significantly reduces staphylococcal virulence. Our data indicate that Cys-phosphorylation is a unique PTM that can play crucial roles in bacterial signaling and regulation.
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Cheung A, Duclos B. Stp1 and Stk1: the Yin and Yang of vancomycin sensitivity and virulence in vancomycin-intermediate Staphylococcus aureus strains. J Infect Dis 2012; 205:1625-7. [PMID: 22492848 DOI: 10.1093/infdis/jis255] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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Control of cell division in Streptococcus pneumoniae by the conserved Ser/Thr protein kinase StkP. Proc Natl Acad Sci U S A 2012; 109:E905-13. [PMID: 22431591 DOI: 10.1073/pnas.1119172109] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
How the human pathogen Streptococcus pneumoniae coordinates cell-wall synthesis during growth and division to achieve its characteristic oval shape is poorly understood. The conserved eukaryotic-type Ser/Thr kinase of S. pneumoniae, StkP, previously was reported to phosphorylate the cell-division protein DivIVA. Consistent with a role in cell division, GFP-StkP and its cognate phosphatase, GFP-PhpP, both localize to the division site. StkP localization depends on its penicillin-binding protein and Ser/Thr-associated domains that likely sense uncross-linked peptidoglycan, because StkP and PhpP delocalize in the presence of antibiotics that target the latest stages of cell-wall biosynthesis and in cells that have stopped dividing. Time-lapse microscopy shows that StkP displays an intermediate timing of recruitment to midcell: StkP arrives shortly after FtsA but before DivIVA. Furthermore, StkP remains at midcell longer than FtsA, until division is complete. Cells mutated for stkP are perturbed in cell-wall synthesis and display elongated morphologies with multiple, often unconstricted, FtsA and DivIVA rings. The data show that StkP plays an important role in regulating cell-wall synthesis and controls correct septum progression and closure. Overall, our results indicate that StkP signals information about the cell-wall status to key cell-division proteins and in this way acts as a regulator of cell division.
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Jadeau F, Grangeasse C, Shi L, Mijakovic I, Deléage G, Combet C. BYKdb: the Bacterial protein tYrosine Kinase database. Nucleic Acids Res 2011; 40:D321-4. [PMID: 22080550 PMCID: PMC3245071 DOI: 10.1093/nar/gkr915] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bacterial tyrosine-kinases share no resemblance with their eukaryotic counterparts and they have been unified in a new protein family named BY-kinases. These enzymes have been shown to control several biological functions in the bacterial cells. In recent years biochemical studies, sequence analyses and structure resolutions allowed the deciphering of a common signature. However, BY-kinase sequence annotations in primary databases remain incomplete. This prompted us to develop a specialized database of computer-annotated BY-kinase sequences: the Bacterial protein tyrosine-kinase database (BYKdb). BY-kinase sequences are first identified, thanks to a workflow developed in a previous work. A second workflow annotates the UniProtKB entries in order to provide the BYKdb entries. The database can be accessed through a web interface that allows static and dynamic queries and offers integrated sequence analysis tools. BYKdb can be found at http://bykdb.ibcp.fr.
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Affiliation(s)
- Fanny Jadeau
- Unité Bases Moléculaires et Structurales des Systèmes Infectieux, UMR 5086 CNRS - Université Claude Bernard Lyon 1, IBCP FR 3302 - 7, Passage du Vercors, 69367 Lyon CEDEX 07, France
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Lima A, Durán R, Schujman GE, Marchissio MJ, Portela MM, Obal G, Pritsch O, de Mendoza D, Cerveñansky C. Serine/threonine protein kinase PrkA of the human pathogen Listeria monocytogenes: Biochemical characterization and identification of interacting partners through proteomic approaches. J Proteomics 2011; 74:1720-34. [DOI: 10.1016/j.jprot.2011.03.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 02/28/2011] [Accepted: 03/03/2011] [Indexed: 12/11/2022]
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Abstract
Genomic studies have revealed the presence of Ser/Thr kinases and phosphatases in many bacterial species, although their physiological roles have largely been unclear. Here we review bacterial Ser/Thr kinases (eSTKs) that show homology in their catalytic domains to eukaryotic Ser/Thr kinases and their partner phosphatases (eSTPs) that are homologous to eukaryotic phosphatases. We first discuss insights into the enzymatic mechanism of eSTK activation derived from structural studies on both the ligand-binding and catalytic domains. We then turn our attention to the identified substrates of eSTKs and eSTPs for a number of species and to the implications of these findings for understanding their physiological roles in these organisms.
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Delivoria-Papadopoulos M, Ashraf QM, Mishra OP. Mechanism of CaM kinase IV activation during hypoxia in neuronal nuclei of the cerebral cortex of newborn piglets: the role of Src kinase. Neurochem Res 2011; 36:1512-9. [PMID: 21516343 DOI: 10.1007/s11064-011-0477-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2011] [Indexed: 12/11/2022]
Abstract
The present study aims to investigate the mechanism of CaM kinase IV activation during hypoxia and tests the hypothesis that hypoxia-induced increased activity of CaM kinase IV is due to Src kinase mediated increased tyrosine phosphorylation of calmodulin and CaM kinase IV in neuronal nuclei of the cerebral cortex of newborn piglets. Piglets were divided into normoxic (Nx, n = 5), hypoxic (Hx, F(i)O(2) of 0.07 for 1 h, n = 5) and hypoxic-pretreated with Src kinase inhibitor PP2 (Hx-Srci, n = 5) groups. Src inhibitor was administered (1.0 mg/kg, I.V.) 30 min prior to hypoxia. Neuronal nuclei were isolated and purified, and tyrosine phosphorylation of calmodulin (Tyr(99)) and CaM kinase IV determined by Western blot using anti-phospho-(pTyr(99))-calmodulin, anti-pTyrosine and anti-CaM kinase IV antibodies. The activity of CaM kinase IV and its consequence the phosphorylation of CREB protein at Ser(133) were determined. Hypoxia resulted in increased tyrosine phosphorylation of calmodulin at Tyr(99), tyrosine phosphorylation of CaM kinase IV, activity of CaM kinase IV and phosphorylation of CREB protein at Ser(133). The data show that administration of Src kinase inhibitor PP2 prevented the hypoxia-induced increased tyrosine phosphorylation of calmodulin (Tyr(99)) and tyrosine phosphorylation of CaM.kinase IV as well as the activity of CaM kinase IV and CREB phosphorylation at Ser(133). We conclude that the mechanism of hypoxia-induced increased activation of CaM kinase IV is mediated by Src kinase-dependent tyrosine phosphorylation of the enzyme and its activator calmodulin. We propose that Tyr(99) phosphorylated calmodulin, as compared to non-phosphorylated, binds with a higher affinity at the calmodulin binding site (rich in basic amino acids) of CaM kinase IV leading to increased activation of CaM kinase IV. Similarly, tyrosine phosphorylated CaM kinase IV binds its substrate with a higher affinity and thus increased tyrosine phosphorylation leads to increased activation of CaM kinase IV resulting in increased CREB phosphorylation that triggers increased transcription of proapoptotic proteins that initiate hypoxic neuronal death.
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Affiliation(s)
- Maria Delivoria-Papadopoulos
- Department of Pediatrics, Drexel University College of Medicine and St. Christopher's Hospital for Children, 245 N 15th Street, New College Building, Room 7410, Mail Stop 1029, Philadelphia, PA 19102, USA.
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Role of PknB kinase in antibiotic resistance and virulence in community-acquired methicillin-resistant Staphylococcus aureus strain USA300. Infect Immun 2010; 78:3637-46. [PMID: 20547748 DOI: 10.1128/iai.00296-10] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The regulation of cellular processes by eukaryote-like serine/threonine kinases is widespread in bacteria. In the last 2 years, several studies have examined the role of serine/threonine kinases in Staphylococcus aureus on cell wall metabolism, autolysis, and virulence, mostly in S. aureus laboratory isolates in the 8325-4 lineage. In this study, we showed that the pknB gene (also called stk1) of methicillin-resistant S. aureus (MRSA) strain COL and the community-acquired MRSA (CA-MRSA) strain USA300 is involved in cell wall metabolism, with the pknB mutant exhibiting enhanced sensitivity to beta-lactam antibiotics but not to other classes of antibiotics, including aminoglycosides, ciprofloxacin, bactrim, and other types of cell wall-active agents (e.g., vancomycin and bacitracin). Additionally, the pknB mutant of USA300 was found to be more resistant to Triton X-100-induced autolysis and also to lysis by lysostaphin. We also showed that pknB is a positive regulator of sigB activity, resulting in compromise in its response to heat and oxidative stresses. In association with reduced sigB activity, the expression levels of RNAII and RNAIII of agr and the downstream effector hla are upregulated while spa expression is downmodulated in the pknB mutant compared to the level in the parent. Consistent with an enhanced agr response in vitro, virulence studies of the pknB mutant of USA300 in a murine cutaneous model of infection showed that the mutant was more virulent than the parental strain. Collectively, our results have linked the pknB gene in CA-MRSA to antibiotic resistance, sigB activity, and virulence and have highlighted important differences in pknB phenotypes (virulence and sigB activity) between laboratory isolates and the prototypic CA-MRSA strain USA300.
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Oxoby M, Moreau F, Durant L, Denis A, Genevard JM, Vongsouthi V, Escaich S, Gerusz V. Towards Gram-positive antivirulence drugs: New inhibitors of Streptococcus agalactiae Stk1. Bioorg Med Chem Lett 2010. [DOI: 10.1016/j.bmcl.2010.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Tyagi N, Anamika K, Srinivasan N. A framework for classification of prokaryotic protein kinases. PLoS One 2010; 5:e10608. [PMID: 20520783 PMCID: PMC2877116 DOI: 10.1371/journal.pone.0010608] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 04/13/2010] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Overwhelming majority of the Serine/Threonine protein kinases identified by gleaning archaeal and eubacterial genomes could not be classified into any of the well known Hanks and Hunter subfamilies of protein kinases. This is owing to the development of Hanks and Hunter classification scheme based on eukaryotic protein kinases which are highly divergent from their prokaryotic homologues. A large dataset of prokaryotic Serine/Threonine protein kinases recognized from genomes of prokaryotes have been used to develop a classification framework for prokaryotic Ser/Thr protein kinases. METHODOLOGY/PRINCIPAL FINDINGS We have used traditional sequence alignment and phylogenetic approaches and clustered the prokaryotic kinases which represent 72 subfamilies with at least 4 members in each. Such a clustering enables classification of prokaryotic Ser/Thr kinases and it can be used as a framework to classify newly identified prokaryotic Ser/Thr kinases. After series of searches in a comprehensive sequence database we recognized that 38 subfamilies of prokaryotic protein kinases are associated to a specific taxonomic level. For example 4, 6 and 3 subfamilies have been identified that are currently specific to phylum proteobacteria, cyanobacteria and actinobacteria respectively. Similarly subfamilies which are specific to an order, sub-order, class, family and genus have also been identified. In addition to these, we also identify organism-diverse subfamilies. Members of these clusters are from organisms of different taxonomic levels, such as archaea, bacteria, eukaryotes and viruses. CONCLUSION/SIGNIFICANCE Interestingly, occurrence of several taxonomic level specific subfamilies of prokaryotic kinases contrasts with classification of eukaryotic protein kinases in which most of the popular subfamilies of eukaryotic protein kinases occur diversely in several eukaryotes. Many prokaryotic Ser/Thr kinases exhibit a wide variety of modular organization which indicates a degree of complexity and protein-protein interactions in the signaling pathways in these microbes.
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Affiliation(s)
- Nidhi Tyagi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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Ohlsen K, Donat S. The impact of serine/threonine phosphorylation in Staphylococcus aureus. Int J Med Microbiol 2010; 300:137-41. [DOI: 10.1016/j.ijmm.2009.08.016] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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