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Carrilero L, Urwin L, Ward E, Choudhury NR, Monk IR, Turner CE, Stinear TP, Corrigan RM. Stringent Response-Mediated Control of GTP Homeostasis Is Required for Long-Term Viability of Staphylococcus aureus. Microbiol Spectr 2023; 11:e0044723. [PMID: 36877013 PMCID: PMC10101089 DOI: 10.1128/spectrum.00447-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 03/07/2023] Open
Abstract
Staphylococcus aureus is an opportunistic bacterial pathogen that often results in difficult-to-treat infections. One mechanism used by S. aureus to enhance survival during infection is the stringent response. This is a stress survival pathway that utilizes the nucleotides (p)ppGpp to reallocate bacterial resources, shutting down growth until conditions improve. Small colony variants (SCVs) of S. aureus are frequently associated with chronic infections, and this phenotype has previously been linked to a hyperactive stringent response. Here, we examine the role of (p)ppGpp in the long-term survival of S. aureus under nutrient-restricted conditions. When starved, a (p)ppGpp-null S. aureus mutant strain ((p)ppGpp0) initially had decreased viability. However, after 3 days we observed the presence and dominance of a population of small colonies. Similar to SCVs, these small colony isolates (p0-SCIs) had reduced growth but remained hemolytic and sensitive to gentamicin, phenotypes that have been tied to SCVs previously. Genomic analysis of the p0-SCIs revealed mutations arising within gmk, encoding an enzyme in the GTP synthesis pathway. We show that a (p)ppGpp0 strain has elevated levels of GTP, and that the mutations in the p0-SCIs all lower Gmk enzyme activity and consequently cellular GTP levels. We further show that in the absence of (p)ppGpp, cell viability can be rescued using the GuaA inhibitor decoyinine, which artificially lowers the intracellular GTP concentration. Our study highlights the role of (p)ppGpp in GTP homeostasis and underscores the importance of nucleotide signaling for long-term survival of S. aureus in nutrient-limiting conditions, such as those encountered during infections. IMPORTANCE Staphylococcus aureus is a human pathogen that upon invasion of a host encounters stresses, such as nutritional restriction. The bacteria respond by switching on a signaling cascade controlled by the nucleotides (p)ppGpp. These nucleotides function to shut down bacterial growth until conditions improve. Therefore, (p)ppGpp are important for bacterial survival and have been implicated in promoting chronic infections. Here, we investigate the importance of (p)ppGpp for long-term survival of bacteria in nutrient-limiting conditions similar to those in a human host. We discovered that in the absence of (p)ppGpp, bacterial viability decreases due to dysregulation of GTP homeostasis. However, the (p)ppGpp-null bacteria were able to compensate by introducing mutations in the GTP synthesis pathway that led to a reduction in GTP build-up and a rescue of viability. This study therefore highlights the importance of (p)ppGpp for the regulation of GTP levels and for long-term survival of S. aureus in restricted environments.
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Affiliation(s)
- Laura Carrilero
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Lucy Urwin
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Ezra Ward
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Naznin R. Choudhury
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Ian R. Monk
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Claire E. Turner
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Rebecca M. Corrigan
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
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Lu F, Wu X, Hu H, He Z, Sun J, Zhang J, Song X, Jin X, Chen G. Emodin Combined with Multiple-Low-Frequency, Low-Intensity Ultrasound To Relieve Osteomyelitis through Sonoantimicrobial Chemotherapy. Microbiol Spectr 2022; 10:e0054422. [PMID: 36069576 PMCID: PMC9603654 DOI: 10.1128/spectrum.00544-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/16/2022] [Indexed: 11/20/2022] Open
Abstract
Treatment of osteomyelitis is still challenging, as conventional antibiotic therapy is limited by the emergence of resistant strains and the formation of biofilms. Sonoantimicrobial chemotherapy (SACT) is a novel therapy of low-frequency and low-intensity ultrasound (LFLIU) combined with a sonosensitizer. Therefore, in our study, a sonosensitizer named emodin (EM) was proposed to be combined with LFLIU to relieve acute osteomyelitis caused by methicillin-resistant Staphylococcus aureus (MRSA) through antibacterial and antibiofilm effects. The efficiencies of different intensities of ultrasound, including single (S-LFLIU, 15 min) and multiple ultrasound (M-LFLIU, 3 times for 5 min at 4-h intervals), against bacteria and biofilms were compared, contributing to developing the best treatment regimen. Our results demonstrated that EM plus S-LFLIU or M-LFLIU (EM+S-LFLIU or EM+M-LFLIU) had significant combined bactericidal and antibiofilm effects, with EM+M-LFLIU in particular exhibiting superior antibiofilm performance. Furthermore, it was suggested that EM+M-LFLIU could produce a large amount of reactive oxygen species (ROS), destroy the integrity of the bacterial membrane and cell wall, and downregulate the expression of genes involved in oxidative stress, membrane wall synthesis, and bacterial virulence, as well as that of other related genes (agrB, pbp3, sgtB, gmk, zwf, and msrA). In vivo studies, micro-computed tomography (micro-CT), hematoxylin and eosin (H&E) staining, enzyme-linked immunosorbent assay (ELISA), and bacterial quantification of bone tissue indicated that EM+M-LFLIU could also relieve osteomyelitis due to MRSA infection. Our work proffers an original approach to bacterial osteomyelitis treatment that weakens drug-resistant bacteria and suppresses and degrades biofilm formation through SACT, which may provide new prospects for clinical treatment. IMPORTANCE Antibiotic therapy is the first choice for clinical treatment of osteomyelitis, but the formation of bacterial biofilms and the emergence of many drug-resistant strains also create an urgent need to find an alternative treatment to effectively eliminate the infection. Recently, LFLIU has come to be considered a safe and promising method of debridement and antibacterial therapy. In this study, we found that ultrasound and EM have a significant combined antibacterial effect in vivo and in vitro, which may play an antibacterial role by stimulating the production of ROS, destroying the bacterial cell wall, and inhibiting the expression of related genes. Our study expands the body of knowledge on the antibacterial effect of drugs-specifically emodin (EM)-through combined physiotherapy. If successfully integrated into clinical practice, these methods may reduce the burden of high concentrations of drugs needed to treat bacterial biofilms and avoid the growing resistance of bacteria to antibiotics.
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Affiliation(s)
- Feng Lu
- Department of Orthopedics, Taizhou Hospital of Zhejiang Province, Zhejiang University, Linhai, China
- Zhejiang University School of Medicine, Hangzhou, China
| | - Xinhui Wu
- Wenzhou Medical University, Wenzhou, China
- Department of Orthopedics, Taizhou Hospital Affiliated with Wenzhou Medical University, Linhai, China
| | - Huiqun Hu
- Zhejiang University School of Medicine, Hangzhou, China
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zixuan He
- Department of Orthopedics, Taizhou Hospital of Zhejiang Province, Zhejiang University, Linhai, China
- Zhejiang University School of Medicine, Hangzhou, China
| | - Jiacheng Sun
- Wenzhou Medical University, Wenzhou, China
- Department of Orthopedics, Taizhou Hospital Affiliated with Wenzhou Medical University, Linhai, China
| | - Jiapeng Zhang
- Wenzhou Medical University, Wenzhou, China
- Department of Orthopedics, Taizhou Hospital Affiliated with Wenzhou Medical University, Linhai, China
| | - Xiaoting Song
- Wenzhou Medical University, Wenzhou, China
- Department of Orthopedics, Taizhou Hospital Affiliated with Wenzhou Medical University, Linhai, China
| | - Xiangang Jin
- Department of Orthopedics, Taizhou Hospital of Zhejiang Province, Zhejiang University, Linhai, China
- Zhejiang University School of Medicine, Hangzhou, China
| | - Guofu Chen
- Department of Orthopedics, Taizhou Hospital Affiliated with Wenzhou Medical University, Linhai, China
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3
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Rodríguez-Rojas A, Nath A, El Shazely B, Santi G, Kim JJ, Weise C, Kuropka B, Rolff J. Antimicrobial Peptide Induced-Stress Renders Staphylococcus aureus Susceptible to Toxic Nucleoside Analogs. Front Immunol 2020; 11:1686. [PMID: 33133056 PMCID: PMC7550632 DOI: 10.3389/fimmu.2020.01686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022] Open
Abstract
Cationic antimicrobial peptides (AMPs) are active immune effectors of multicellular organisms and are also considered as new antimicrobial drug candidates. One of the problems encountered when developing AMPs as drugs is the difficulty of reaching sufficient killing concentrations under physiological conditions. Here, using pexiganan, a cationic peptide derived from a host defense peptide of the African clawed frog and the first AMP developed into an antibacterial drug, we studied whether sub-lethal effects of AMPs can be harnessed to devise treatment combinations. We studied the pexiganan stress response of Staphylococcus aureus at sub-lethal concentrations using quantitative proteomics. Several proteins involved in nucleotide metabolism were elevated, suggesting a metabolic demand. We then show that Staphylococcus aureus is highly susceptible to antimetabolite nucleoside analogs when exposed to pexiganan, even at sub-inhibitory concentrations. These findings could be used to enhance pexiganan potency while decreasing the risk of resistance emergence, and our findings can likely be extended to other antimicrobial peptides.
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Affiliation(s)
| | - Arpita Nath
- Institut für Biologie, Evolutionary Biology, Freie Universität Berlin, Berlin, Germany
| | - Baydaa El Shazely
- Institut für Biologie, Evolutionary Biology, Freie Universität Berlin, Berlin, Germany
- Zoology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Greta Santi
- Institut für Biologie, Evolutionary Biology, Freie Universität Berlin, Berlin, Germany
| | - Joshua Jay Kim
- Institut für Biologie, Evolutionary Biology, Freie Universität Berlin, Berlin, Germany
| | - Christoph Weise
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Jens Rolff
- Institut für Biologie, Evolutionary Biology, Freie Universität Berlin, Berlin, Germany
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4
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Pedro L, Cross M, Hofmann A, Mak T, Quinn RJ. Development of an HPLC-based guanosine monophosphate kinase assay and application to Plasmodium vivax guanylate kinase. Anal Biochem 2019; 575:63-69. [PMID: 30943378 PMCID: PMC6494078 DOI: 10.1016/j.ab.2019.03.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 03/18/2019] [Accepted: 03/29/2019] [Indexed: 11/12/2022]
Abstract
The development of a high-performance liquid chromatography (HPLC)-based method, for guanosine monophosphate kinase activity assays, is presented. The method uses the intrinsic UV absorption (at 260 nm) of substrates and products of the enzymatic reaction (GMP, ATP, ADP and GDP) to unambiguously determine percent conversion of substrate into product. It uses a commercially available C18 column which can separate reaction samples by elution under isocratic conditions in 12 min per run. The kinetics of the forward reaction catalyzed by Plasmodium vivax guanylate kinase (PvGK), a potential drug target against malaria, was determined. The relative concentrations of the two substrates (GMP and ATP) have a distinct effect on reaction velocity. Kinetic analyses showed the PvGK-catalyzed reaction to be associated with atypical kinetics, where substrate inhibition kinetics and non-Michaelis-Menten (sigmoidal) kinetics were found with respect to GMP and ATP, respectively. Additionally, the method was used in inhibition assays to screen twenty fragment-like compounds. The assays were robust and reproducible, with a signal window of 3.8 and a Z’ factor of 0.6. For the best inhibitor, an IC50 curve was generated. Simple HPLC separation of nucleotides involved in the guanylate kinase reaction. Direct and unambiguous determination of percent conversion of substrate into product. Successful application to Plasmodium vivax guanylate kinase (PvGK) activity studies. Reaction catalyzed by PvGK found to be associated with atypical kinetics. Robust and reproducible inhibition assay for compound screening.
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Affiliation(s)
- Liliana Pedro
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Megan Cross
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Andreas Hofmann
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Tin Mak
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia.
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5
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Khan N, Shah PP, Ban D, Trigo-Mouriño P, Carneiro MG, DeLeeuw L, Dean WL, Trent JO, Beverly LJ, Konrad M, Lee D, Sabo TM. Solution structure and functional investigation of human guanylate kinase reveals allosteric networking and a crucial role for the enzyme in cancer. J Biol Chem 2019; 294:11920-11933. [PMID: 31201273 DOI: 10.1074/jbc.ra119.009251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/12/2019] [Indexed: 01/13/2023] Open
Abstract
Human guanylate kinase (hGMPK) is the only known enzyme responsible for cellular GDP production, making it essential for cellular viability and proliferation. Moreover, hGMPK has been assigned a critical role in metabolic activation of antiviral and antineoplastic nucleoside-analog prodrugs. Given that hGMPK is indispensable for producing the nucleotide building blocks of DNA, RNA, and cGMP and that cancer cells possess elevated GTP levels, it is surprising that a detailed structural and functional characterization of hGMPK is lacking. Here, we present the first high-resolution structure of hGMPK in the apo form, determined with NMR spectroscopy. The structure revealed that hGMPK consists of three distinct regions designated as the LID, GMP-binding (GMP-BD), and CORE domains and is in an open configuration that is nucleotide binding-competent. We also demonstrate that nonsynonymous single-nucleotide variants (nsSNVs) of the hGMPK CORE domain distant from the nucleotide-binding site of this domain modulate enzymatic activity without significantly affecting hGMPK's structure. Finally, we show that knocking down the hGMPK gene in lung adenocarcinoma cell lines decreases cellular viability, proliferation, and clonogenic potential while not altering the proliferation of immortalized, noncancerous human peripheral airway cells. Taken together, our results provide an important step toward establishing hGMPK as a potential biomolecular target, from both an orthosteric (ligand-binding sites) and allosteric (location of CORE domain-located nsSNVs) standpoint.
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Affiliation(s)
- Nazimuddin Khan
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - Parag P Shah
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - Pablo Trigo-Mouriño
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Marta G Carneiro
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Lynn DeLeeuw
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - William L Dean
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - John O Trent
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - Levi J Beverly
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - Manfred Konrad
- Enzyme Biochemistry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
| | - T Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202
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6
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Khan N, Ban D, Trigo-Mourino P, Carneiro MG, Konrad M, Lee D, Sabo TM. 1H, 13C and 15N resonance assignment of human guanylate kinase. BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:11-14. [PMID: 28861857 DOI: 10.1007/s12104-017-9771-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
Human guanylate kinase (hGMPK) is a critical enzyme that, in addition to phosphorylating its physiological substrate (d)GMP, catalyzes the second phosphorylation step in the conversion of anti-viral and anti-cancer nucleoside analogs to their corresponding active nucleoside analog triphosphates. Until now, a high-resolution structure of hGMPK is unavailable and thus, we studied free hGMPK by NMR and assigned the chemical shift resonances of backbone and side chain 1H, 13C, and 15N nuclei as a first step towards the enzyme's structural and mechanistic analysis with atomic resolution.
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Affiliation(s)
- Nazimuddin Khan
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY, 40202, USA
- Enzyme Biochemistry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - David Ban
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY, 40202, USA
| | - Pablo Trigo-Mourino
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Marta G Carneiro
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
- ZoBio B.V., Biopartner building 2, J.H. Oortweg 19, 2333 CH, Leiden, The Netherlands
| | - Manfred Konrad
- Enzyme Biochemistry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Donghan Lee
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY, 40202, USA
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - T Michael Sabo
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY, 40202, USA.
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
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7
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Pan H, Xu J, Kweon OG, Zou W, Feng J, He GX, Cerniglia CE, Chen H. Differential gene expression in Staphylococcus aureus exposed to Orange II and Sudan III azo dyes. J Ind Microbiol Biotechnol 2015; 42:745-57. [PMID: 25720844 DOI: 10.1007/s10295-015-1599-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/10/2015] [Indexed: 12/22/2022]
Abstract
We previously demonstrated the effects of azo dyes and their reduction metabolites on bacterial cell growth and cell viability. In this report, the effects of Orange II and Sudan III on gene expression profiling in Staphylococcus aureus ATCC BAA 1556 were analyzed using microarray and quantitative RT-PCR technology. Upon exposure to 6 μg/ml Orange II for 18 h, 21 genes were found to be differently expressed. Among them, 8 and 13 genes were up- and down-regulated, respectively. Most proteins encoded by these differentially expressed genes involve stress response caused by drug metabolism, oxidation, and alkaline shock indicating that S. aureus could adapt to Orange II exposure through a balance between up and down regulated gene expression. Whereas, after exposure to 6 μg/ml Sudan III for 18 h, 57 genes were differentially expressed. In which, 51 genes were up-regulated and 6 were down-regulated. Most proteins encoded by these differentially expressed genes involve in cell wall/membrane biogenesis and biosynthesis, nutrient uptake, transport and metabolite, and stress response, suggesting that Sudan III damages the bacterial cell wall or/and membrane due to binding of the dye. Further analysis indicated that all differentially expressed genes encoded membrane proteins were up-regulated and most of them serve as transporters. The result suggested that these genes might contribute to survival, persistence and growth in the presence of Sudan III. Only one gene msrA, which plays an important role in oxidative stress resistance, was found to be down-regulated after exposure to both Orange II and Sudan III. The present results suggested that both these two azo dyes can cause stress in S. aureus and the response of the bacterium to the stress is mainly related to characteristics of the azo dyes.
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Affiliation(s)
- Hongmiao Pan
- Division of Microbiology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, AR, 72079-9502, USA
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8
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Molecular mechanism and evolution of guanylate kinase regulation by (p)ppGpp. Mol Cell 2015; 57:735-749. [PMID: 25661490 PMCID: PMC4336630 DOI: 10.1016/j.molcel.2014.12.037] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 11/07/2014] [Accepted: 12/22/2014] [Indexed: 01/07/2023]
Abstract
The nucleotide (p)ppGpp mediates bacterial stress responses, but its targets and underlying mechanisms of action vary among bacterial species and remain incompletely understood. Here, we characterize the molecular interaction between (p)ppGpp and guanylate kinase (GMK), revealing the importance of this interaction in adaptation to starvation. Combining structural and kinetic analyses, we show that (p)ppGpp binds the GMK active site and competitively inhibits the enzyme. The (p)ppGpp-GMK interaction prevents the conversion of GMP to GDP, resulting in GMP accumulation upon amino acid downshift. Abolishing this interaction leads to excess (p)ppGpp and defective adaptation to amino acid starvation. A survey of GMKs from phylogenetically diverse bacteria shows that the (p)ppGpp-GMK interaction is conserved in members of Firmicutes, Actinobacteria, and Deinococcus-Thermus, but not in Proteobacteria, where (p)ppGpp regulates RNA polymerase (RNAP). We propose that GMK is an ancestral (p)ppGpp target and RNAP evolved more recently as a direct target in Proteobacteria.
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Delalande O, Sacquin-Mora S, Baaden M. Enzyme closure and nucleotide binding structurally lock guanylate kinase. Biophys J 2011; 101:1440-9. [PMID: 21943425 DOI: 10.1016/j.bpj.2011.07.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 07/15/2011] [Accepted: 07/28/2011] [Indexed: 02/02/2023] Open
Abstract
We investigate the conformational dynamics and mechanical properties of guanylate kinase (GK) using a multiscale approach combining high-resolution atomistic molecular dynamics and low-resolution Brownian dynamics simulations. The GK enzyme is subject to large conformational changes, leading from an open to a closed form, which are further influenced by the presence of nucleotides. As suggested by recent work on simple coarse-grained models of apo-GK, we primarily focus on GK's closure mechanism with the aim to establish a detailed picture of the hierarchy and chronology of structural events essential for the enzymatic reaction. We have investigated open-versus-closed, apo-versus-holo, and substrate-versus-product-loaded forms of the GK enzyme. Bound ligands significantly modulate the mechanical and dynamical properties of GK and rigidity profiles of open and closed states hint at functionally important differences. Our data emphasizes the role of magnesium, highlights a water channel permitting active site hydration, and reveals a structural lock that stabilizes the closed form of the enzyme.
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Affiliation(s)
- Olivier Delalande
- Institut de Biologie Physico-Chimique, Laboratoire de Biochimie Théorique, Centre National de la Recherche Scientifique, UPR9080, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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10
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Kandeel M, Kitade Y. Binding dynamics and energetic insight into the molecular forces driving nucleotide binding by guanylate kinase. J Mol Recognit 2010; 24:322-32. [PMID: 21360614 DOI: 10.1002/jmr.1074] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 07/16/2010] [Accepted: 07/16/2010] [Indexed: 11/11/2022]
Abstract
Plasmodium deoxyguanylate pathways are an attractive area of investigation for future metabolic and drug discovery studies due to their unique substrate specificities. We investigated the energetic contribution to guanylate kinase substrate binding and the forces underlying ligand recognition. In the range from 20 to 35°C, the thermodynamic profiles displayed marked decrease in binding enthalpy, while the free energy of binding showed little changes. GMP produced a large binding heat capacity change of -356 cal mol(-1) K(-1), indicating considerable conformational changes upon ligand binding. Interestingly, the calculated ΔCp was -32 cal mol(-1) K(-1), indicating that the accessible surface area is not the central change in substrate binding, and that other entropic forces, including conformational changes, are more predominant. The thermodynamic signature for GMP is inconsistent with rigid-body association, while dGMP showed more or less rigid-body association. These binding profiles explain the poor catalytic efficiency and low affinity for dGMP compared with GMP. At low temperature, the ligands bind to the receptor site under the effect of hydrophobic forces. Interestingly, by increasing the temperature, the entropic forces gradually vanish and proceed to a nonfavorable contribution, and the interaction occurs mainly through bonding, electrostatic forces, and van der Waals interactions.
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Affiliation(s)
- Mahmoud Kandeel
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafr El-Shikh University, Kafr El-Shikh 33516, Egypt.
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11
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Keegan RM, Winn MD. MrBUMP: an automated pipeline for molecular replacement. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2008; 64:119-24. [PMID: 18094475 PMCID: PMC2394800 DOI: 10.1107/s0907444907037195] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Accepted: 07/30/2007] [Indexed: 11/10/2022]
Abstract
A novel automation pipeline for macromolecular structure solution by molecular replacement is described. There is a special emphasis on the discovery and preparation of a large number of search models, all of which can be passed to the core molecular-replacement programs. For routine molecular-replacement problems, the pipeline automates what a crystallographer might do and its value is simply one of convenience. For more difficult cases, the pipeline aims to discover the particular template structure and model edits required to produce a viable search model and may succeed in finding an efficacious combination that would be missed otherwise. An overview of MrBUMP is given and some recent additions to its functionality are highlighted.
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Affiliation(s)
- Ronan M. Keegan
- Computational Science and Engineering Department, STFC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, England
| | - Martyn D. Winn
- Computational Science and Engineering Department, STFC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, England
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