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Dokuz S, Tasdurmazli S, Acar T, Duran GN, Ozdemir C, Ozbey U, Ozbil M, Karadayi S, Bayrak OF, Derman S, Chen JYS, Ozbek T. Evaluation of bacteriophage ϕ11 host recognition protein and its host-binding peptides for diagnosing/targeting Staphylococcus aureus infections. Int J Antimicrob Agents 2024; 64:107230. [PMID: 38824973 DOI: 10.1016/j.ijantimicag.2024.107230] [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: 01/28/2024] [Revised: 05/14/2024] [Accepted: 05/28/2024] [Indexed: 06/04/2024]
Abstract
BACKGROUND Evaluating the potential of using both synthetic and biological products as targeting agents for the diagnosis, imaging, and treatment of infections due to particularly antibiotic-resistant pathogens is important for controlling infections. This study examined the interaction between Gp45, a receptor-binding protein of the ϕ11 lysogenic phage, and its host Staphylococcus aureus (S. aureus), a common cause of nosocomial infections. METHODS Using molecular dynamics and docking simulations, this study identified the peptides that bind to S. aureus wall teichoic acids via Gp45. It compared the binding affinity of Gp45 and the two highest-scoring peptide sequences (P1 and P3) and their scrambled forms using microscopy, spectroscopy, and ELISA. RESULTS It was found that rGp45 (recombinant Gp45) and chemically synthesised P1 had a higher binding affinity for S. aureus compared with all other peptides, except for Escherichia coli. Furthermore, rGp45 had a capture efficiency of > 86%; P1 had a capture efficiency of > 64%. CONCLUSION These findings suggest that receptor-binding proteins such as rGp45, which provide a critical initiation of the phage life cycle for host adsorption, might play an important role in the diagnosis, imaging, and targeting of bacterial infections. Studying such proteins could accordingly enable the development of effective strategies for controlling infections.
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Affiliation(s)
- Senanur Dokuz
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Turkey
| | - Semra Tasdurmazli
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Turkey
| | - Tayfun Acar
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Istanbul, Turkey
| | - Gizem Nur Duran
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
| | - Cilem Ozdemir
- Department of Medical Biology, Health Sciences Institution, Mugla Sitki Kocman University, Mugla, Turkey
| | - Utku Ozbey
- Department of Medical Genetics, School of Medicine, Yeditepe University, Istanbul, Turkey
| | - Mehmet Ozbil
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
| | - Sukriye Karadayi
- Department of Medical Laboratory Techniques, Vocational School of Health Services, Altınbas University, Istanbul, Turkey
| | - Omer Faruk Bayrak
- Department of Medical Genetics, School of Medicine, Yeditepe University, Istanbul, Turkey
| | - Serap Derman
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Istanbul, Turkey
| | - John Yu-Shen Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Tulin Ozbek
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Turkey.
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Escal J, Neel T, Hodin S, Boussoualim K, Amouzougan A, Coassy A, Locrelle H, Thomas T, Delavenne X, Marotte H. Proteomics analyses of human plasma reveal triosephosphate isomerase as a potential blood marker of methotrexate resistance in rheumatoid arthritis. Rheumatology (Oxford) 2024; 63:1368-1376. [PMID: 37527020 DOI: 10.1093/rheumatology/kead390] [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: 04/26/2023] [Revised: 07/02/2023] [Accepted: 07/09/2023] [Indexed: 08/03/2023] Open
Abstract
OBJECTIVE The objective of this study was to assess differentially expressed blood proteins between patients with active RA and patients in remission after MTX treatment, with the aim of identifying a biomarker of MTX resistance (MTXR). METHODS Two populations of RA patients treated with a stable dose of s.c. MTX for at least 3 months were constituted according to the DAS28: remission (DAS28 < 2.6; n = 24) and active disease (DAS28 > 3.2; n = 32). The two groups of RA patients were homogeneous regarding their epidemiological characteristics, except for the duration of treatment, which was longer in the remission group. After collection of a blood sample, plasma protein digestion was performed, followed by untargeted proteomics analysis. Then, a targeted analysis was performed to confirm the results of the untargeted approach. RESULTS Untargeted proteomics analysis revealed eight plasma proteins that were differentially expressed between the two groups of patients. Among them, triosephosphate isomerase (TPI-1) and glucose-6-phosphate isomerase (GPI), which are main actors in glycolysis, were found down-regulated in the active group. This result was confirmed for TPI-1 in the targeted proteomics analysis. CONCLUSION A first step was achieved in the search for biomarkers of MTXR, with the identification of two actors in glycolysis (TPI-1 and GPI). The next step will be to confirm these results in a larger cohort, including samples from treatment-naive patients, to assess the predictive potential of these protein markers.
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Affiliation(s)
- Jean Escal
- Université Jean Monnet Saint-Étienne, CHU Saint-Etienne, Laboratoire de Pharmacologie et Toxicologie, INSERM, SAINBIOSE U1059, Saint-Etienne, France
| | - Tiphany Neel
- CHU Saint-Étienne, Service de Rhumatologie, Saint-Etienne, France
| | - Sophie Hodin
- Université Jean Monnet Saint-Étienne, INSERM, SAINBIOSE U1059, Saint-Etienne, France
| | | | | | - Astrid Coassy
- CHU Saint-Étienne, Service de Rhumatologie, Saint-Etienne, France
| | - Hervé Locrelle
- CHU Saint-Étienne, Service de Rhumatologie, Saint-Etienne, France
| | - Thierry Thomas
- Université Jean Monnet Saint-Étienne, CHU Saint-Étienne, Service de Rhumatologie, Mines Saint-Etienne, INSERM, SAINBIOSE U1059, Saint-Etienne, France
| | - Xavier Delavenne
- Université Jean Monnet Saint-Étienne, CHU Saint-Etienne, Laboratoire de Pharmacologie et Toxicologie, INSERM, SAINBIOSE U1059, Saint-Etienne, France
| | - Hubert Marotte
- Université Jean Monnet Saint-Étienne, CHU Saint-Étienne, Service de Rhumatologie, Mines Saint-Etienne, INSERM, SAINBIOSE U1059, Saint-Etienne, France
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Tasdurmazli S, Dokuz S, Erdogdu B, Var I, Chen JYS, Ozbek T. The evaluation of biotechnological potential of Gp144, the key molecule of natural predator bacteriophage K in Staphylococcus aureus hunting mechanism. Biotechnol J 2023; 18:e2300145. [PMID: 37300362 DOI: 10.1002/biot.202300145] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/25/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
Bacteriophages, which selectively infect bacteria, and phage-derived structures are considered promising agents for the diagnosis and treatment of bacterial infections due to the increasing antibiotic resistance. The binding of phages to their specific receptors on host bacteria is highly specific and irreversible, and therefore, the characterization of receptor-binding proteins(RBPs), which are key determinants of phage specificity, is crucial for the development of new diagnostic and therapeutic products. This study highlights the biotechnological potential of Gp144, an RBP located in the tail baseplate of bacteriophage K and responsible for adsorption of phageK to S. aureus. Once it was established that recombinant Gp144 (rGp144)is biocompatible and does not exhibit lytic effects on bacteria, its interaction with the host, the binding efficiency and performance were assessed in vitro using microscopic and serological methods. Results showed that rGp144 has a capture efficiency (CE) of over 87% and the best CE score is %96 which captured 9 CFU mL-1 out of 10 CFU mL-1 bacteria, indicating that very low number of bacteria could be detected. Additionally, it was shown for the first time in the literature that rGp144 binds to both S. aureus and methicillin-resistant S. aureus (MRSA) cells in vitro, while its affinity to different Gram-positive bacteria (E. faecalis and B. cereus) was not observed. The findings suggest that rGp144 can be effectively used for the diagnosis of S. aureus and MRSA, and that the use of RBPs in host-phage interaction can be a novel and effective strategy for imaging and diagnosing the site of infection.
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Affiliation(s)
- Semra Tasdurmazli
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Turkey
| | - Senanur Dokuz
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Turkey
| | - Berna Erdogdu
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Turkey
| | - Isil Var
- Department of Food Engineering, Faculty of Agricultural, Cukurova University, Sarıcam-Adana, Turkey
| | - John Yu-Shen Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Tulin Ozbek
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Turkey
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Kim HA, Jung HA, Kim TY. Identification of Genes Regulated by IL-1β Using Integrative microRNA and mRNA Genomic Analysis in Human Articular Chondrocytes. JOURNAL OF RHEUMATIC DISEASES 2011. [DOI: 10.4078/jrd.2011.18.4.264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Hyun Ah Kim
- Department of Internal Medicine, Hallym University Sacred Heart Hospital, Anyang, Korea
| | - Hyun A Jung
- Department of Internal Medicine, Hallym University Sacred Heart Hospital, Anyang, Korea
| | - Tae Young Kim
- Department of Orthopedic Surgery, Hallym University Sacred Heart Hospital, Anyang, Korea
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Yamamoto H, Miwa H, Kunishima N. Crystal Structure of Glucose-6-Phosphate Isomerase from Thermus thermophilus HB8 Showing a Snapshot of Active Dimeric State††H.Y. performed structural determination and biochemical and biophysical experiments, and wrote this paper. H.M. contributed to large-scale protein production. N.K. supervised this work. J Mol Biol 2008; 382:747-62. [DOI: 10.1016/j.jmb.2008.07.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 07/11/2008] [Accepted: 07/16/2008] [Indexed: 11/26/2022]
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Lagana A, Goetz JG, Y N, Altschuler Y, Nabi IR. pH-specific sequestration of phosphoglucose isomerase/autocrine motility factor by fibronectin and heparan sulphate. J Cell Sci 2005; 118:4175-85. [PMID: 16141236 DOI: 10.1242/jcs.02538] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Phosphoglucose isomerase (PGI) is a glycolytic enzyme that moonlights as a cytokine under the aliases autocrine motility factor (AMF), neuroleukin and maturation factor. The cytokine function of PGI/AMF targets multiple cell types however mechanisms that regulate and sequester this ubiquitous, circulating cytokine remain largely unidentified. PGI/AMF is shown here to exhibit fibronectin (FN)-dependent cell surface association at both neutral and acid pH. Direct PGI/AMF binding to FN and fluorescence resonance energy transfer (FRET) between PGI/AMF and FN were detected only at pH 5. At neutral pH, the interaction of PGI/AMF with FN is receptor-mediated requiring prior clathrin-dependent endocytosis. PGI/AMF and FN do not co-internalize and PGI/AMF undergoes a second round of endocytosis upon recycling to the plasma membrane indicating that recycling PGI/AMF receptor complexes associate with FN fibrils. Heparan sulphate does not affect cell association of PGI/AMF at neutral pH but enhances the FN-independent cell surface association of PGI/AMF at acid pH identifying two distinct mechanisms for PGI/AMF sequestration under acidic conditions. However, only PGI/AMF sequestration by FN at acid pH was able to stimulate cell motility upon pH neutralization identifying FN as a pH-dependent cytokine trap for PGI/AMF. The multiple ways of cellular association of PGI/AMF may represent acquired mechanisms to regulate and harness the cytokine function of PGI/AMF.
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Affiliation(s)
- Annick Lagana
- Département de pathologie et biologie cellulaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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Boonacker E, Stap J, Koehler A, Van Noorden CJF. The need for metabolic mapping in living cells and tissues. Acta Histochem 2005; 106:89-96. [PMID: 15147629 DOI: 10.1016/j.acthis.2004.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2003] [Revised: 01/16/2004] [Accepted: 01/27/2004] [Indexed: 01/09/2023]
Abstract
The ultimate activity of an enzyme depends on many regulatory steps from transcription of the gene up to complex formation of the enzyme. Therefore, gene expression (mRNA levels) or protein expression (protein levels) are not reliable parameters to predict the functional activity of an enzyme. Activity measurements in cell homogenates or in frozen or fixed (and thus dead) cell preparations are not appropriate either because post-translational regulation mechanisms that exist in living cells may be lost by homogenization or freezing or chemical fixation of cells. Therefore, metabolic mapping in living cells or, in other words, visualization and quantification using microscopy and image analysis of enzyme reactions in living cells is the approach of choice to understand the functional role of enzymes in vivo as is demonstrated here with a number of examples in recent literature.
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Affiliation(s)
- Emil Boonacker
- Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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