1
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Fang N, Wu L, Duan S, Li J. The Structural and Molecular Mechanisms of Mycobacterium tuberculosis Translational Elongation Factor Proteins. Molecules 2024; 29:2058. [PMID: 38731549 PMCID: PMC11085428 DOI: 10.3390/molecules29092058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Targeting translation factor proteins holds promise for developing innovative anti-tuberculosis drugs. During protein translation, many factors cause ribosomes to stall at messenger RNA (mRNA). To maintain protein homeostasis, bacteria have evolved various ribosome rescue mechanisms, including the predominant trans-translation process, to release stalled ribosomes and remove aberrant mRNAs. The rescue systems require the participation of translation elongation factor proteins (EFs) and are essential for bacterial physiology and reproduction. However, they disappear during eukaryotic evolution, which makes the essential proteins and translation elongation factors promising antimicrobial drug targets. Here, we review the structural and molecular mechanisms of the translation elongation factors EF-Tu, EF-Ts, and EF-G, which play essential roles in the normal translation and ribosome rescue mechanisms of Mycobacterium tuberculosis (Mtb). We also briefly describe the structure-based, computer-assisted study of anti-tuberculosis drugs.
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Affiliation(s)
- Ning Fang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
| | - Lingyun Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
| | - Shuyan Duan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang 277160, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China; (N.F.); (L.W.)
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2
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Fang W, Xu J, Wei Z, Wu J, Wu W, Wang Y, Chen S. Enhancing bactericidal activities of ciprofloxacin by targeting the trans-translation system that is involved in stress responses in Klebsiella pneumoniae. Arch Microbiol 2024; 206:154. [PMID: 38478112 DOI: 10.1007/s00203-024-03872-1] [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: 12/03/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 04/16/2024]
Abstract
Although the trans-translation system is a promising target for antcibiotic development, its antibacterial mechanism in Klebsiella pneumoniae (KP) is unclear. Considering that tmRNA was the core component of trans-translation, this study firstly investigated phenotypic changes caused by various environmental stresses in KP lacking trans-translation activities (tmRNA-deleted), and then aimed to evaluate antibacterial activities of the trans-translation-targeting antibiotic combination (tobramycin/ciprofloxacin) in clinical KP isolates based on inhibition activities of aminoglycosides against trans-translation. We found that the tmRNA-deleted strain P4325/ΔssrA was significantly more susceptible than the wild-type KP strain P4325 under environments with hypertonicity (0.5 and 1 M NaCl), hydrogen peroxide (40 mM), and UV irradiation. No significant differences in biofilm formation and survivals under human serum were observed between P4325/ΔssrA and P4325. tmRNA deletion caused twofold lower MIC values for aminoglycosides. As for the membrane permeability, tmRNA deletion increased ethidium bromide (EtBr) uptake of KP in the presence or absence of verapamil and carbonyl cyanide-m-chlorophenylhydrazone (CCCP), decreased EtBr uptake in presence of reserpine in P4325/ΔssrA, and reduced EtBr efflux in P4325/ΔssrA in the presence of CCCP. The time-kill curve and in vitro experiments revealed significant bactericidal activities of the tmRNA-targeting aminoglycoside-based antibiotic combination (tobramycin/ciprofloxacin). Thus, the corresponding tmRNA-targeting antibiotic combinations (aminoglycoside-based) might be effective and promising treatment options against multi-drug resistant KP.
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Affiliation(s)
- Wendong Fang
- Department of Laboratory Medicine, The PLA 307 Clinical College, Fifth Clinical Medical College of Anhui Medical University, Beijing, China
- Department of Laboratory Medicine, Fifth Medical Center of Chinese, PLA General Hospital, Beijing, China
| | - Jie Xu
- Department of Laboratory Medicine, The PLA 307 Clinical College, Fifth Clinical Medical College of Anhui Medical University, Beijing, China
- Department of Laboratory Medicine, Fifth Medical Center of Chinese, PLA General Hospital, Beijing, China
| | - Zilan Wei
- Department of Laboratory Medicine, Fifth Medical Center of Chinese, PLA General Hospital, Beijing, China
- Medical School of Chinese PLA, Beijing, China
| | - Jiahui Wu
- Department of Laboratory Medicine, Fifth Medical Center of Chinese, PLA General Hospital, Beijing, China
- Medical School of Chinese PLA, Beijing, China
| | - Weihui Wu
- Department of Microbiology, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, China.
| | | | - Shuiping Chen
- Department of Laboratory Medicine, The PLA 307 Clinical College, Fifth Clinical Medical College of Anhui Medical University, Beijing, China.
- Department of Laboratory Medicine, Fifth Medical Center of Chinese, PLA General Hospital, Beijing, China.
- Medical School of Chinese PLA, Beijing, China.
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3
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Svetlov MS, Dunand CF, Nakamoto JA, Atkinson GC, Safdari HA, Wilson DN, Vázquez-Laslop N, Mankin AS. Peptidyl-tRNA hydrolase is the nascent chain release factor in bacterial ribosome-associated quality control. Mol Cell 2024; 84:715-726.e5. [PMID: 38183984 DOI: 10.1016/j.molcel.2023.12.002] [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: 08/25/2023] [Revised: 11/08/2023] [Accepted: 12/01/2023] [Indexed: 01/08/2024]
Abstract
Rescuing stalled ribosomes often involves their splitting into subunits. In many bacteria, the resultant large subunits bearing peptidyl-tRNAs are processed by the ribosome-associated quality control (RQC) apparatus that extends the C termini of the incomplete nascent polypeptides with polyalanine tails to facilitate their degradation. Although the tailing mechanism is well established, it is unclear how the nascent polypeptides are cleaved off the tRNAs. We show that peptidyl-tRNA hydrolase (Pth), the known role of which has been to hydrolyze ribosome-free peptidyl-tRNA, acts in concert with RQC factors to release nascent polypeptides from large ribosomal subunits. Dislodging from the ribosomal catalytic center is required for peptidyl-tRNA hydrolysis by Pth. Nascent protein folding may prevent peptidyl-tRNA retraction and interfere with the peptide release. However, oligoalanine tailing makes the peptidyl-tRNA ester bond accessible for Pth-catalyzed hydrolysis. Therefore, the oligoalanine tail serves not only as a degron but also as a facilitator of Pth-catalyzed peptidyl-tRNA hydrolysis.
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Affiliation(s)
- Maxim S Svetlov
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
| | - Clémence F Dunand
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jose A Nakamoto
- Department of Experimental Medicine, University of Lund, 221 00 Lund, Sweden
| | - Gemma C Atkinson
- Department of Experimental Medicine, University of Lund, 221 00 Lund, Sweden
| | - Haaris A Safdari
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
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4
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Marathe N, Nguyen HA, Alumasa JN, Kuzmishin Nagy AB, Vazquez M, Dunham CM, Keiler KC. Antibiotic that inhibits trans-translation blocks binding of EF-Tu to tmRNA but not to tRNA. mBio 2023; 14:e0146123. [PMID: 37681945 PMCID: PMC10653918 DOI: 10.1128/mbio.01461-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 09/09/2023] Open
Abstract
IMPORTANCE Elongation factor thermo-unstable (EF-Tu) is a universally conserved translation factor that mediates productive interactions between tRNAs and the ribosome. In bacteria, EF-Tu also delivers transfer-messenger RNA (tmRNA)-SmpB to the ribosome during trans-translation. We report the first small molecule, KKL-55, that specifically inhibits EF-Tu activity in trans-translation without affecting its activity in normal translation. KKL-55 has broad-spectrum antibiotic activity, suggesting that compounds targeted to the tmRNA-binding interface of EF-Tu could be developed into new antibiotics to treat drug-resistant infections.
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Affiliation(s)
- Neeraja Marathe
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ha An Nguyen
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, Georgia, USA
| | - John N. Alumasa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Alexandra B. Kuzmishin Nagy
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, Georgia, USA
| | - Michael Vazquez
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Christine M. Dunham
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
- Emory Antibiotic Resistance Center (ARC), Emory University, Atlanta, Georgia, USA
| | - Kenneth C. Keiler
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
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5
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Girgis MM, Christodoulides M. Vertebrate and Invertebrate Animal and New In Vitro Models for Studying Neisseria Biology. Pathogens 2023; 12:782. [PMID: 37375472 DOI: 10.3390/pathogens12060782] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/03/2023] [Accepted: 05/18/2023] [Indexed: 06/29/2023] Open
Abstract
The history of Neisseria research has involved the use of a wide variety of vertebrate and invertebrate animal models, from insects to humans. In this review, we itemise these models and describe how they have made significant contributions to understanding the pathophysiology of Neisseria infections and to the development and testing of vaccines and antimicrobials. We also look ahead, briefly, to their potential replacement by complex in vitro cellular models.
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Affiliation(s)
- Michael M Girgis
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Myron Christodoulides
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
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Zhai X, Wu G, Tao X, Yang S, Lv L, Zhu Y, Dong D, Xiang H. Success stories of natural product-derived compounds from plants as multidrug resistance modulators in microorganisms. RSC Adv 2023; 13:7798-7817. [PMID: 36909750 PMCID: PMC9994607 DOI: 10.1039/d3ra00184a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/01/2023] [Indexed: 03/14/2023] Open
Abstract
Microorganisms evolve resistance to antibiotics as a function of evolution. Antibiotics have accelerated bacterial resistance through mutations and acquired resistance through a combination of factors. In some cases, multiple antibiotic-resistant determinants are encoded in these genes, immediately making the recipient organism a "superbug". Current antimicrobials are no longer effective against infections caused by pathogens that have developed antimicrobial resistance (AMR), and the problem has become a crisis. Microorganisms that acquire resistance to chemotherapy (multidrug resistance) are a major obstacle for successful treatments. Pharmaceutical industries should be highly interested in natural product-derived compounds, as they offer new sources of chemical entities for the development of new drugs. Phytochemical research and recent experimental advances are discussed in this review in relation to the antimicrobial efficacy of selected natural product-derived compounds as well as details of synergistic mechanisms and structures. The present review recognizesand amplifies the importance of compounds with natural origins, which can be used to create safer and more effective antimicrobial drugs by combating microorganisms that are resistant to multiple types of drugs.
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Affiliation(s)
- Xiaohan Zhai
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University Dalian China
| | - Guoyu Wu
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University Dalian China
| | - Xufeng Tao
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University Dalian China
| | - Shilei Yang
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University Dalian China
| | - Linlin Lv
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University Dalian China
| | - Yanna Zhu
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University Dalian China
| | - Deshi Dong
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University Dalian China
| | - Hong Xiang
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University Dalian China
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7
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D'Urso G, Guyomar C, Chat S, Giudice E, Gillet R. Insights into the ribosomal trans-translation rescue system: lessons from recent structural studies. FEBS J 2023; 290:1461-1472. [PMID: 35015931 DOI: 10.1111/febs.16349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/27/2021] [Accepted: 01/10/2022] [Indexed: 11/29/2022]
Abstract
The arrest of protein synthesis caused when ribosomes stall on an mRNA lacking a stop codon is a deadly risk for all cells. In bacteria, this situation is remedied by the trans-translation quality control system. Trans-translation occurs because of the synergistic action of two main partners, transfer-messenger RNA (tmRNA) and small protein B (SmpB). These act in complex to monitor protein synthesis, intervening when necessary to rescue stalled ribosomes. During this process, incomplete nascent peptides are tagged for destruction, problematic mRNAs are degraded and the previously stalled ribosomes are recycled. In this 'Structural Snapshot' article, we describe the mechanism at the molecular level, a view updated after the most recent structural studies using cryo-electron microscopy.
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Affiliation(s)
- Gaetano D'Urso
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
| | - Charlotte Guyomar
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
| | - Sophie Chat
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
| | - Emmanuel Giudice
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
| | - Reynald Gillet
- Institut de Génétique et Développement de Rennes (IGDR), CNRS, Univ. Rennes, France
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8
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Complete blood platelet and lymphocyte ratios increase diagnostic accuracy of periprosthetic joint infection following total hip arthroplasty. Arch Orthop Trauma Surg 2023; 143:1441-1449. [PMID: 35098356 DOI: 10.1007/s00402-021-04309-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 12/04/2021] [Indexed: 02/09/2023]
Abstract
INTRODUCTION Systemically, changes in serum platelet to lymphocyte ratio (PLR), platelet count to mean platelet volume ratio (PVR), neutrophil to lymphocyte ratio (NLR) and monocyte to lymphocyte (MLR) represent primary responses to early inflammation and infection. This study aimed to determine whether PLR, PVR, NLR, and MLR can be useful in diagnosing periprosthetic joint infection (PJI) in total hip arthroplasty (THA) patients. METHODS A total of 464 patients that underwent revision THA with calculable PLR, PVR, NLR, and MLR in 2 groups was evaluated: 1) 191 patients with a pre-operative diagnosis of PJI, and 2) 273 matched patients treated for revision THA for aseptic complications. RESULTS The sensitivity and specificity of PLR combined with erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), synovial white blood cell count (WBC) and synovial polymorphonuclear leukocytes (PMN) (97.9%; 98.5%) is significantly higher than only ESR combined with CRP, synovial WBC and synovial PMN (94.2%; 94.5%; p < 0.01). The sensitivity and specificity of PVR combined with ESR, CRP and synovial WBC, and synovial PMN (98.4%; 98.2%) is higher than only ESR combined with CRP, synovial WBC and synovial PMN (94.2%; 94.5%; p < 0.01). CONCLUSION The study results demonstrate that both PLR and PVR calculated from complete blood counts when combined with serum and synovial fluid markers have increased diagnostic sensitivity and specificity in diagnosing periprosthetic joint infection in THA patients. LEVEL OF EVIDENCE III, case-control retrospective analysis.
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Klemt C, Padmanabha A, Esposito JG, Laurencin S, Smith EJ, Kwon YM. Elevated ESR and CRP Prior to Second-Stage Reimplantation Knee Revision Surgery for Periprosthetic Joint Infection Are Associated with Increased Reinfection Rates. J Knee Surg 2023; 36:354-361. [PMID: 34375998 DOI: 10.1055/s-0041-1733902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although two-stage revision surgery is considered as the most effective treatment for managing chronic periprosthetic joint infection (PJI), there is no current consensus on the predictors of optimal timing to second-stage reimplantation. This study aimed to compare clinical outcomes between patients with elevated erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) prior to second-stage reimplantation and those with normalized ESR and CRP prior to second-stage reimplantation. We retrospectively reviewed 198 patients treated with two-stage revision total knee arthroplasty for chronic PJI. Cohorts included patients with: (1) normal level of serum ESR and CRP (n = 96) and (2) elevated level of serum ESR and CRP prior to second-stage reimplantation (n = 102). Outcomes including reinfection rates and readmission rates were compared between both cohorts. At a mean follow-up of 4.4 years (2.8-6.5 years), the elevated ESR and CRP cohort demonstrated significantly higher reinfection rates compared with patients with normalized ESR and CRP prior to second-stage reimplantation (33.3% vs. 14.5%, p < 0.01). Patients with both elevated ESR and CRP demonstrated significantly higher reinfection rates, when compared with patients with elevated ESR and normalized CRP (33.3% vs. 27.6%, p = 0.02) as well as normalized ESR and elevated CRP (33.3% vs. 26.3%, p < 0.01). This study demonstrates that elevated serum ESR and/or CRP levels prior to reimplantation in two-stage knee revision surgery for chronic PJI are associated with increased reinfection rate after surgery. Elevation of both ESR and CRP were associated with a higher risk of reinfection compared with elevation of either ESR or CRP, suggesting the potential benefits of normalizing ESR and CRP prior to reimplantation in treatment of chronic PJI.
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Affiliation(s)
- Christian Klemt
- Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Anand Padmanabha
- Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - John G Esposito
- Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Samuel Laurencin
- Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Evan J Smith
- Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Young-Min Kwon
- Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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10
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Chauhan S, Marotta NJ, Karls AC, Weinert EE. Binding of 2',3'-Cyclic Nucleotide Monophosphates to Bacterial Ribosomes Inhibits Translation. ACS CENTRAL SCIENCE 2022; 8:1518-1526. [PMID: 36439312 PMCID: PMC9686202 DOI: 10.1021/acscentsci.2c00681] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Indexed: 06/16/2023]
Abstract
The intracellular small molecules 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) have recently been rediscovered within both prokaryotes and eukaryotes. Studies in bacteria have demonstrated that 2',3'-cNMP levels affect bacterial phenotypes, such as biofilm formation, motility, and growth, and modulate expression of numerous genes, suggesting that 2',3'-cNMP levels are monitored by cells. In this study, 2',3'-cNMP-linked affinity chromatography resins were used to identify Escherichia coli proteins that bind 2',3'-cNMPs, with the top hits including all of the ribosomal proteins, and to confirm direct binding of purified ribosomes. Using in vitro translation assays, we have demonstrated that 2',3'-cNMPs inhibit translation at concentrations found in amino acid-starved cells. In addition, a genetically encoded tool to increase cellular 2',3'-cNMP levels was developed and was demonstrated to decrease E. coli growth rates. Taken together, this work suggests a mechanism for 2',3-cNMP levels to modulate bacterial phenotypes by rapidly affecting translation.
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Affiliation(s)
- Shikha
S. Chauhan
- Department
of Biochemistry and Molecular Biology, Penn
State University, University
Park, Pennsylvania 16802, United States
| | - Nick J. Marotta
- Graduate
Program in Molecular, Cellular, and Integrative Biosciences, Penn State University, University Park, Pennsylvania 16802, United States
| | - Anna C. Karls
- Department
of Microbiology, University of Georgia, Athens, Georgia 30602, United States
| | - Emily E. Weinert
- Department
of Biochemistry and Molecular Biology, Penn
State University, University
Park, Pennsylvania 16802, United States
- Department
of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
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Abstract
Despite having a highly reduced genome, Chlamydia trachomatis undergoes a complex developmental cycle in which the bacteria differentiate between the following two functionally and morphologically distinct forms: the infectious, nonreplicative elementary body (EB) and the noninfectious, replicative reticulate body (RB). The transitions between EBs and RBs are not mediated by division events that redistribute intracellular proteins. Rather, both primary (EB to RB) and secondary (RB to EB) differentiation likely require bulk protein turnover. One system for targeted protein degradation is the trans-translation system for ribosomal rescue, where polypeptides stalled during translation are marked with an SsrA tag encoded by a hybrid tRNA-mRNA, tmRNA. ClpX recognizes the SsrA tag, leading to ClpXP-mediated degradation. We hypothesize that ClpX functions in chlamydial differentiation through targeted protein degradation. We found that mutation of a key residue (R230A) within the specific motif in ClpX associated with the recognition of SsrA-tagged substrates resulted in abrogated secondary differentiation while not reducing chlamydial replication or developmental cycle progression as measured by transcripts. Furthermore, inhibition of trans-translation through chemical and targeted genetic approaches also impeded chlamydial development. Knockdown of tmRNA and subsequent complementation with an allele mutated in the SsrA tag closely phenocopied the overexpression of ClpXR230A, thus suggesting that ClpX recognition of SsrA-tagged substrates plays a critical function in secondary differentiation. Taken together, these data provide mechanistic insight into the requirements for transitions between chlamydial developmental forms. IMPORTANCE Chlamydia trachomatis is the leading cause of bacterial sexually transmitted infections and preventable infectious blindness. This unique organism undergoes developmental transitions between infectious, nondividing forms and noninfectious, dividing forms. Therefore, the chlamydial developmental cycle is an attractive target for Chlamydia-specific antibiotics, which would minimize effects of broad-spectrum antibiotics on the spread of antibiotic resistance in other organisms. However, the lack of knowledge about chlamydial development on a molecular level impedes the identification of specific, druggable targets. This work describes a mechanism through which both the fundamental processes of trans-translation and proteomic turnover by ClpXP contribute to chlamydial differentiation, a critical facet of chlamydial growth and survival. Given the almost universal presence of trans-translation and ClpX in eubacteria, this mechanism may be conserved in developmental cycles of other bacterial species. Additionally, this study expands the fields of trans-translation and Clp proteases by emphasizing the functional diversity of these systems throughout bacterial evolution.
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Dhumal D, Maron B, Malach E, Lyu Z, Ding L, Marson D, Laurini E, Tintaru A, Ralahy B, Giorgio S, Pricl S, Hayouka Z, Peng L. Dynamic self-assembling supramolecular dendrimer nanosystems as potent antibacterial candidates against drug-resistant bacteria and biofilms. NANOSCALE 2022; 14:9286-9296. [PMID: 35649277 DOI: 10.1039/d2nr02305a] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The alarming and prevailing antibiotic resistance crisis urgently calls for innovative "outside of the box" antibacterial agents, which can differ substantially from conventional antibiotics. In this context, we have established antibacterial candidates based on dynamic supramolecular dendrimer nanosystems self-assembled with amphiphilic dendrimers composed of a long hydrophobic alkyl chain and a small hydrophilic poly(amidoamine) dendron bearing distinct terminal functionalities. Remarkably, the amphiphilic dendrimer with amine terminals exhibited strong antibacterial activity against both Gram-positive and Gram-negative as well as drug-resistant bacteria, and prevented biofilm formation. Multidisciplinary studies combining experimental approaches and computer modelling together demonstrate that the dendrimer interacts and binds via electrostatic interactions with the bacterial membrane, where it becomes enriched and then dynamically self-assembles into supramolecular nanoassemblies for stronger and multivalent interactions. These, in turn, rapidly promote the insertion of the hydrophobic dendrimer tail into the bacterial membrane thereby inducing bacterial cell lysis and constituting powerful antibacterial activity. Our study presents a novel concept for creating nanotechnology-based antibacterial candidates via dynamic self-assembly and offers a new perspective for combatting recalcitrant bacterial infection.
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Affiliation(s)
- Dinesh Dhumal
- Aix Marseille Univ, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), UMR 7325, Equipe Labelisée Ligue Contre le Cancer, Parc Scientifique et Technologique de Luminy, Marseille, France.
| | - Bar Maron
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Einav Malach
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Zhenbin Lyu
- Aix Marseille Univ, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), UMR 7325, Equipe Labelisée Ligue Contre le Cancer, Parc Scientifique et Technologique de Luminy, Marseille, France.
| | - Ling Ding
- Aix Marseille Univ, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), UMR 7325, Equipe Labelisée Ligue Contre le Cancer, Parc Scientifique et Technologique de Luminy, Marseille, France.
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Trieste, Italy
| | - Aura Tintaru
- Aix Marseille Univ, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), UMR 7325, Equipe Labelisée Ligue Contre le Cancer, Parc Scientifique et Technologique de Luminy, Marseille, France.
| | - Brigino Ralahy
- Aix Marseille Univ, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), UMR 7325, Equipe Labelisée Ligue Contre le Cancer, Parc Scientifique et Technologique de Luminy, Marseille, France.
| | - Suzanne Giorgio
- Aix Marseille Univ, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), UMR 7325, Equipe Labelisée Ligue Contre le Cancer, Parc Scientifique et Technologique de Luminy, Marseille, France.
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Trieste, Italy
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Zvi Hayouka
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Ling Peng
- Aix Marseille Univ, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), UMR 7325, Equipe Labelisée Ligue Contre le Cancer, Parc Scientifique et Technologique de Luminy, Marseille, France.
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13
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Naclerio GA, Onyedibe KI, Karanja CW, Aryal UK, Sintim HO. Comparative Studies to Uncover Mechanisms of Action of N-(1,3,4-Oxadiazol-2-yl)benzamide Containing Antibacterial Agents. ACS Infect Dis 2022; 8:865-877. [PMID: 35297603 PMCID: PMC9188027 DOI: 10.1021/acsinfecdis.1c00613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Drug-resistant bacterial pathogens still cause high levels of mortality annually despite the availability of many antibiotics. Methicillin-resistant Staphylococcus aureus (MRSA) is especially problematic, and the rise in resistance to front-line treatments like vancomycin and linezolid calls for new chemical modalities to treat chronic and relapsing MRSA infections. Halogenated N-(1,3,4-oxadiazol-2-yl)benzamides are an interesting class of antimicrobial agents, which have been described by multiple groups to be effective against different bacterial pathogens. The modes of action of a few N-(1,3,4-oxadiazol-2-yl)benzamides have been elucidated. For example, oxadiazoles KKL-35 and MBX-4132 have been described as inhibitors of trans-translation (a ribosome rescue pathway), while HSGN-94 was shown to inhibit lipoteichoic acid (LTA). However, other similarly halogenated N-(1,3,4-oxadiazol-2-yl)benzamides neither inhibit trans-translation nor LTA biosynthesis but are potent antimicrobial agents. For example, HSGN-220, -218, and -144 are N-(1,3,4-oxadiazol-2-yl)benzamides that are modified with OCF3, SCF3, or SF5 and have remarkable minimum inhibitory concentrations ranging from 1 to 0.06 μg/mL against MRSA clinical isolates and show a low propensity to develop resistance to MRSA over 30 days. The mechanism of action of these highly potent oxadiazoles is however unknown. To provide insights into how these halogenated N-(1,3,4-oxadiazol-2-yl)benzamides inhibit bacterial growth, we performed global proteomics and RNA expression analysis of some essential genes of S. aureus treated with HSGN-220, -218, and -144. These studies revealed that the oxadiazoles HSGN-220, -218, and -144 are multitargeting antibiotics that regulate menaquinone biosynthesis and other essential proteins like DnaX, Pol IIIC, BirA, LexA, and DnaC. In addition, these halogenated N-(1,3,4-oxadiazol-2-yl)benzamides were able to depolarize bacterial membranes and regulate siderophore biosynthesis and heme regulation. Iron starvation appears to be part of the mechanism of action that led to bacterial killing. This study demonstrates that N-(1,3,4-oxadiazol-2-yl)benzamides are indeed privileged scaffolds for the development of antibacterial agents and that subtle modifications lead to changes to the mechanism of action.
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Affiliation(s)
- George A. Naclerio
- Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Kenneth I. Onyedibe
- Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Institute for Inflammation, Immunology, and Infectious Diseases, West Lafayette, Indiana 47907, United States
| | - Caroline W. Karanja
- Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Uma K. Aryal
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907, United States
| | - Herman O. Sintim
- Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Institute for Inflammation, Immunology, and Infectious Diseases, West Lafayette, Indiana 47907, United States
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14
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Scurtu LG, Jinga V, Simionescu O. Fascinating Molecular and Immune Escape Mechanisms in the Treatment of STIs (Syphilis, Gonorrhea, Chlamydia, and Herpes Simplex). Int J Mol Sci 2022; 23:ijms23073550. [PMID: 35408911 PMCID: PMC8998805 DOI: 10.3390/ijms23073550] [Citation(s) in RCA: 2] [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: 02/19/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 02/04/2023] Open
Abstract
The incidence of syphilis, gonorrhea, chlamydia, and herpes simplex has increased over the last decade, despite the numerous prevention strategies. Worldwide scientists report a surge in drug-resistant infections, particularly in immunocompromised patients. Antigenic variations in syphilis enable long-term infection, but benzathine penicillin G maintains its efficiency, whereas macrolides should be recommended with caution. Mupirocin and zoliflodacin were recently introduced as therapies against ceftriaxone-resistant gonococcus, which poses a larger global threat. The gastrointestinal and prostatic potential reservoirs of Chlamydia trachomatis may represent the key towards complete eradication. Similar to syphilis, macrolides resistance has to be considered in genital chlamydiosis. Acyclovir-resistant HSV may respond to the novel helicase-primase inhibitors and topical imiquimod, particularly in HIV-positive patients. Novel drugs can overcome these challenges while nanocarriers enhance their potency, particularly in mucosal areas. This review summarizes the most recent and valuable discoveries regarding the immunopathogenic mechanisms of these sexually transmitted infections and discusses the challenges and opportunities of the novel molecules and nanomaterials.
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Affiliation(s)
- Lucian G. Scurtu
- Department of Dermatology I, Colentina Clinical Hospital, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020125 Bucharest, Romania;
| | - Viorel Jinga
- Department of Urology, Clinical Hospital Prof. Dr. Th. Burghele, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 030167 Bucharest, Romania;
| | - Olga Simionescu
- Department of Dermatology I, Colentina Clinical Hospital, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020125 Bucharest, Romania;
- Correspondence:
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15
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Campos-Silva R, D’Urso G, Delalande O, Giudice E, Macedo AJ, Gillet R. Trans-Translation Is an Appealing Target for the Development of New Antimicrobial Compounds. Microorganisms 2021; 10:3. [PMID: 35056452 PMCID: PMC8778911 DOI: 10.3390/microorganisms10010003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/09/2021] [Accepted: 12/16/2021] [Indexed: 01/06/2023] Open
Abstract
Because of the ever-increasing multidrug resistance in microorganisms, it is crucial that we find and develop new antibiotics, especially molecules with different targets and mechanisms of action than those of the antibiotics in use today. Translation is a fundamental process that uses a large portion of the cell's energy, and the ribosome is already the target of more than half of the antibiotics in clinical use. However, this process is highly regulated, and its quality control machinery is actively studied as a possible target for new inhibitors. In bacteria, ribosomal stalling is a frequent event that jeopardizes bacterial wellness, and the most severe form occurs when ribosomes stall at the 3'-end of mRNA molecules devoid of a stop codon. Trans-translation is the principal and most sophisticated quality control mechanism for solving this problem, which would otherwise result in inefficient or even toxic protein synthesis. It is based on the complex made by tmRNA and SmpB, and because trans-translation is absent in eukaryotes, but necessary for bacterial fitness or survival, it is an exciting and realistic target for new antibiotics. Here, we describe the current and future prospects for developing what we hope will be a novel generation of trans-translation inhibitors.
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Affiliation(s)
- Rodrigo Campos-Silva
- CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, University of Rennes, 35000 Rennes, France; (R.C.-S.); (G.D.); (O.D.); (E.G.)
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia and Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90610-000, Brazil;
| | - Gaetano D’Urso
- CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, University of Rennes, 35000 Rennes, France; (R.C.-S.); (G.D.); (O.D.); (E.G.)
| | - Olivier Delalande
- CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, University of Rennes, 35000 Rennes, France; (R.C.-S.); (G.D.); (O.D.); (E.G.)
| | - Emmanuel Giudice
- CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, University of Rennes, 35000 Rennes, France; (R.C.-S.); (G.D.); (O.D.); (E.G.)
| | - Alexandre José Macedo
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia and Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90610-000, Brazil;
| | - Reynald Gillet
- CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, University of Rennes, 35000 Rennes, France; (R.C.-S.); (G.D.); (O.D.); (E.G.)
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16
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Abstract
Translation of the genetic information into proteins, performed by the ribosome, is a key cellular process in all organisms. Translation usually proceeds smoothly, but, unfortunately, undesirable events can lead to stalling of translating ribosomes. To rescue these faulty arrested ribosomes, bacterial cells possess three well-characterized quality control systems, tmRNA, ArfA, and ArfB. Recently, an additional ribosome rescue mechanism has been discovered in Bacillus subtilis. In contrast to the "canonical" systems targeting the 70S bacterial ribosome, this latter mechanism operates by first splitting the ribosome into the small (30S) and large (50S) subunits to then clearing the resultant jammed large subunit from the incomplete nascent polypeptide. Here, I will discuss the recent microbiological, biochemical, and structural data regarding functioning of this novel rescue system.
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Affiliation(s)
- Maxim S Svetlov
- Center for Biomolecular Sciences, Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
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17
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Connolly KL, Pilligua-Lucas M, Gomez C, Costenoble-Caherty AC, Soc A, Underwood K, Macintyre AN, Sempowski GD, Jerse AE. Preclinical Testing of Vaccines and Therapeutics for Gonorrhea in Female Mouse Models of Lower and Upper Reproductive Tract Infection. J Infect Dis 2021; 224:S152-S160. [PMID: 34396408 DOI: 10.1093/infdis/jiab211] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Murine models of Neisseria gonorrhoeae lower reproductive tract infection are valuable systems for studying N. gonorrhoeae adaptation to the female host and immune responses to infection. These models have also accelerated preclinical testing of candidate therapeutic and prophylactic products against gonorrhea. However, because N. gonorrhoeae infection is restricted to the murine cervicovaginal region, there is a need for an in vivo system for translational work on N. gonorrhoeae pelvic inflammatory disease (PID). Here we discuss the need for well-characterized preclinical upper reproductive tract infection models for developing candidate products against N. gonorrhoeae PID, and report a refinement of the gonorrhea mouse model that supports sustained upper reproductive tract infection. To establish this new model for vaccine testing, we also tested the licensed meningococcal 4CMenB vaccine, which cross-protects against murine N. gonorrhoeae lower reproductive tract infection, for efficacy against N. gonorrhoeae in the endometrium and oviducts following transcervical or vaginal challenge.
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Affiliation(s)
- Kristie L Connolly
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | - Michelle Pilligua-Lucas
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | - Carolina Gomez
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | | | - Anthony Soc
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | - Knashka Underwood
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | - Andrew N Macintyre
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Ann E Jerse
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
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18
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Structures of tmRNA and SmpB as they transit through the ribosome. Nat Commun 2021; 12:4909. [PMID: 34389707 PMCID: PMC8363625 DOI: 10.1038/s41467-021-24881-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/13/2021] [Indexed: 01/01/2023] Open
Abstract
In bacteria, trans-translation is the main rescue system, freeing ribosomes stalled on defective messenger RNAs. This mechanism is driven by small protein B (SmpB) and transfer-messenger RNA (tmRNA), a hybrid RNA known to have both a tRNA-like and an mRNA-like domain. Here we present four cryo-EM structures of the ribosome during trans-translation at resolutions from 3.0 to 3.4 Å. These include the high-resolution structure of the whole pre-accommodated state, as well as structures of the accommodated state, the translocated state, and a translocation intermediate. Together, they shed light on the movements of the tmRNA-SmpB complex in the ribosome, from its delivery by the elongation factor EF-Tu to its passage through the ribosomal A and P sites after the opening of the B1 bridges. Additionally, we describe the interactions between the tmRNA-SmpB complex and the ribosome. These explain why the process does not interfere with canonical translation.
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