1
|
Danti G, Popella L, Vogel J, Maric HM. High-Throughput Tiling of Essential mRNAs Increases Potency of Antisense Antibiotics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025:e2504284. [PMID: 40304263 DOI: 10.1002/advs.202504284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2025] [Revised: 04/08/2025] [Indexed: 05/02/2025]
Abstract
Antimicrobial resistance is outpacing drug discovery, creating an urgent need for precision-based strategies to counteract resistant pathogens. Peptide nucleic acid (PNA)-based antisense molecules offer a promising approach by selectively inhibiting essential bacterial mRNAs, but their design rules for optimal efficacy remain incompletely understood. Here, a scalable high-throughput platform is developed for the nanomolar-scale one-shot synthesis of PNAs as carrier peptide conjugates (PPNAs). Parallel synthesis of up to 1,536 PPNAs composed of up to 21 PNA or peptide building blocks enabled systematic, base-by-base analysis of RNA hybridization, mRNA inhibition, and antimicrobial activity across nine essential genes in uropathogenic Escherichia coli. The accuracy and robustness of this high-throughput tiling platform are demonstrated through in-depth analysis of the acpP mRNA and identify potent antisense inhibitors of rpsH, ftsZ, and murA. This approach provides an efficient and scalable route to design and optimize PNA-based antimicrobials, facilitating empirical testing across diverse bacterial targets. By enabling large-scale exploration of the relevant mRNA sequence space, the sequence tiling platform accelerates the discovery of antisense-based antimicrobials, offering a scalable strategy to develop precision therapies against various pathogens and combat resistance.
Collapse
Affiliation(s)
- Giorgia Danti
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97080, Würzburg, Germany
| | - Linda Popella
- Institute for Molecular Infection Biology (IMIB), Faculty of Medicine, University of Würzburg, 97080, Würzburg, Germany
- Cluster for Nucleic Acid Therapeutics Munich (CNATM), 80802, Munich, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Faculty of Medicine, University of Würzburg, 97080, Würzburg, Germany
- Cluster for Nucleic Acid Therapeutics Munich (CNATM), 80802, Munich, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080, Würzburg, Germany
| | - Hans M Maric
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97080, Würzburg, Germany
| |
Collapse
|
2
|
Parkhill SL, Johnson EO. Integrating bacterial molecular genetics with chemical biology for renewed antibacterial drug discovery. Biochem J 2024; 481:839-864. [PMID: 38958473 PMCID: PMC11346456 DOI: 10.1042/bcj20220062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
The application of dyes to understanding the aetiology of infection inspired antimicrobial chemotherapy and the first wave of antibacterial drugs. The second wave of antibacterial drug discovery was driven by rapid discovery of natural products, now making up 69% of current antibacterial drugs. But now with the most prevalent natural products already discovered, ∼107 new soil-dwelling bacterial species must be screened to discover one new class of natural product. Therefore, instead of a third wave of antibacterial drug discovery, there is now a discovery bottleneck. Unlike natural products which are curated by billions of years of microbial antagonism, the vast synthetic chemical space still requires artificial curation through the therapeutics science of antibacterial drugs - a systematic understanding of how small molecules interact with bacterial physiology, effect desired phenotypes, and benefit the host. Bacterial molecular genetics can elucidate pathogen biology relevant to therapeutics development, but it can also be applied directly to understanding mechanisms and liabilities of new chemical agents with new mechanisms of action. Therefore, the next phase of antibacterial drug discovery could be enabled by integrating chemical expertise with systematic dissection of bacterial infection biology. Facing the ambitious endeavour to find new molecules from nature or new-to-nature which cure bacterial infections, the capabilities furnished by modern chemical biology and molecular genetics can be applied to prospecting for chemical modulators of new targets which circumvent prevalent resistance mechanisms.
Collapse
Affiliation(s)
- Susannah L. Parkhill
- Systems Chemical Biology of Infection and Resistance Laboratory, The Francis Crick Institute, London, U.K
- Faculty of Life Sciences, University College London, London, U.K
| | - Eachan O. Johnson
- Systems Chemical Biology of Infection and Resistance Laboratory, The Francis Crick Institute, London, U.K
- Faculty of Life Sciences, University College London, London, U.K
- Department of Chemistry, Imperial College, London, U.K
- Department of Chemistry, King's College London, London, U.K
| |
Collapse
|
3
|
MacNair CR, Rutherford ST, Tan MW. Alternative therapeutic strategies to treat antibiotic-resistant pathogens. Nat Rev Microbiol 2024; 22:262-275. [PMID: 38082064 DOI: 10.1038/s41579-023-00993-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2023] [Indexed: 04/19/2024]
Abstract
Resistance threatens to render antibiotics - which are essential for modern medicine - ineffective, thus posing a threat to human health. The discovery of novel classes of antibiotics able to overcome resistance has been stalled for decades, with the developmental pipeline relying almost entirely on variations of existing chemical scaffolds. Unfortunately, this approach has been unable to keep pace with resistance evolution, necessitating new therapeutic strategies. In this Review, we highlight recent efforts to discover non-traditional antimicrobials, specifically describing the advantages and limitations of antimicrobial peptides and macrocycles, antibodies, bacteriophages and antisense oligonucleotides. These approaches have the potential to stem the tide of resistance by expanding the physicochemical property space and target spectrum occupied by currently approved antibiotics.
Collapse
Affiliation(s)
- Craig R MacNair
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
| |
Collapse
|
4
|
Mallik S, Dodia H, Ghosh A, Srinivasan R, Good L, Raghav SK, Beuria TK. FtsE, the Nucleotide Binding Domain of the ABC Transporter Homolog FtsEX, Regulates Septal PG Synthesis in E. coli. Microbiol Spectr 2023; 11:e0286322. [PMID: 37014250 PMCID: PMC10269673 DOI: 10.1128/spectrum.02863-22] [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: 08/01/2022] [Accepted: 03/11/2023] [Indexed: 04/05/2023] Open
Abstract
The peptidoglycan (PG) layer, a crucial component of the tripartite E.coli envelope, is required to maintain cellular integrity, protecting the cells from mechanical stress resulting from intracellular turgor pressure. Thus, coordinating synthesis and hydrolysis of PG during cell division (septal PG) is crucial for bacteria. The FtsEX complex directs septal PG hydrolysis through the activation of amidases; however, the mechanism and regulation of septal PG synthesis are unclear. In addition, how septal PG synthesis and hydrolysis are coordinated has remained unclear. Here, we have shown that overexpression of FtsE leads to a mid-cell bulging phenotype in E.coli, which is different from the filamentous phenotype observed during overexpression of other cell division proteins. Silencing of the common PG synthesis genes murA and murB reduced bulging, confirming that this phenotype is due to excess PG synthesis. We further demonstrated that septal PG synthesis is independent of FtsE ATPase activity and FtsX. These observations and previous results suggest that FtsEX plays a role during septal PG hydrolysis, whereas FtsE alone coordinates septal PG synthesis. Overall, our study findings support a model in which FtsE plays a role in coordinating septal PG synthesis with bacterial cell division. IMPORTANCE The peptidoglycan (PG) layer is an essential component of the E.coli envelope that is required to maintain cellular shape and integrity. Thus, coordinating PG synthesis and hydrolysis at the mid-cell (septal PG) is crucial during bacterial division. The FtsEX complex directs septal PG hydrolysis through the activation of amidases; however, its role in regulation of septal PG synthesis is unclear. Here, we demonstrate that overexpression of FtsE in E.coli leads to a mid-cell bulging phenotype due to excess PG synthesis. This phenotype was reduced upon silencing of common PG synthesis genes murA and murB. We further demonstrated that septal PG synthesis is independent of FtsE ATPase activity and FtsX. These observations suggest that the FtsEX complex plays a role during septal PG hydrolysis, whereas FtsE alone coordinates septal PG synthesis. Our study indicates that FtsE plays a role in coordinating septal PG synthesis with bacterial cell division.
Collapse
Affiliation(s)
- Sunanda Mallik
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Hiren Dodia
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
- Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Arup Ghosh
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
| | - Ramanujam Srinivasan
- National Institute of Science Education and Research, Bhubaneswar, Odisha, India
| | - Liam Good
- The Royal Veterinary College, University of London, London, United Kingdom
| | | | | |
Collapse
|
5
|
Popella L, Jung J, Do PT, Hayward RJ, Barquist L, Vogel J. Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli. Nucleic Acids Res 2022; 50:6435-6452. [PMID: 35687096 PMCID: PMC9226493 DOI: 10.1093/nar/gkac362] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/05/2022] [Accepted: 06/08/2022] [Indexed: 12/13/2022] Open
Abstract
Antisense peptide nucleic acids (PNAs) that target mRNAs of essential bacterial genes exhibit specific bactericidal effects in several microbial species, but our mechanistic understanding of PNA activity and their target gene spectrum is limited. Here, we present a systematic analysis of PNAs targeting 11 essential genes with varying expression levels in uropathogenic Escherichia coli (UPEC). We demonstrate that UPEC is susceptible to killing by peptide-conjugated PNAs, especially when targeting the widely-used essential gene acpP. Our evaluation yields three additional promising target mRNAs for effective growth inhibition, i.e.dnaB, ftsZ and rpsH. The analysis also shows that transcript abundance does not predict target vulnerability and that PNA-mediated growth inhibition is not universally associated with target mRNA depletion. Global transcriptomic analyses further reveal PNA sequence-dependent but also -independent responses, including the induction of envelope stress response pathways. Importantly, we show that 9mer PNAs are generally as effective in inhibiting bacterial growth as their 10mer counterparts. Overall, our systematic comparison of a range of PNAs targeting mRNAs of different essential genes in UPEC suggests important features for PNA design, reveals a general bacterial response to PNA conjugates and establishes the feasibility of using PNA antibacterials to combat UPEC.
Collapse
Affiliation(s)
- Linda Popella
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080, Würzburg, Germany
| | - Jakob Jung
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080, Würzburg, Germany
| | - Phuong Thao Do
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080, Würzburg, Germany
| | - Regan J Hayward
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080, Würzburg, Germany
- Faculty of Medicine, University of Würzburg, D-97080, Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080, Würzburg, Germany
- Faculty of Medicine, University of Würzburg, D-97080, Würzburg, Germany
| |
Collapse
|
6
|
Hogan AM, Cardona ST. Gradients in gene essentiality reshape antibacterial research. FEMS Microbiol Rev 2022; 46:fuac005. [PMID: 35104846 PMCID: PMC9075587 DOI: 10.1093/femsre/fuac005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 01/14/2022] [Accepted: 01/24/2022] [Indexed: 02/03/2023] Open
Abstract
Essential genes encode the processes that are necessary for life. Until recently, commonly applied binary classifications left no space between essential and non-essential genes. In this review, we frame bacterial gene essentiality in the context of genetic networks. We explore how the quantitative properties of gene essentiality are influenced by the nature of the encoded process, environmental conditions and genetic background, including a strain's distinct evolutionary history. The covered topics have important consequences for antibacterials, which inhibit essential processes. We argue that the quantitative properties of essentiality can thus be used to prioritize antibacterial cellular targets and desired spectrum of activity in specific infection settings. We summarize our points with a case study on the core essential genome of the cystic fibrosis pathobiome and highlight avenues for targeted antibacterial development.
Collapse
Affiliation(s)
- Andrew M Hogan
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Winnipeg, Manitoba R3T 2N2, Canada
| | - Silvia T Cardona
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
| |
Collapse
|
7
|
Patil NA, Thombare VJ, Li R, He X, Lu J, Yu HH, Wickremasinghe H, Pamulapati K, Azad MAK, Velkov T, Roberts KD, Li J. An Efficient Approach for the Design and Synthesis of Antimicrobial Peptide-Peptide Nucleic Acid Conjugates. Front Chem 2022; 10:843163. [PMID: 35372270 PMCID: PMC8964499 DOI: 10.3389/fchem.2022.843163] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/16/2022] [Indexed: 01/23/2023] Open
Abstract
Peptide-Peptide Nucleic Acid (PNA) conjugates targeting essential bacterial genes have shown significant potential in developing novel antisense antimicrobials. The majority of efforts in this area are focused on identifying different PNA targets and the selection of peptides to deliver the peptide-PNA conjugates to Gram-negative bacteria. Notably, the selection of a linkage strategy to form peptide-PNA conjugate plays an important role in the effective delivery of PNAs. Recently, a unique Cysteine- 2-Cyanoisonicotinamide (Cys-CINA) click chemistry has been employed for the synthesis of cyclic peptides. Considering the high selectivity of this chemistry, we investigated the efficiency of Cys-CINA conjugation to synthesize novel antimicrobial peptide-PNA conjugates. The PNA targeting acyl carrier protein gene (acpP), when conjugated to the membrane-active antimicrobial peptides (polymyxin), showed improvement in antimicrobial activity against multidrug-resistant Gram-negative Acinetobacter baumannii. Thus, indicating that the Cys-CINA conjugation is an effective strategy to link the antisense oligonucleotides with antimicrobial peptides. Therefore, the Cys-CINA conjugation opens an exciting prospect for antimicrobial drug development.
Collapse
Affiliation(s)
- Nitin A. Patil
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- *Correspondence: Nitin A. Patil,
| | - Varsha J. Thombare
- Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC, Australia
| | - Rong Li
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Xiaoji He
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Jing Lu
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC, Australia
| | - Heidi H. Yu
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Hasini Wickremasinghe
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Kavya Pamulapati
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Mohammad A. K. Azad
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Tony Velkov
- Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC, Australia
| | - Kade D. Roberts
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Jian Li
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| |
Collapse
|
8
|
Potentiating the Anti-Tuberculosis Efficacy of Peptide Nucleic Acids through Combinations with Permeabilizing Drugs. Microbiol Spectr 2022; 10:e0126221. [PMID: 35171048 PMCID: PMC8849056 DOI: 10.1128/spectrum.01262-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The emergence of antimicrobial resistance warrants for the development of improved treatment approaches. In this regard, peptide nucleic acids (PNAs) have shown great promise, exhibiting antibiotic properties through the targeting of cellular nucleic acids. We aimed to study the efficacy of PNA as an anti-tuberculosis agent. Since the efficacy of PNA is limited by its low penetration into the cell, we also investigated combinatorial treatments using permeabilizing drugs to improve PNA efficacy. Various concentrations of anti-inhA PNA, permeabilizing drugs, and their combinations were screened against extracellular and intracellular mycobacteria.0.625 to 5 μM anti-inhA PNA was observed to merely inhibit the growth of extracellular M. smegmatis, while low intracellular bacterial load was reduced by 2 or 2.5 log-fold when treated with 2.5 or 5 μM PNA, respectively. Anti-inhA PNA against M. tuberculosis H37Ra exhibited bactericidal properties at 2.5 and 5 μM and enabled a slight reduction in intracellular M. tuberculosis at concentrations from 2.5 to 20 μM. Of the permeabilizing drugs tested, ethambutol showed the most permeabilizing potential and ultimately potentiated anti-inhA PNA to the greatest extent, reducing its efficacious concentration to 1.25 μM against both M. smegmatis and M. tuberculosis. Furthermore, an enhanced clearance of 1.3 log-fold was observed for ethambutol-anti-inhA PNA combinations against intracellular M. tuberculosis. Thus, permeabilizing drug-PNA combinations indeed exhibit improved efficacies. We therefore propose that anti-inhA PNA could improve therapy even when applied in minute doses as an addition to the current anti-tuberculosis drug regimen. IMPORTANCE Peptide nucleic acids have great potential in therapeutics as anti-gene/anti-sense agents. However, their limited uptake in cells has curtailed their widespread application. Through this study, we explore a PNA-drug combinatorial strategy to improve the efficacy of PNAs and reduce their effective concentrations. This work also focuses on improving tuberculosis treatment, which is hindered by the emergence of antimicrobial-resistant strains of Mycobacterium tuberculosis. It is observed that the antibacterial efficacy of anti-inhA PNA is enhanced when it is combined with permeabilizing drugs, particularly ethambutol. This indicates that the addition of even small concentrations of anti-inhA PNA to the current TB regimen could potentiate their therapeutic efficiency. We hypothesize that this system would also overcome isoniazid resistance, since the resistance mutations lie outside the designed anti-inhA PNA target site.
Collapse
|
9
|
Popella L, Jung J, Popova K, Ðurica-Mitić S, Barquist L, Vogel J. Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics. Nucleic Acids Res 2021; 49:4705-4724. [PMID: 33849070 PMCID: PMC8096218 DOI: 10.1093/nar/gkab242] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
Antisense peptide nucleic acids (PNAs) inhibiting mRNAs of essential genes provide a straight-forward way to repurpose our knowledge of bacterial regulatory RNAs for development of programmable species-specific antibiotics. While there is ample proof of PNA efficacy, their target selectivity and impact on bacterial physiology are poorly understood. Moreover, while antibacterial PNAs are typically designed to block mRNA translation, effects on target mRNA levels are not well-investigated. Here, we pioneer the use of global RNA-seq analysis to decipher PNA activity in a transcriptome-wide manner. We find that PNA-based antisense oligomer conjugates robustly decrease mRNA levels of the widely-used target gene, acpP, in Salmonella enterica, with limited off-target effects. Systematic analysis of several different PNA-carrier peptides attached not only shows different bactericidal efficiency, but also activation of stress pathways. In particular, KFF-, RXR- and Tat-PNA conjugates especially induce the PhoP/Q response, whereas the latter two additionally trigger several distinct pathways. We show that constitutive activation of the PhoP/Q response can lead to Tat-PNA resistance, illustrating the utility of RNA-seq for understanding PNA antibacterial activity. In sum, our study establishes an experimental framework for the design and assessment of PNA antimicrobials in the long-term quest to use these for precision editing of microbiota.
Collapse
Affiliation(s)
- Linda Popella
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Jakob Jung
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Kristina Popova
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Svetlana Ðurica-Mitić
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
| |
Collapse
|
10
|
Martínez-Guitián M, Vázquez-Ucha JC, Álvarez-Fraga L, Conde-Pérez K, Bou G, Poza M, Beceiro A. Antisense inhibition of lpxB gene expression in Acinetobacter baumannii by peptide-PNA conjugates and synergy with colistin. J Antimicrob Chemother 2021; 75:51-59. [PMID: 31586411 DOI: 10.1093/jac/dkz409] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 08/28/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND LpxB is an enzyme involved in the biosynthesis pathway of lipid A, a component of LPS. OBJECTIVES To evaluate the lpxB gene in Acinetobacter baumannii as a potential therapeutic target and to propose antisense agents such as peptide nucleic acids (PNAs) as a tool to combat bacterial infection, either alone or in combination with known antimicrobial therapies. METHODS RNA-seq analysis of the A. baumannii ATCC 17978 strain in a murine pneumonia model was performed to study the in vivo expression of lpxB. Protein expression was studied in the presence or absence of anti-lpxB (KFF)3K-PNA (pPNA). Time-kill curve analyses and protection assays of infected A549 cells were performed. The chequerboard technique was used to test for synergy between pPNA and colistin. A Galleria mellonella infection model was used to test the in vivo efficacy of pPNA. RESULTS The lpxB gene was overexpressed during pneumonia. Treatment with a specific pPNA inhibited LpxB expression in vitro, decreased survival of the ATCC 17978 strain and increased the survival rate of infected A549 cells. Synergy was observed between pPNA and colistin in colistin-susceptible strains. In vivo assays confirmed that a combination treatment of anti-lpxB pPNA and colistin was more effective than colistin in monotherapy. CONCLUSIONS The lpxB gene is essential for A. baumannii survival. Anti-lpxB pPNA inhibits LpxB expression, causing bacterial death. This pPNA showed synergy with colistin and increased the survival rate in G. mellonella. The data suggest that antisense pPNA molecules blocking the lpxB gene could be used as antibacterial agents.
Collapse
Affiliation(s)
- Marta Martínez-Guitián
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Juan Carlos Vázquez-Ucha
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Laura Álvarez-Fraga
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Kelly Conde-Pérez
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Germán Bou
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Margarita Poza
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| |
Collapse
|
11
|
Silencing Antibiotic Resistance with Antisense Oligonucleotides. Biomedicines 2021; 9:biomedicines9040416. [PMID: 33921367 PMCID: PMC8068983 DOI: 10.3390/biomedicines9040416] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/07/2021] [Accepted: 04/10/2021] [Indexed: 02/06/2023] Open
Abstract
Antisense technologies consist of the utilization of oligonucleotides or oligonucleotide analogs to interfere with undesirable biological processes, commonly through inhibition of expression of selected genes. This field holds a lot of promise for the treatment of a very diverse group of diseases including viral and bacterial infections, genetic disorders, and cancer. To date, drugs approved for utilization in clinics or in clinical trials target diseases other than bacterial infections. Although several groups and companies are working on different strategies, the application of antisense technologies to prokaryotes still lags with respect to those that target other human diseases. In those cases where the focus is on bacterial pathogens, a subset of the research is dedicated to produce antisense compounds that silence or reduce expression of antibiotic resistance genes. Therefore, these compounds will be adjuvants administered with the antibiotic to which they reduce resistance levels. A varied group of oligonucleotide analogs like phosphorothioate or phosphorodiamidate morpholino residues, as well as peptide nucleic acids, locked nucleic acids and bridge nucleic acids, the latter two in gapmer configuration, have been utilized to reduce resistance levels. The major mechanisms of inhibition include eliciting cleavage of the target mRNA by the host’s RNase H or RNase P, and steric hindrance. The different approaches targeting resistance to β-lactams include carbapenems, aminoglycosides, chloramphenicol, macrolides, and fluoroquinolones. The purpose of this short review is to summarize the attempts to develop antisense compounds that inhibit expression of resistance to antibiotics.
Collapse
|
12
|
Chen W, Dong B, Liu W, Liu Z. Recent Advances in Peptide Nucleic Acids as Antibacterial Agents. Curr Med Chem 2021; 28:1104-1125. [PMID: 32484766 DOI: 10.2174/0929867327666200602132504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/06/2020] [Accepted: 05/13/2020] [Indexed: 11/22/2022]
Abstract
The emergence of antibiotic-resistant bacteria and the slow progress in searching for new antimicrobial agents makes it hard to treat bacterial infections and cause problems for the healthcare system worldwide, including high costs, prolonged hospitalizations, and increased mortality. Therefore, the discovery of effective antibacterial agents is of great importance. One attractive alternative is antisense peptide nucleic acid (PNA), which inhibits or eliminates gene expression by binding to the complementary messenger RNA (mRNA) sequence of essential genes or the accessible and functionally important regions of the ribosomal RNA (rRNA). Following 30 years of development, PNAs have played an extremely important role in the treatment of Gram-positive, Gram-negative, and acidfast bacteria due to their desirable stability of hybrid complex with target RNA, the strong affinity for target mRNA/rRNA, and the stability against nucleases. PNA-based antisense antibiotics can strongly inhibit the growth of pathogenic and antibiotic-resistant bacteria in a sequence-specific and dose-dependent manner at micromolar concentrations. However, several fundamental challenges, such as intracellular delivery, solubility, physiological stability, and clearance still need to be addressed before PNAs become broadly applicable in clinical settings. In this review, we summarize the recent advances in PNAs as antibacterial agents and the challenges that need to be overcome in the future.
Collapse
Affiliation(s)
- Wei Chen
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics Central South University, Changsha 410083, China
| | - Bo Dong
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics Central South University, Changsha 410083, China
| | - Wenen Liu
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha 410008, China
| | - Zhengchun Liu
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics Central South University, Changsha 410083, China
| |
Collapse
|
13
|
Zink IA, Fouqueau T, Tarrason Risa G, Werner F, Baum B, Bläsi U, Schleper C. Comparative CRISPR type III-based knockdown of essential genes in hyperthermophilic Sulfolobales and the evasion of lethal gene silencing. RNA Biol 2021; 18:421-434. [PMID: 32957821 PMCID: PMC7951960 DOI: 10.1080/15476286.2020.1813411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/22/2020] [Accepted: 08/16/2020] [Indexed: 02/07/2023] Open
Abstract
CRISPR type III systems, which are abundantly found in archaea, recognize and degrade RNA in their specific response to invading nucleic acids. Therefore, these systems can be harnessed for gene knockdown technologies even in hyperthermophilic archaea to study essential genes. We show here the broader usability of this posttranscriptional silencing technology by expanding the application to further essential genes and systematically analysing and comparing silencing thresholds and escape mutants. Synthetic guide RNAs expressed from miniCRISPR cassettes were used to silence genes involved in cell division (cdvA), transcription (rpo8), and RNA metabolism (smAP2) of the two crenarchaeal model organisms Saccharolobus solfataricus and Sulfolobus acidocaldarius. Results were systematically analysed together with those obtained from earlier experiments of cell wall biogenesis (slaB) and translation (aif5A). Comparison of over 100 individual transformants revealed gene-specific silencing maxima ranging between 40 and 75%, which induced specific knockdown phenotypes leading to growth retardation. Exceedance of this threshold by strong miniCRISPR constructs was not tolerated and led to specific mutation of the silencing miniCRISPR array and phenotypical reversion of cultures. In two thirds of sequenced reverted cultures, the targeting spacers were found to be precisely excised from the miniCRISPR array, indicating a still hypothetical, but highly active recombination system acting on the dynamics of CRISPR spacer arrays. Our results indicate that CRISPR type III - based silencing is a broadly applicable tool to study in vivo functions of essential genes in Sulfolobales which underlies a specific mechanism to avoid malignant silencing overdose.
Collapse
Affiliation(s)
- Isabelle Anna Zink
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Thomas Fouqueau
- RNAP Lab, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Gabriel Tarrason Risa
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Finn Werner
- RNAP Lab, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Buzz Baum
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Udo Bläsi
- Max Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| |
Collapse
|
14
|
Shahriar S, Ahsan T, Khan A, Akhteruzzaman S, Shehreen S, Sajib AA. Aspartame, acesulfame K and sucralose- influence on the metabolism of Escherichia coli. Metabol Open 2020; 8:100072. [PMID: 33336183 PMCID: PMC7732866 DOI: 10.1016/j.metop.2020.100072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/18/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Gut microbes play a crucial role in the maintenance of human health. Components in the diet of the host affect their metabolism and diversity. Here, we investigated the influences of three commonly used non-caloric artificial sweeteners-aspartame, acesulfame K and sucralose-on the growth and metabolism of an omnipresent gut microbe Escherichia coli K-12. Methods: Growth of E. coli in the presence of aspartame, acesulfame K and sucralose in media was assessed and the influences of these artificial sweeteners on metabolism were investigated by relative expression analysis of genes encoding the rate limiting steps of important metabolic pathways as well as their global metabolomic profiles. Results: As a whole, E. coli growth was inhibited by aspartame and induced by acesulfame potassium, while the effect of sucralose on growth was less prominent. Although the expressions of multiple key enzymes that regulate important metabolic pathways were significantly altered by all three sweeteners, acesulfame K caused the most notable changes in this regard. In multivariate analysis with the metabolite profiles, the sucralose-treated cells clustered the closest to the untreated cells, while the acesulfame potassium treated cells were the most distant. These sweeteners affect multiple metabolic pathways in E. coli, which include propanoate, phosphonate, phosphinate and fatty acid metabolism, pentose phosphate pathway, and biosynthesis of several amino acids including lysine and the aromatic amino acids. Similar to the gene expression pattern, acesulfame potassium treated E. coli showed the largest deviation in their metabolite profiles compared to the untreated cells.
Collapse
Affiliation(s)
- Shayan Shahriar
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Tamim Ahsan
- Department of Genetic Engineering & Biotechnology, Bangabandhu Sheikh Mujibur Rahman Maritime University, Dhaka, Bangladesh
| | - Abira Khan
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Sharif Akhteruzzaman
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Saadlee Shehreen
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Abu Ashfaqur Sajib
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| |
Collapse
|
15
|
Correlated chromosomal periodicities according to the growth rate and gene expression. Sci Rep 2020; 10:15531. [PMID: 32968121 PMCID: PMC7511328 DOI: 10.1038/s41598-020-72389-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/10/2020] [Indexed: 12/02/2022] Open
Abstract
Linking genetic information to population fitness is crucial to understanding living organisms. Despite the abundant knowledge of the genetic contribution to growth, the overall patterns/features connecting genes, their expression, and growth remain unclear. To reveal the quantitative and direct connections, systematic growth assays of single-gene knockout Escherichia coli strains under both rich and poor nutritional conditions were performed; subsequently, the resultant growth rates were associated with the original expression levels of the knockout genes in the parental genome. Comparative analysis of growth and the transcriptome identified not only the nutritionally differentiated fitness cost genes but also a significant correlation between the growth rates of the single-gene knockout strains and the original expression levels of these knockout genes in the parental strain, regardless of the nutritional variation. In addition, the coordinated chromosomal periodicities of the wild-type transcriptome and the growth rates of the strains lacking the corresponding genes were observed. The common six-period periodicity was somehow attributed to the essential genes, although the underlying mechanism remains to be addressed. The correlated chromosomal periodicities associated with the gene expression-growth dataset were highly valuable for bacterial growth prediction and discovering the working principles governing minimal genetic information.
Collapse
|
16
|
Montazersaheb S, Avci ÇB, Bagca BG, Ay NPO, Tarhriz V, Nielsen PE, Charoudeh HN, Hejazi MS. Targeting TdT gene expression in Molt-4 cells by PNA-octaarginine conjugates. Int J Biol Macromol 2020; 164:4583-4590. [PMID: 32941907 DOI: 10.1016/j.ijbiomac.2020.09.081] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 12/11/2022]
Abstract
Peptide nucleic acid (PNA) is an amide based structural nucleic acid mimic with potential applications in gene therapeutic drug discovery. In the present study, we evaluated and compared the effects on gene expression, cell viability and apoptosis of two antisense PNA-d-octaarginine conjugates, targeting sequences at the AUG translation start site or the 5'-UTR of the TdT (terminal deoxynucleotidyl transferase) gene, as well as a sense oligomer corresponding to the 5'-UTR-antisense, in Molt-4 cells. The protein level of TdT was determined by flow cytometry, and qPCR was used for mRNA expression analysis. Mismatch PNAs were used as control to address the sequence/target spcifity of the biological effects. The results showed that treatment with the AUG- and to slightly lesser extent with the 5'-UTR-antisense PNAs reduced the TdT mRNA as wel as the protein level, whereas only very low effect was observed for the 5'-UTR-sense PNA. A parallel effect was observed on reduced cell survival and increased rate of apoptosis. Our findings suggest that antisense PNAs can inhibit expression of the TdT gene and induce apoptosis in Molt-4 cells.
Collapse
Affiliation(s)
- Soheila Montazersaheb
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Çığır Biray Avci
- Faculty of Medicine, Department of Medical Biology, Ege University, Izmir, Turkey
| | - Bakiye Goker Bagca
- Faculty of Medicine, Department of Medical Biology, Ege University, Izmir, Turkey
| | | | - Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | | | - Mohammad Saeid Hejazi
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
| |
Collapse
|
17
|
Pifer R, Greenberg DE. Antisense antibacterial compounds. Transl Res 2020; 223:89-106. [PMID: 32522669 DOI: 10.1016/j.trsl.2020.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/28/2020] [Accepted: 06/01/2020] [Indexed: 02/08/2023]
Abstract
Extensive antibiotic use combined with poor historical drug stewardship practices have created a medical crisis in which once treatable bacterial infections are now increasingly unmanageable. To combat this, new antibiotics will need to be developed and safeguarded. An emerging class of antibiotics based upon nuclease-stable antisense technologies has proven valuable in preclinical testing against a variety of bacterial pathogens. This review describes the current state of development of antisense-based antibiotics, the mechanisms thus far employed by these compounds, and possible future avenues of research.
Collapse
Affiliation(s)
- Reed Pifer
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - David E Greenberg
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas; Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas.
| |
Collapse
|
18
|
Antimicrobial antisense RNA delivery to F-pili producing multidrug-resistant bacteria via a genetically engineered bacteriophage. Biochem Biophys Res Commun 2020; 530:533-540. [PMID: 32739024 DOI: 10.1016/j.bbrc.2020.06.088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 06/18/2020] [Indexed: 12/16/2022]
Abstract
Multidrug-resistant bacteria are a growing issue worldwide. This study developed a convenient and effective method to downregulate the expression of a specific gene to produce a novel antimicrobial tool using a small (140 nucleotide) RNA with a 24-nucleotide antisense (as) region from an arabinose-inducible expression phagemid vector in Escherichia coli. Knockdown effects of rpoS encoding RNA polymerase sigma factor were observed using this inducible artificial asRNA approach. asRNAs targeting several essential E. coli genes produced significant growth defects, especially when targeted to acpP and ribosomal protein coding genes rplN, rplL, and rpsM. Growth inhibited phenotypes were facilitated in hfq- conditions. Phage lysates were prepared from cells harboring phagemids as a lethal-agent delivery tool. Targeting the rpsM gene by phagemid-derived M13 phage infection of E. coli containing a carbapenem-producing F-plasmid and multidrug-resistant Klebsiella pneumoniae containing an F-plasmid resulted in the death of over 99.99% of infected bacteria. This study provides a possible strategy for treating bacterial infection and can be applied to any F-pilus producing bacterial species.
Collapse
|
19
|
Abstract
The antibacterial efficacy of the tetracycline antibiotics has been greatly reduced by the development of resistance, hence a decline in their clinical use. The hok/sok locus is a type I toxin/antitoxin plasmid stability element, often associated with multi-drug resistance plasmids, especially ESBL-encoding plasmids. It enhances host cell survivability and pathogenicity in stressful growth conditions, and increases bacterial tolerance to β-lactam antibiotics. The hok/sok locus forms dsRNA by RNA:RNA interactions between the toxin encoding mRNA and antitoxin non-coding RNA, and doxycycline has been reported to bind dsRNA structures and inhibit their cleavage/processing by the dsRNase, RNase III. This study investigated the antibacterial activities of doxycycline in hok/sok host bacteria cells, the effects on hok/sok-induced changes in growth and the mechanism(s) involved. Diverse strains of E. coli were transformed with hok/sok plasmids and assessed for doxycycline susceptibility and growth changes. The results show that the hok/sok locus increases bacterial susceptibility to doxycycline, which is more apparent in strains with more pronounced hok/sok-induced growth effects. The increased doxycycline susceptibility occurs despite β-lactam resistance imparted by hok/sok. Doxycycline was found to induce bacterial death in a manner phenotypically characteristic of Hok toxin expression, suggesting that it inhibits the toxin/antitoxin dsRNA degradation, leading to Hok toxin expression and cell death. In this way, doxycycline could counteract the multi-drug resistance plasmid maintenance/propagation, persistence and pathogenicity mechanisms associated with the hok/sok locus, which could potentially help in efforts to mitigate the rise of antimicrobial resistance.
Collapse
|
20
|
Adebowale OO, Goh S, Good L. The development of species-specific antisense peptide nucleic acid method for the treatment and detection of viable Salmonella. Heliyon 2020; 6:e04110. [PMID: 32566778 PMCID: PMC7298406 DOI: 10.1016/j.heliyon.2020.e04110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/20/2020] [Accepted: 05/27/2020] [Indexed: 11/25/2022] Open
Abstract
Genotypic based detection methods using specific target sites in the pathogen genome can complement phenotypic identification. We report the development of species-specific antisense peptide nucleic acid (PNA) combined with selective and differential enrichment growth conditions for Salmonella treatment and detection. An antisense PNA oligomer targeting the Salmonella ftsZ gene and conjugated with a cell-penetrating peptide ((KFF)3K) was exploited to probe bacteria cultured in three different growth media (Muller Hinton broth (MHB), Rappaport-Vassiliadis Soya Peptone Broth (RVS, Oxoid), and in-house modified Rappaport-Vassiliadis Soya Peptone Broths (mRVSs). Also, water and milk artificially contaminated with bacteria were probed. Antisense PNA provided detectable changes in Salmonella growth and morphology in all media and artificially contaminated matrices except RVS. Salmonella was detected as elongated cells. On the contrary, treated Escherichia coli did not elongate, providing evidence of differentiation and selectivity for Salmonella. Similarly, Salmonella probed with mismatched PNAs did not elongate. Antisense oligomers targeted ftsZ mRNA in combination with selective growth conditions can provide a detection strategy for viable Salmonella in a single reaction, and act as a potential tool for bacteria detection in real food and environmental samples.
Collapse
|
21
|
Goltermann L, Nielsen PE. PNA Antisense Targeting in Bacteria: Determination of Antibacterial Activity (MIC) of PNA-Peptide Conjugates. Methods Mol Biol 2020; 2105:231-239. [PMID: 32088874 DOI: 10.1007/978-1-0716-0243-0_14] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Antisense PNA-peptide conjugates targeting essential bacterial genes have shown interesting potential for discovery of novel precision antibiotics. In this context, the minimal inhibitory concentration (MIC) assay is used to assess and compare the antimicrobial activity of natural as well as synthetic antimicrobial compounds. Here, we describe the determination of the minimal inhibitory concentration of peptide-PNA conjugates against Escherichia coli. This method can be expanded to include minimal bactericidal concentration (MBC) determination and kill-curve kinetics.
Collapse
Affiliation(s)
- Lise Goltermann
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
22
|
Lee HT, Kim SK, Lee JB, Yoon JW. A Novel Peptide Nucleic Acid against the Cytidine Monophosphate Kinase of S. aureus Inhibits Staphylococcal Infection In Vivo. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:245-252. [PMID: 31581048 PMCID: PMC6796767 DOI: 10.1016/j.omtn.2019.08.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/01/2019] [Accepted: 08/21/2019] [Indexed: 01/15/2023]
Abstract
Here, we report a novel bactericidal peptide nucleic acid (PNA) that can induce the antisense effect on the cytidine monophosphate kinase (Cmk) of Staphylococcus aureus, a putative essential component for bacterial species. Based on the genome sequence of S. aureus N315, a set of PNA conjugates with a bacterial penetration peptide, (KFF)3K, were synthesized to target the seven potentially essential genes (cmk, deoD, ligA, smpB, glmU, pyrH, and ftsA) and further evaluated for their antibacterial properties in vitro as well as in vivo. The results demonstrated that two peptide-conjugated PNAs (P-PNAs), antisense P-PNA (ASP)-cmk1 and ASP-deoD1, targeting either the cmk or the deoD genes, had the strongest inhibitory effects on the growth of S. aureus ATCC 29740 (a bovine mastitic milk isolate) in a dose-dependent manner. In vivo application of ASP-cmk1 resulted in a significant reduction of bacterial loads in mice intraperitoneally infected with a sublethal dose of S. aureus. Moreover, ASP-cmk1 significantly increased the survival rate of the breast-fed infant mice after intramammary infection of the lactating CD-1 mice. Taken together, our characterization of ASP-cmk1 demonstrated its bactericidal activity against S. aureus as well as its effectiveness in vivo.
Collapse
Affiliation(s)
- Hyung Tae Lee
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Se Kye Kim
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Jun Bong Lee
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Jang Won Yoon
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea.
| |
Collapse
|
23
|
Giedyk M, Jackowska A, Równicki M, Kolanowska M, Trylska J, Gryko D. Vitamin B 12 transports modified RNA into E. coli and S. Typhimurium cells. Chem Commun (Camb) 2019; 55:763-766. [PMID: 30480264 DOI: 10.1039/c8cc05064c] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Specifically designed, antisense oligonucleotides are promising candidates for antibacterial drugs. They suppress the correct expression of bacterial genes by complementary binding to essential sequences of bacterial DNA or RNA. The main obstacle in fully utilizing their potential as therapeutic agents comes from the fact that bacteria do not uptake oligonucleotides from their environment. Herein, we report that vitamin B12 can transport oligonucleotides into Escherichia coli and Salmonella typhimurium cells. 5'-Aminocobalamin with an alkyne linker and azide-modified oligonucleotides enabled the synthesis of vitamin B12-2'OMeRNA conjugates using an efficient "click" methodology. Inhibition of protein expression in E. coli and S. Typhimurium cells indicates an unprecedented transport of 2'OMeRNA oligomers into bacterial cells via the vitamin B12 delivery pathway.
Collapse
Affiliation(s)
- Maciej Giedyk
- Institute of Organic Chemistry Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | | | | | | | | | | |
Collapse
|
24
|
Równicki M, Pieńko T, Czarnecki J, Kolanowska M, Bartosik D, Trylska J. Artificial Activation of Escherichia coli mazEF and hipBA Toxin-Antitoxin Systems by Antisense Peptide Nucleic Acids as an Antibacterial Strategy. Front Microbiol 2018; 9:2870. [PMID: 30534121 PMCID: PMC6275173 DOI: 10.3389/fmicb.2018.02870] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/08/2018] [Indexed: 12/14/2022] Open
Abstract
The search for new, non-standard targets is currently a high priority in the design of new antibacterial compounds. Bacterial toxin-antitoxin systems (TAs) are genetic modules that encode a toxin protein that causes growth arrest by interfering with essential cellular processes, and a cognate antitoxin, which neutralizes the toxin activity. TAs have no human analogs, are highly abundant in bacterial genomes, and therefore represent attractive alternative targets for antimicrobial drugs. This study demonstrates how artificial activation of Escherichia coli mazEF and hipBA toxin-antitoxin systems using sequence-specific antisense peptide nucleic acid oligomers is an innovative antibacterial strategy. The growth arrest observed in E. coli resulted from the inhibition of translation of the antitoxins by the antisense oligomers. Furthermore, two other targets, related to the activities of mazEF and hipBA, were identified as promising sites of action for antibacterials. These results show that TAs are susceptible to sequence-specific antisense agents and provide a proof-of-concept for their further exploitation in antimicrobial strategies.
Collapse
Affiliation(s)
- Marcin Równicki
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
| | - Tomasz Pieńko
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Department of Drug Chemistry, Faculty of Pharmacy with the Laboratory Medicine Division, Medical University of Warsaw, Warsaw, Poland
| | - Jakub Czarnecki
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Unit of Bacterial Genome Plasticity, Department of Genomes and Genetics, Pasteur Institute, Paris, France
| | - Monika Kolanowska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Genomic Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| |
Collapse
|
25
|
Sugimoto S, Maeda H, Kitamatsu M, Nishikawa I, Shida M. Selective growth inhibition of Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans by antisense peptide nucleic acids. Mol Cell Probes 2018; 43:45-49. [PMID: 30471338 DOI: 10.1016/j.mcp.2018.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/13/2018] [Accepted: 11/20/2018] [Indexed: 10/27/2022]
Abstract
Peptide nucleic acids (PNA) are DNA/RNA analogs in which the sugar-phosphate backbone is replaced by N-2-aminoethylglycine. PNA are widely used for experimental antisense therapy due to their strong affinity to mRNA. By targeting specific genes, protein synthesis and the growth of bacteria or cancer cells can be inhibited by PNA. Here, we report the design and evaluation of antisense PNA for selective growth inhibition of Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans, potent pathogens associated with periodontitis. Antisense PNA against groEL and acpP were prepared with carrier peptide (KFFKFFKFFK). Anti-groEL PNA for P. gingivalis specifically inhibited growth in a dose-dependent manner, and growth was inhibited for 5 h at a concentration of 3 μM. Anti-groEL PNA for A. actinomycetemcomitans inhibited growth for 2 h at a concentration of 3 μM with reduced GroEL protein expression. Anti-acpP PNA did not show a marked growth inhibitory effect on either species. Although further studies are needed to develop more effective antisense PNA for both species, anti-groEL PNA may be potentially useful species-specific antibacterial tools against oral pathogens.
Collapse
Affiliation(s)
- Sadaomi Sugimoto
- Department of Endodontics, Osaka Dental University, 8-1 Kuzuhahanazonocho, Hirakata, Osaka, 573-1121, Japan
| | - Hiroshi Maeda
- Department of Endodontics, Osaka Dental University, 8-1 Kuzuhahanazonocho, Hirakata, Osaka, 573-1121, Japan.
| | - Mizuki Kitamatsu
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka, 577-8502, Japan
| | - Ikuo Nishikawa
- Department of Endodontics, Osaka Dental University, 8-1 Kuzuhahanazonocho, Hirakata, Osaka, 573-1121, Japan
| | - Muneyasu Shida
- Department of Endodontics, Osaka Dental University, 8-1 Kuzuhahanazonocho, Hirakata, Osaka, 573-1121, Japan
| |
Collapse
|
26
|
Geller BL, Li L, Martinez F, Sully E, Sturge CR, Daly SM, Pybus C, Greenberg DE. Morpholino oligomers tested in vitro, in biofilm and in vivo against multidrug-resistant Klebsiella pneumoniae. J Antimicrob Chemother 2018; 73:1611-1619. [PMID: 29506074 PMCID: PMC6251509 DOI: 10.1093/jac/dky058] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/24/2018] [Accepted: 01/29/2018] [Indexed: 01/07/2023] Open
Abstract
Background Klebsiella pneumoniae is an opportunistic pathogen and many strains are multidrug resistant. KPC is one of the most problematic resistance mechanisms, as it confers resistance to most β-lactams, including carbapenems. A promising platform technology for treating infections caused by MDR pathogens is the nucleic acid-like synthetic oligomers that silence bacterial gene expression by an antisense mechanism. Objectives To test a peptide-conjugated phosphorodiamidate morpholino oligomer (PPMO) in a mouse model of K. pneumoniae infection. Methods PPMOs were designed to target various essential genes of K. pneumoniae and screened in vitro against a panel of diverse strains. The most potent PPMOs were further tested for their bactericidal effects in broth cultures and in established biofilms. Finally, a PPMO was used to treat mice infected with a KPC-expressing strain. Results The most potent PPMOs targeted acpP, rpmB and ftsZ and had MIC75s of 0.5, 4 and 4 μM, respectively. AcpP PPMOs were bactericidal at 1-2 × MIC and reduced viable cells and biofilm mass in established biofilms. In a mouse pneumonia model, therapeutic intranasal treatment with ∼30 mg/kg AcpP PPMO improved survival by 89% and reduced bacterial burden in the lung by ∼3 logs. Survival was proportional to the dose of AcpP PPMO. Delaying treatment by 2, 8 or 24 h post-infection improved survival compared with control groups treated with PBS or scrambled sequence (Scr) PPMOs. Conclusions PPMOs have the potential to be effective therapeutic agents against KPC-expressing, MDR K. pneumoniae.
Collapse
Affiliation(s)
- Bruce L Geller
- Department of Microbiology, 226 Nash Hall, Oregon State University, Corvallis, OR 97331, USA
| | - Lixin Li
- Department of Microbiology, 226 Nash Hall, Oregon State University, Corvallis, OR 97331, USA
| | - Fabian Martinez
- Department of Microbiology, 226 Nash Hall, Oregon State University, Corvallis, OR 97331, USA
| | - Erin Sully
- Department of Microbiology, 226 Nash Hall, Oregon State University, Corvallis, OR 97331, USA
| | - Carolyn R Sturge
- Department of Internal Medicine, 5323 Harry Hines Blvd., University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Seth M Daly
- Department of Internal Medicine, 5323 Harry Hines Blvd., University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christine Pybus
- Department of Internal Medicine, 5323 Harry Hines Blvd., University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David E Greenberg
- Department of Internal Medicine, 5323 Harry Hines Blvd., University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Microbiology, 5323 Harry Hines Blvd., University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
27
|
Phenotypic indications of FtsZ inhibition in hok/sok-induced bacterial growth changes and stress response. Microb Pathog 2017; 114:393-401. [PMID: 29233778 DOI: 10.1016/j.micpath.2017.12.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 12/06/2017] [Accepted: 12/08/2017] [Indexed: 11/22/2022]
Abstract
The hok/sok locus has been shown to enhance the growth of bacteria in adverse growth conditions such as high temperature, low starting-culture densities and antibiotic treatment. This is in addition to their well-established plasmid-stabilization effect via post-segregational killing of plasmid-free daughter cells. It delays the onset of growth by prolonging the lag phase of bacterial culture, and increases the rate of exponential growth when growth eventually begins. This enables the cells adapt to the prevailing growth conditions and enhance their survival in stressful conditions. These effects functionally complement defective SOS response mechanism, and appear analogous to the growth effects of FtsZ in the SOS pathway. In this study, the role of FtsZ in the hok/sok-induced changes in bacterial growth and cell division was investigated. Morphologic studies of early growth-phase cultures and cells growing under temperature stress showed elongated cells typical of FtsZ inhibition/deficiency. Both ftsZ silencing and over-expression produced comparable growth effects in control cells, and altered the growth changes observed otherwise in the hok/sok+ cells. These changes were diminished in SOS-deficient strain containing mutant FtsZ. The involvement of FtsZ in the hok/sok-induced growth changes may be exploited as drug target in host bacteria, which often propagate antibiotic resistance elements.
Collapse
|
28
|
Równicki M, Wojciechowska M, Wierzba AJ, Czarnecki J, Bartosik D, Gryko D, Trylska J. Vitamin B 12 as a carrier of peptide nucleic acid (PNA) into bacterial cells. Sci Rep 2017; 7:7644. [PMID: 28794451 PMCID: PMC5550456 DOI: 10.1038/s41598-017-08032-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/06/2017] [Indexed: 01/02/2023] Open
Abstract
Short modified oligonucleotides targeted at bacterial DNA or RNA could serve as antibacterial agents provided that they are efficiently taken up by bacterial cells. However, the uptake of such oligonucleotides is hindered by the bacterial cell wall. To overcome this problem, oligomers have been attached to cell-penetrating peptides, but the efficiency of delivery remains poor. Thus, we have investigated the ability of vitamin B12 to transport peptide nucleic acid (PNA) oligomers into cells of Escherichia coli and Salmonella Typhimurium. Vitamin B12 was covalently linked to a PNA oligomer targeted at the mRNA of a reporter gene expressing Red Fluorescent Protein. Cu-catalyzed 1,3-dipolar cycloaddition was employed for the synthesis of PNA-vitamin B12 conjugates; namely the vitamin B12 azide was reacted with PNA possessing the terminal alkyne group. Different types of linkers and spacers between vitamin B12 and PNA were tested, including a disulfide bond. We found that vitamin B12 transports antisense PNA into E. coli cells more efficiently than the most widely used cell-penetrating peptide (KFF)3K. We also determined that the structure of the linker impacts the antisense effect. The results of this study provide the foundation for developing vitamin B12 as a carrier of PNA oligonucleotides into bacterial cells.
Collapse
Affiliation(s)
- Marcin Równicki
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, Banacha 2c, 02-097, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Monika Wojciechowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Aleksandra J Wierzba
- Institute of Organic Chemistry, Polish Academy of Sciences, M. Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Jakub Czarnecki
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Dorota Gryko
- Institute of Organic Chemistry, Polish Academy of Sciences, M. Kasprzaka 44/52, 01-224, Warsaw, Poland.
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
| |
Collapse
|
29
|
Peptide nucleic acids (PNAs): currently potential bactericidal agents. Biomed Pharmacother 2017; 93:580-588. [PMID: 28686972 DOI: 10.1016/j.biopha.2017.06.092] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 06/12/2017] [Accepted: 06/23/2017] [Indexed: 01/09/2023] Open
Abstract
In recent years, the emergence of ESBL-producing and multi-drug resistant bacteria have been increased and designing novel components is necessary for confrontation these bacteria. Peptide nucleic acids (PNAs) are one of the synthetic components that bind to single strand DNA and RNA. Applications of these components are wide while, and one of the important applications of these components is inhibition of gene expression and knock downing the target gene follow as inhibition of bacterial growth. For PNA targeting gene, peptide-PNAs (PPNA) activity cannot be occurred without sequence homology, at the same time, it has been affected by sequence-based specific target and dose-dependent-based manner. Choosing the conserved sequence in different bacterial genus can provide broad-spectrum antimicrobial activity. In this review article, we studied several research papers and extract PNA targeting genes that cause gene knock down and inhibition of bacterial growth. Some novel opportunities for advancement and the design ultra-narrow-spectrum antimicrobial drugs against multi-drug can be accessible by utilizing PNA against necessary genes of pathogens. These results open novel vision for therapeutic intervention. Future researches are required to evaluate the safety, toxicity and pharmacokinetics properties of PPNAs in order to be utilized in clinical treatment.
Collapse
|
30
|
Wan G, Ruan L, Yin Y, Yang T, Ge M, Cheng X. Effects of silver nanoparticles in combination with antibiotics on the resistant bacteria Acinetobacter baumannii. Int J Nanomedicine 2016; 11:3789-800. [PMID: 27574420 PMCID: PMC4990392 DOI: 10.2147/ijn.s104166] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Acinetobacter baumannii resistance to carbapenem antibiotics is a serious clinical challenge. As a newly developed technology, silver nanoparticles (AgNPs) show some excellent characteristics compared to older treatments, and are a candidate for combating A. baumannii infection. However, its mechanism of action remains unclear. In this study, we combined AgNPs with antibiotics to treat carbapenem-resistant A. baumannii (aba1604). Our results showed that single AgNPs completely inhibited A. baumannii growth at 2.5 μg/mL. AgNP treatment also showed synergistic effects with the antibiotics polymixin B and rifampicin, and an additive effect with tigecyline. In vivo, we found that AgNPs-antibiotic combinations led to better survival ratios in A. baumannii-infected mouse peritonitis models than that by single drug treatment. Finally, we employed different antisense RNA-targeted Escherichia coli strains to elucidate the synergistic mechanism involved in bacterial responses to AgNPs and antibiotics.
Collapse
Affiliation(s)
- Guoqing Wan
- School of Life Science and Technology, China Pharmaceutical University, Nanjing; Shanghai Laiyi Center for Biopharmaceutical R&D
| | - Lingao Ruan
- Shanghai Laiyi Center for Biopharmaceutical R&D; School of Pharmacy, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yu Yin
- Shanghai Laiyi Center for Biopharmaceutical R&D; School of Pharmacy, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Tian Yang
- Shanghai Laiyi Center for Biopharmaceutical R&D; School of Pharmacy, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Mei Ge
- Shanghai Laiyi Center for Biopharmaceutical R&D
| | - Xiaodong Cheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing; Department of Integrative Biology & Pharmacology, The University of Texas Health Science Center, Houston, TX, USA
| |
Collapse
|
31
|
The antimicrobial polymer PHMB enters cells and selectively condenses bacterial chromosomes. Sci Rep 2016; 6:23121. [PMID: 26996206 PMCID: PMC4800398 DOI: 10.1038/srep23121] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/29/2016] [Indexed: 11/08/2022] Open
Abstract
To combat infection and antimicrobial resistance, it is helpful to elucidate drug mechanism(s) of action. Here we examined how the widely used antimicrobial polyhexamethylene biguanide (PHMB) kills bacteria selectively over host cells. Contrary to the accepted model of microbial membrane disruption by PHMB, we observed cell entry into a range of bacterial species, and treated bacteria displayed cell division arrest and chromosome condensation, suggesting DNA binding as an alternative antimicrobial mechanism. A DNA-level mechanism was confirmed by observations that PHMB formed nanoparticles when mixed with isolated bacterial chromosomal DNA and its effects on growth were suppressed by pairwise combination with the DNA binding ligand Hoechst 33258. PHMB also entered mammalian cells, but was trapped within endosomes and excluded from nuclei. Therefore, PHMB displays differential access to bacterial and mammalian cellular DNA and selectively binds and condenses bacterial chromosomes. Because acquired resistance to PHMB has not been reported, selective chromosome condensation provides an unanticipated paradigm for antimicrobial action that may not succumb to resistance.
Collapse
|
32
|
Goh S, Loeffler A, Lloyd DH, Nair SP, Good L. Oxacillin sensitization of methicillin-resistant Staphylococcus aureus and methicillin-resistant Staphylococcus pseudintermedius by antisense peptide nucleic acids in vitro. BMC Microbiol 2015; 15:262. [PMID: 26560174 PMCID: PMC4642645 DOI: 10.1186/s12866-015-0599-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 11/05/2015] [Indexed: 01/29/2023] Open
Abstract
Background Antibiotic resistance genes can be targeted by antisense agents, which can reduce their expression and thus restore cellular susceptibility to existing antibiotics. Antisense inhibitors can be gene and pathogen specific, or designed to inhibit a group of bacteria having conserved sequences within resistance genes. Here, we aimed to develop antisense peptide nucleic acids (PNAs) that could be used to effectively restore susceptibility to β-lactams in methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant Staphylococcus pseudintermedius (MRSP). Results Antisense PNAs specific for conserved regions of the mobilisable gene mecA, and the growth essential gene, ftsZ, were designed. Clinical MRSA and MRSP strains of high oxacillin resistance were treated with PNAs and assayed for reduction in colony forming units on oxacillin plates, reduction in target gene mRNA levels, and cell size. Anti-mecA PNA at 7.5 and 2.5 μM reduced mecA mRNA in MRSA and MRSP (p < 0.05). At these PNA concentrations, 66 % of MRSA and 92 % of MRSP cells were killed by oxacillin (p < 0.01). Anti-ftsZ PNA at 7.5 and 2.5 μM reduced ftsZ mRNA in MRSA and MRSP, respectively (p ≤ 0.05). At these PNA concentrations, 86 % of MRSA cells and 95 % of MRSP cells were killed by oxacillin (p < 0.05). Anti-ftsZ PNAs resulted in swelling of bacterial cells. Scrambled PNA controls did not affect MRSA but sensitized MRSP moderately to oxacillin without affecting mRNA levels. Conclusions The antisense PNAs effects observed provide in vitro proof of concept that this approach can be used to reverse β-lactam resistance in staphylococci. Further studies are warranted as clinical treatment alternatives are needed. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0599-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shan Goh
- Pathology and Pathogen Biology, Royal Veterinary College, Hawkshead Lane, Hatfield, Hertfordshire, UK.
| | - Anette Loeffler
- Clinical Sciences and Services, Royal Veterinary College, Hawkshead Lane, Hatfield, Hertfordshire, UK
| | - David H Lloyd
- Clinical Sciences and Services, Royal Veterinary College, Hawkshead Lane, Hatfield, Hertfordshire, UK
| | - Sean P Nair
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, UK
| | - Liam Good
- Pathology and Pathogen Biology, Royal Veterinary College, Royal College Street, London, UK
| |
Collapse
|
33
|
George R, Cavalcante R, Jr CC, Marques E, Waugh JB, Unlap MT. Use of siRNA molecular beacons to detect and attenuate mycobacterial infection in macrophages. World J Exp Med 2015; 5:164-181. [PMID: 26309818 PMCID: PMC4543811 DOI: 10.5493/wjem.v5.i3.164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 05/05/2015] [Accepted: 06/11/2015] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis is one of the leading infectious diseases plaguing mankind and is mediated by the facultative pathogen, Mycobacterium tuberculosis (MTB). Once the pathogen enters the body, it subverts the host immune defenses and thrives for extended periods of time within the host macrophages in the lung granulomas, a condition called latent tuberculosis (LTB). Persons with LTB are prone to reactivation of the disease when the body’s immunity is compromised. Currently there are no reliable and effective diagnosis and treatment options for LTB, which necessitates new research in this area. The mycobacterial proteins and genes mediating the adaptive responses inside the macrophage is largely yet to be determined. Recently, it has been shown that the mce operon genes are critical for host cell invasion by the mycobacterium and for establishing a persistent infection in both in vitro and in mouse models of tuberculosis. The YrbE and Mce proteins which are encoded by the MTB mce operons display high degrees of homology to the permeases and the surface binding protein of the ABC transports, respectively. Similarities in structure and cell surface location impute a role in cell invasion at cholesterol rich regions and immunomodulation. The mce4 operon is also thought to encode a cholesterol transport system that enables the mycobacterium to derive both energy and carbon from the host membrane lipids and possibly generating virulence mediating metabolites, thus enabling the bacteria in its long term survival within the granuloma. Various deletion mutation studies involving individual or whole mce operon genes have shown to be conferring varying degrees of attenuation of infectivity or at times hypervirulence to the host MTB, with the deletion of mce4A operon gene conferring the greatest degree of attenuation of virulence. Antisense technology using synthetic siRNAs has been used in knocking down genes in bacteria and over the years this has evolved into a powerful tool for elucidating the roles of various genes mediating infectivity and survival in mycobacteria. Molecular beacons are a newer class of antisense RNA tagged with a fluorophore/quencher pair and their use for in vivo detection and knockdown of mRNA is rapidly gaining popularity.
Collapse
|
34
|
Silencing of Essential Genes within a Highly Coordinated Operon in Escherichia coli. Appl Environ Microbiol 2015; 81:5650-9. [PMID: 26070674 DOI: 10.1128/aem.01444-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 06/08/2015] [Indexed: 01/13/2023] Open
Abstract
Essential bacterial genes located within operons are particularly challenging to study independently because of coordinated gene expression and the nonviability of knockout mutants. Essentiality scores for many operon genes remain uncertain. Antisense RNA (asRNA) silencing or in-frame gene disruption of genes may help establish essentiality but can lead to polar effects on genes downstream or upstream of the target gene. Here, the Escherichia coli ribF-ileS-lspA-fkpB-ispH operon was used to evaluate the possibility of independently studying an essential gene using expressed asRNA and target gene overexpression to deregulate coupled expression. The gene requirement for growth in conditional silencing strains was determined by the relationship of target mRNA reduction with growth inhibition as the minimum transcript level required for 50% growth (MTL50). Mupirocin and globomycin, the protein inhibitors of IleS and LspA, respectively, were used in sensitization assays of strains containing both asRNA-expressing and open reading frame-expressing plasmids to examine deregulation of the overlapping ileS-lspA genes. We found upstream and downstream polar silencing effects when either ileS or lspA was silenced, indicating coupled expression. Weighted MTL50 values (means and standard deviations) of ribF, ileS, and lspA were 0.65 ± 0.18, 0.64 ± 0.06, and 0.76 ± 0.10, respectively. However, they were not significantly different (P = 0.71 by weighted one-way analysis of variance). The gene requirement for ispH could not be determined due to insufficient growth reduction. Mupirocin and globomycin sensitization experiments indicated that ileS-lspA expression could not be decoupled. The results highlight the inherent challenges associated with genetic analyses of operons; however, coupling of essential genes may provide opportunities to improve RNA-silencing antimicrobials.
Collapse
|
35
|
Chaudhary AK, Na D, Lee EY. Rapid and high-throughput construction of microbial cell-factories with regulatory noncoding RNAs. Biotechnol Adv 2015; 33:914-30. [PMID: 26027891 DOI: 10.1016/j.biotechadv.2015.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/27/2015] [Accepted: 05/27/2015] [Indexed: 12/11/2022]
Abstract
Due to global crises such as pollution and depletion of fossil fuels, sustainable technologies based on microbial cell-factories have been garnering great interest as an alternative to chemical factories. The development of microbial cell-factories is imperative in cutting down the overall manufacturing cost. Thus, diverse metabolic engineering strategies and engineering tools have been established to obtain a preferred genotype and phenotype displaying superior productivity. However, these tools are limited to only a handful of genes with permanent modification of a genome and significant labor costs, and this is one of the bottlenecks associated with biofactory construction. Therefore, a groundbreaking rapid and high-throughput engineering tool is needed for efficient construction of microbial cell-factories. During the last decade, copious small noncoding RNAs (ncRNAs) have been discovered in bacteria. These are involved in substantial regulatory roles like transcriptional and post-transcriptional gene regulation by modulating mRNA elongation, stability, or translational efficiency. Because of their vulnerability, ncRNAs can be used as another layer of conditional control over gene expression without modifying chromosomal sequences, and hence would be a promising high-throughput tool for metabolic engineering. Here, we review successful design principles and applications of ncRNAs for high-throughput metabolic engineering or physiological studies of diverse industrially important microorganisms.
Collapse
Affiliation(s)
- Amit Kumar Chaudhary
- Department of Chemical Engineering, Kyung Hee University, Gyeonggi-do 446-701, Republic of Korea
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 156-756, Republic of Korea.
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Gyeonggi-do 446-701, Republic of Korea.
| |
Collapse
|
36
|
Soheili S, Ghafourian S, Sekawi Z, Neela VK, Sadeghifard N, Taherikalani M, Khosravi A, Ramli R, Hamat RA. The mazEF toxin-antitoxin system as an attractive target in clinical isolates of Enterococcus faecium and Enterococcus faecalis. DRUG DESIGN DEVELOPMENT AND THERAPY 2015; 9:2553-61. [PMID: 26005332 PMCID: PMC4428366 DOI: 10.2147/dddt.s77263] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The toxin–antitoxin (TA) system is a regulatory system where two sets of genes encode the toxin and its corresponding antitoxin. In this study, the prevalence of TA systems in independently isolated clinical isolates of Enterococcus faecium and Enterococcus faecalis was determined, the dominant TA system was identified, different virulence genes in E. faecium and E. faecalis were surveyed, the level of expression of the virulence and TA genes in normal and stress conditions was determined, and finally their associations with the TA genes were defined. Remarkably, the analysis demonstrated higBA and mazEF in all clinical isolates, and their locations were on chromosomes and plasmids, respectively. On the other hand, a quantitative analysis of TA and virulence genes revealed that the expression level in both genes is different under normal and stress conditions. The results obtained by anti-mazF peptide nucleic acids demonstrated that the expression level of virulence genes had decreased. These findings demonstrate an association between TA systems and virulence factors. The mazEF on the plasmids and the higBA TA genes on the chromosomes of all E. faecium and E. faecalis strains were dominant. Additionally, there was a decrease in the expression of virulence genes in the presence of anti-mazF peptide nucleic acids. Therefore, it is suggested that mazEF TA systems are potent and sensitive targets in all E. faecium and E. faecalis strains.
Collapse
Affiliation(s)
- Sara Soheili
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Sobhan Ghafourian
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Zamberi Sekawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Vasantha Kumari Neela
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Nourkhoda Sadeghifard
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Morovat Taherikalani
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Afra Khosravi
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Ramliza Ramli
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaakob Latif, Bandar Tun Razak, Kuala Lumpur, Malaysia
| | - Rukman Awang Hamat
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health sciences, Universiti Putra Malaysia, Serdang, Malaysia
| |
Collapse
|
37
|
Resveratrol antibacterial activity against Escherichia coli is mediated by Z-ring formation inhibition via suppression of FtsZ expression. Sci Rep 2015; 5:10029. [PMID: 25942564 PMCID: PMC4419592 DOI: 10.1038/srep10029] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 03/06/2015] [Indexed: 01/14/2023] Open
Abstract
Resveratrol exhibits a potent antimicrobial activity. However, the mechanism underlying its antibacterial activity has not been shown. In this study, the antibacterial mechanism of resveratrol was investigated. To investigate induction of the SOS response, a strain containing the lacZ+gene under the control of an SOS-inducible sulA promoter was constructed. DNA damage was measured by pulse-field gel electrophoresis (PFGE). After resveratrol treatment, the cells were observed by confocal microscopy. For the RNA silencing assay, ftsZ-specific antisense peptide nucleic acid (PNA) was used. Reactive oxygen species (ROS) production increased in Escherichia coli after resveratrol treatment; however, cell growth was not recovered by ROS quenching, indicating that, in this experiment, ROS formation and cell death following resveratrol treatment were not directly correlated. Resveratrol treatment increased DNA fragmentation in cells, while SOS response-related gene expression levels increased in a dose-dependent manner. Cell elongation was observed after resveratrol treatment. Elongation was induced by inhibiting FtsZ, an essential cell-division protein in prokaryotes, and resulted in significant inhibition of Z-ring the formation in E. coli. The expression of ftsZ mRNA was suppressed by resveratrol. Our results indicate that resveratrol inhibits bacterial cell growth by suppressing FtsZ expression and Z-ring formation.
Collapse
|
38
|
The role of the hok/sok locus in bacterial response to stressful growth conditions. Microb Pathog 2015; 79:70-9. [PMID: 25625568 DOI: 10.1016/j.micpath.2015.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/26/2014] [Accepted: 01/23/2015] [Indexed: 11/23/2022]
Abstract
The hok/sok locus is renowned for its plasmid stabilization effect via post-segregational killing of plasmid-free daughter cells. However, the function(s) of the chromosome-encoded loci, which are more abundant in pathogenic strains of a broad range of enteric bacteria, are yet to be understood. Also, the frequent occurrence of this toxin/antitoxin addiction system in multi-drug resistance plasmids suggests additional roles. In this study, the effects of the hok/sok locus on the growth of bacteria in stressful growth-limiting conditions such as high temperature and antibiotic burden were investigated using hok/sok plasmids. The results showed that the hok/sok locus prolonged the lag phase of host cell cultures, thereby enabling the cells to adapt, respond to the stress and eventually thrive in these growth-limiting conditions by increasing the growth rate at exponential phase. The hok/sok locus also enhanced the survival and growth of cells in low cell density cultures irrespective of unfavourable growth conditions, and may complement existing or defective SOS mechanism. In addition to the plasmid stabilization function, these effects would enhance the ability of pathogenic bacteria to establish infections and propagate the antibiotic resistance elements carried on these plasmids, thereby contributing to the virulence of such bacteria.
Collapse
|
39
|
Saeedinia AR, Zeinoddini M, Soleimani M, Sadeghizadeh M. A new method for simultaneous gene deletion and down-regulation in Brucella melitensis Rev.1. Microbiol Res 2015; 170:114-123. [PMID: 25249309 DOI: 10.1016/j.micres.2014.08.007] [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: 03/05/2014] [Revised: 08/17/2014] [Accepted: 08/24/2014] [Indexed: 10/24/2022]
Abstract
In this study, our aim was to integrate an antisense expression cassette in bacterial chromosome for providing a long-term expression down-regulation in a bid to develop a new approach for simultaneous deletion and down-regulation of target genes in bacterial system. Therefore, we were used this approach for simultaneous deletion of the perosamine synthetase (per) gene and down-regulation of the virB1 expression in Brucella melitensis Rev.1. The per gene, which is one of the LPS O-chain coding genes, was replaced by homologous recombination with an antisense virB1 expression cassette together with kanamycin resistance cassette (kan(R)). Deletion of the per gene was characterized by PCR analysis and DNA sequencing. The expression of antisense virB1 cassette was confirmed by RT-PCR. Down-regulation of the virB1 mRNA expression was quantified by real-time RT-PCR using virB1 specific primers relative to the groEL reference gene. The survival rate of mutant strain was evaluated by CFU count in the BALB/c mice. The virB1 mRNA expression was down-regulated on average 10-fold in mutant strain as compared to parental strain. The loss of per gene function and decrease of the virB1 mRNA expression resulted in reduced entry and survival of the mutant Rev.1 strain in BALB/c mice splenocytes. We propose that this method can be used for simultaneous regulation of multiple genes expression.
Collapse
Affiliation(s)
- Ali Reza Saeedinia
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box: 14115-175, Tehran, Iran.
| | - Mehdi Zeinoddini
- Department of Genetics, Science and Biotechnology Research Center, Mallek-Ashtar University of Technology, P.O. Box: 15875-1774, Tehran, Iran.
| | - Masoud Soleimani
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box: 14115-111, Tehran, Iran.
| | - Majid Sadeghizadeh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box: 14115-175, Tehran, Iran.
| |
Collapse
|
40
|
Worley-Morse TO, Gunsch CK. A computational analysis of antisense off-targets in prokaryotic organisms. Genomics 2014; 105:123-30. [PMID: 25486012 DOI: 10.1016/j.ygeno.2014.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 11/14/2014] [Accepted: 11/19/2014] [Indexed: 10/24/2022]
Abstract
The adoption of antisense gene silencing as a novel disinfectant for prokaryotic organisms is hindered by poor silencing efficiencies. Few studies have considered the effects of off-targets on silencing efficiencies, especially in prokaryotic organisms. In this computational study, a novel algorithm was developed that determined and sorted the number of off-targets as a function of alignment length in Escherichia coli K-12 MG1655 and Mycobacterium tuberculosis H37Rv. The mean number of off-targets per a single location was calculated to be 14.1 ± 13.3 and 36.1 ± 58.5 for the genomes of E. coli K-12 MG1655 and M. tuberculosis H37Rv, respectively. Furthermore, when the entire transcriptome was analyzed, it was found that there was no general gene location that could be targeted to minimize or maximize the number of off-targets. In an effort to determine the effects of off-targets on silencing efficiencies, previously published studies were used. Analyses with acpP, ino1, and marORAB revealed a statistically significant relationship between the number of short alignment length off-targets hybrids and the efficacy of the antisense gene silencing, suggesting that the minimization of off-targets may be beneficial for antisense gene silencing in prokaryotic organisms.
Collapse
Affiliation(s)
- Thomas O Worley-Morse
- Department of Civil and Environmental Engineering, Duke University, Box 90287, Durham, NC 27708, USA
| | - Claudia K Gunsch
- Department of Civil and Environmental Engineering, Duke University, Box 90287, Durham, NC 27708, USA.
| |
Collapse
|
41
|
Abstract
Peptide nucleic acids (PNAs) are a class of artificial DNA/RNA analogues that have unique physicochemical properties, which include a high chemical stability, resistance to nucleases and proteases and higher mismatch sensitivity than DNA. PNAs were initially anticipated to be useful for application in antisense and antigene therapies; however, their poor cellular uptake has limited their use for such purposes in the "real world". Recently, it has been shown that the addition of metal complexes to these oligonucleotide analogues could open up new avenues for their utilization in various research fields. Such metallo-constructs have shown great promise, for a diverse range of applications, most notably in the biosensing area. In this chapter, we report on the recent synthetic advances towards the preparation of these "(multi)-metallic PNAs" on the solid phase.
Collapse
|
42
|
Kiran D, Sriranganathan N. The antimicrobial effect of anti-dnaKpeptide nucleic acids on multidrug resistant strains ofEscherichia coliandSalmonella entericaserovar Typhimurium. ACTA ACUST UNITED AC 2014. [DOI: 10.1893/0005-3155-85.1.48] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
43
|
Mondhe M, Chessher A, Goh S, Good L, Stach JEM. Species-selective killing of bacteria by antimicrobial peptide-PNAs. PLoS One 2014; 9:e89082. [PMID: 24558473 PMCID: PMC3928365 DOI: 10.1371/journal.pone.0089082] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 01/19/2014] [Indexed: 12/31/2022] Open
Abstract
Broad-spectrum antimicrobials kill indiscriminately, a property that can lead to negative clinical consequences and an increase in the incidence of resistance. Species-specific antimicrobials that could selectively kill pathogenic bacteria without targeting other species in the microbiome could limit these problems. The pathogen genome presents an excellent target for the development of such antimicrobials. In this study we report the design and evaluation of species-selective peptide nucleic acid (PNA) antibacterials. Selective growth inhibition of B. subtilis, E. coli, K. pnuemoniae and S. enterica serovar Typhimurium in axenic or mixed culture could be achieved with PNAs that exploit species differences in the translation initiation region of essential genes. An S. Typhimurium-specific PNA targeting ftsZ resulted in elongated cells that were not observed in E. coli, providing phenotypic evidence of the selectivity of PNA-based antimicrobials. Analysis of the genomes of E. coli and S. Typhimurium gave a conservative estimate of >150 PNA targets that could potentially discriminate between these two closely related species. This work provides a basis for the development of a new class of antimicrobial with a tuneable spectrum of activity.
Collapse
Affiliation(s)
- Madhav Mondhe
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ashley Chessher
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Shan Goh
- Department of Pathology and Infectious Diseases, Royal Veterinary College, University of London, London, United Kingdom
| | | | - James E. M. Stach
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
- * E-mail:
| |
Collapse
|
44
|
Nakashima N, Miyazaki K. Bacterial cellular engineering by genome editing and gene silencing. Int J Mol Sci 2014; 15:2773-93. [PMID: 24552876 PMCID: PMC3958881 DOI: 10.3390/ijms15022773] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 01/27/2014] [Accepted: 01/28/2014] [Indexed: 12/18/2022] Open
Abstract
Genome editing is an important technology for bacterial cellular engineering, which is commonly conducted by homologous recombination-based procedures, including gene knockout (disruption), knock-in (insertion), and allelic exchange. In addition, some new recombination-independent approaches have emerged that utilize catalytic RNAs, artificial nucleases, nucleic acid analogs, and peptide nucleic acids. Apart from these methods, which directly modify the genomic structure, an alternative approach is to conditionally modify the gene expression profile at the posttranscriptional level without altering the genomes. This is performed by expressing antisense RNAs to knock down (silence) target mRNAs in vivo. This review describes the features and recent advances on methods used in genomic engineering and silencing technologies that are advantageously used for bacterial cellular engineering.
Collapse
Affiliation(s)
- Nobutaka Nakashima
- Bioproduction Research Institute, National Institute of Advanced Industrial Sciences and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.
| | - Kentaro Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Sciences and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.
| |
Collapse
|
45
|
Janßen HJ, Steinbüchel A. Fatty acid synthesis in Escherichia coli and its applications towards the production of fatty acid based biofuels. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:7. [PMID: 24405789 PMCID: PMC3896788 DOI: 10.1186/1754-6834-7-7] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/24/2013] [Indexed: 05/04/2023]
Abstract
The idea of renewable and regenerative resources has inspired research for more than a hundred years. Ideally, the only spent energy will replenish itself, like plant material, sunlight, thermal energy or wind. Biodiesel or ethanol are examples, since their production relies mainly on plant material. However, it has become apparent that crop derived biofuels will not be sufficient to satisfy future energy demands. Thus, especially in the last decade a lot of research has focused on the production of next generation biofuels. A major subject of these investigations has been the microbial fatty acid biosynthesis with the aim to produce fatty acids or derivatives for substitution of diesel. As an industrially important organism and with the best studied microbial fatty acid biosynthesis, Escherichia coli has been chosen as producer in many of these studies and several reviews have been published in the fields of E. coli fatty acid biosynthesis or biofuels. However, most reviews discuss only one of these topics in detail, despite the fact, that a profound understanding of the involved enzymes and their regulation is necessary for efficient genetic engineering of the entire pathway. The first part of this review aims at summarizing the knowledge about fatty acid biosynthesis of E. coli and its regulation, and it provides the connection towards the production of fatty acids and related biofuels. The second part gives an overview about the achievements by genetic engineering of the fatty acid biosynthesis towards the production of next generation biofuels. Finally, the actual importance and potential of fatty acid-based biofuels will be discussed.
Collapse
Affiliation(s)
- Helge Jans Janßen
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, D-48149, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, D-48149, Münster, Germany
- Environmental Sciences Department, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
46
|
A vector library for silencing central carbon metabolism genes with antisense RNAs in Escherichia coli. Appl Environ Microbiol 2013; 80:564-73. [PMID: 24212579 DOI: 10.1128/aem.02376-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We describe here the construction of a series of 71 vectors to silence central carbon metabolism genes in Escherichia coli. The vectors inducibly express antisense RNAs called paired-terminus antisense RNAs, which have a higher silencing efficacy than ordinary antisense RNAs. By measuring mRNA amounts, measuring activities of target proteins, or observing specific phenotypes, it was confirmed that all the vectors were able to silence the expression of target genes efficiently. Using this vector set, each of the central carbon metabolism genes was silenced individually, and the accumulation of metabolites was investigated. We were able to obtain accurate information on ways to increase the production of pyruvate, an industrially valuable compound, from the silencing results. Furthermore, the experimental results of pyruvate accumulation were compared to in silico predictions, and both sets of results were consistent. Compared to the gene disruption approach, the silencing approach has an advantage in that any E. coli strain can be used and multiple gene silencing is easily possible in any combination.
Collapse
|
47
|
Alajlouni RA, Seleem MN. Targeting listeria monocytogenes rpoA and rpoD genes using peptide nucleic acids. Nucleic Acid Ther 2013; 23:363-7. [PMID: 23859300 DOI: 10.1089/nat.2013.0426] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Treating intracellular pathogens remains a considerable medical challenge because of the inefficient intracellular delivery of antimicrobials and the frequent emergence of bacterial resistance to therapeutic agents deemed the drugs of last resort. We investigated the capability of antisense peptide nucleic acids (PNAs) conjugated to the (KFF)3K cell penetrating peptide to target RNA polymerase α subunit (rpoA) and RNA polymerase sigma 70 (rpoD) in the intracellular pathogen Listeria monocytogenes. The PNAs tested displayed a concentration dependent inhibition of L. monocytogenes growth in pure culture at the micromolar level and significantly reduced intracellular L. monocytogenes in infected cell culture and Caenorhabditis elegans whole animal model. In vitro, the combined PNAs treatment was synergistic resulting in a clearance of L. monocytogenes at 0.5× the individual PNA concentration. This study demonstrates the potential of anti-rpoA PNA as an antibacterial agent and will provide the basis for improving and developing these PNAs to better target intracellular pathogens like Listeria. This study also establishes C. elegans as a potential model for the screening of PNAs.
Collapse
Affiliation(s)
- Ruba A Alajlouni
- Department of Comparative Pathobiology, Purdue University College of Veterinary Medicine West Lafayette, Indiana, USA
| | | |
Collapse
|
48
|
Synthetic RNA Silencing of Actinorhodin Biosynthesis in Streptomyces coelicolor A3(2). PLoS One 2013; 8:e67509. [PMID: 23826310 PMCID: PMC3694883 DOI: 10.1371/journal.pone.0067509] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 05/24/2013] [Indexed: 01/15/2023] Open
Abstract
We demonstrate the first application of synthetic RNA gene silencers in Streptomyces coelicolor A3(2). Peptide nucleic acid and expressed antisense RNA silencers successfully inhibited actinorhodin production. Synthetic RNA silencing was target-specific and is a new tool for gene regulation and metabolic engineering studies in Streptomyces.
Collapse
|
49
|
Nakashima N, Tamura T. Gene silencing in Escherichia coli using antisense RNAs expressed from doxycycline-inducible vectors. Lett Appl Microbiol 2013; 56:436-42. [PMID: 23480057 DOI: 10.1111/lam.12066] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 02/15/2013] [Accepted: 03/02/2013] [Indexed: 11/30/2022]
Abstract
UNLABELLED Here, we report on the construction of doxycycline (tetracycline analogue)-inducible vectors that express antisense RNAs in Escherichia coli. Using these vectors, the expression of genes of interest can be silenced conditionally. The expression of antisense RNAs from the vectors was more tightly regulated than the previously constructed isopropyl-β-D-galactopyranoside-inducible vectors. Furthermore, expression levels of antisense RNAs were enhanced by combining the doxycycline-inducible promoter with the T7 promoter-T7 RNA polymerase system; the T7 RNA polymerase gene, under control of the doxycycline-inducible promoter, was integrated into the lacZ locus of the genome without leaving any antibiotic marker. These vectors are useful for investigating gene functions or altering cell phenotypes for biotechnological and industrial applications. SIGNIFICANCE AND IMPACT OF THE STUDY A gene silencing method using antisense RNAs in Escherichia coli is described, which facilitates the investigation of bacterial gene function. In particular, the method is suitable for comprehensive analyses or phenotypic analyses of genes essential for growth. Here, we describe expansion of vector variations for expressing antisense RNAs, allowing choice of a vector appropriate for the target genes or experimental purpose.
Collapse
Affiliation(s)
- N Nakashima
- Bioproduction Research Institute, National Institute of Advanced Industrial Sciences and Technology AIST, Sapporo 062-8517, Japan.
| | | |
Collapse
|
50
|
Downregulation of yidC in Escherichia coli by antisense RNA expression results in sensitization to antibacterial essential oils eugenol and carvacrol. PLoS One 2013; 8:e57370. [PMID: 23469191 PMCID: PMC3587592 DOI: 10.1371/journal.pone.0057370] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 01/21/2013] [Indexed: 11/19/2022] Open
Abstract
Background The rising drug resistance in pathogenic bacteria and inefficiency of current antibiotics to meet clinical requirements has augmented the need to establish new and innovative approaches for antibacterial drug discovery involving identification of novel antibacterial targets and inhibitors. Being obligatory for bacterial growth, essential gene products are considered vital as drug targets. The bacterial protein YidC is highly conserved among pathogens and is essential for membrane protein insertion due to which it holds immense potential as a promising target for antibacterial therapy. Methods/Principal Findings The aim of this study was to explore the feasibility and efficacy of expressed antisense-mediated gene silencing for specific downregulation of yidC in Escherichia coli. We induced RNA silencing of yidC which resulted in impaired growth of the host cells. This was followed by a search for antibacterial compounds sensitizing the YidC depleted cells as they may act as inhibitors of the essential protein or its products. The present findings affirm that reduction of YidC synthesis results in bacterial growth retardation, which warrants the use of this enzyme as a viable target in search of novel antibacterial agents. Moreover, yidC antisense expression in E. coli resulted in sensitization to antibacterial essential oils eugenol and carvacrol. Fractional Inhibitory Concentration Indices (FICIs) point towards high level of synergy between yidC silencing and eugenol/carvacrol treatment. Finally, as there are no known YidC inhibitors, the RNA silencing approach applied in this study put forward rapid means to screen novel potential YidC inhibitors. Conclusions/Significance The present results suggest that YidC is a promising candidate target for screening antibacterial agents. High level of synergy reported here between yidC silencing and eugenol/carvacrol treatment is indicative of a potential antibacterial therapy. This is the first report indicating that the essential gene yidC is a therapeutic target of the antibacterial essential oils eugenol and carvacrol in E. coli.
Collapse
|