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Mao C, Wang Y, Yang Y, Li L, Yuan K, Cao H, Qiu Z, Guo G, Wu J, Peng J. Cec4-Derived Peptide Inhibits Planktonic and Biofilm-Associated Methicillin Resistant Staphylococcus epidermidis. Microbiol Spectr 2022; 10:e0240922. [PMID: 36453944 PMCID: PMC9769716 DOI: 10.1128/spectrum.02409-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/08/2022] [Indexed: 12/05/2022] Open
Abstract
Staphylococcus epidermidis is part of the normal microbiota that colonizes the skin and mucosal surfaces of human beings. Previous studies suggested that S. epidermidis possessed low virulence, but recent studies confirmed that it can acquire high virulence from Staphylococcus aureus and with the increasing detection of methicillin-resistant S. epidermidis. It has become a major pathogen of graft-associated and hospital-acquired infections. In previous studies, we modified the antimicrobial peptide Cec4 (41 amino acids) and obtained the derived peptide C9 (16 amino acids) showing better antimicrobial activity against S. epidermidis with an MIC value of 8 μg/mL. The peptide has rapid bactericidal activity without detectable high-level resistance, showing certain inhibition and eradication ability on S. epidermidis biofilms. The damage of cell membrane structures by C9 was observed by scanning emission microscopy (SEM) and transmission electron microscopy (TEM). In addition, C9 altered the S. epidermidis cell membrane permeability, depolarization levels, fluidity, and reactive oxygen species (ROS) accumulation and possessed the ability to bind genomic DNA. Analysis of the transcriptional profiles of C9-treated cells revealed changes in genes involved in cell wall and ribosome biosynthesis, membrane protein transport, oxidative stress, and DNA transcription regulation. At the same time, the median lethal dose of C9 in mice was more than 128 mg/kg, and the intraperitoneal administration of 64 mg/kg was less toxic to the liver and kidneys of mice. Furthermore, C9 also showed a certain therapeutic effect on the mouse bacteremia model. In conclusion, C9 may be a candidate drug against S. epidermidis, which has the potential to be further developed as an antibacterial therapeutic agent. IMPORTANCE S. epidermidis is one of the most important pathogens of graft-related infection and hospital-acquired infection. The growing problem of antibiotic resistance, as well as the emergence of bacterial pathogenicity, highlights the need for antimicrobials with new modes of action. Antimicrobial peptides have been extensively studied over the past 30 years as ideal alternatives to antibiotics, and we report here that the derived peptide C9 is characterized by rapid bactericidal and antibiofilm activity, avoiding the development of resistance by acting on multiple nonspecific targets of the cell membrane or cell components. In addition, it has therapeutic potential against S. epidermidis infection in vivo. This study provides a rationale for the further development and application of C9 as an effective candidate antibiotic.
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Affiliation(s)
- Chengju Mao
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Cellular Immunotherapy Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- The Key and Characteristic Laboratory of Modern Pathogen Biology, Basic Medical College, Guizhou Medical University, Guiyang, China
| | - Yue Wang
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Cellular Immunotherapy Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- The Key and Characteristic Laboratory of Modern Pathogen Biology, Basic Medical College, Guizhou Medical University, Guiyang, China
| | - Yifan Yang
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Cellular Immunotherapy Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- The Key and Characteristic Laboratory of Modern Pathogen Biology, Basic Medical College, Guizhou Medical University, Guiyang, China
| | - Lu Li
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Cellular Immunotherapy Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Kexin Yuan
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Cellular Immunotherapy Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Huijun Cao
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Zhilang Qiu
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Cellular Immunotherapy Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, China
- The Key and Characteristic Laboratory of Modern Pathogen Biology, Basic Medical College, Guizhou Medical University, Guiyang, China
| | - Guo Guo
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, China
- The Key and Characteristic Laboratory of Modern Pathogen Biology, Basic Medical College, Guizhou Medical University, Guiyang, China
| | - Jianwei Wu
- The Key and Characteristic Laboratory of Modern Pathogen Biology, Basic Medical College, Guizhou Medical University, Guiyang, China
| | - Jian Peng
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Cellular Immunotherapy Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, China
- The Key and Characteristic Laboratory of Modern Pathogen Biology, Basic Medical College, Guizhou Medical University, Guiyang, China
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Sulaiman JE, Long L, Qian PY, Lam H. Proteome profiling of evolved methicillin-resistant Staphylococcus aureus strains with distinct daptomycin tolerance and resistance phenotypes. Front Microbiol 2022; 13:970146. [PMID: 35992709 PMCID: PMC9386379 DOI: 10.3389/fmicb.2022.970146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/13/2022] [Indexed: 12/04/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a highly dangerous pathogen, and daptomycin has been increasingly used to treat its infections in clinics. Recently, several groups have shown that tolerance and resistance of microbes can evolve rapidly under cyclic antibiotic exposure. We have previously shown that the same tolerance and resistance development occurs in MRSA treated with daptomycin in an adaptive laboratory evolution (ALE) experiment. In the present study, we performed proteomic analysis to compare six daptomycin-tolerant and resistant MRSA strains that were evolved from the same ancestral strain. The strain with a higher tolerance level than the others had the most different proteome and response to antibiotic treatment, resembling those observed in persister cells, which are small subpopulations of bacteria that survive lethal antibiotics treatment. By comparing the proteome changes across strains with similar phenotypes, we identified the key proteins that play important roles in daptomycin tolerance and resistance in MRSA. We selected two candidates to be confirmed by gene overexpression analysis. Overexpression of EcsA1 and FabG, which were up-regulated in all of the tolerant evolved strains, led to increased daptomycin tolerance in wild-type MRSA. The proteomics data also suggested that cell wall modulations were implicated in both resistance and tolerance, but in different ways. While the resistant strains had peptidoglycan changes and a more positive surface charge to directly repel daptomycin, the tolerant strains possessed different cell wall changes that do not involve the peptidoglycan nor alterations of the surface charge. Overall, our study showed the differential proteome profiles among multiple tolerant and resistant strains, pinpointed the key proteins for the two phenotypes and revealed the differences in cell wall modulations between the daptomycin-tolerant/resistant strains.
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Affiliation(s)
- Jordy Evan Sulaiman
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Lexin Long
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
- *Correspondence: Henry Lam,
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Subramanian D, Natarajan J. Leveraging big data bioinformatics approaches to extract knowledge from Staphylococcus aureus public omics data. Crit Rev Microbiol 2022; 49:391-413. [PMID: 35468027 DOI: 10.1080/1040841x.2022.2065905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Staphylococcus aureus is a notorious pathogen posing challenges in the medical industry due to drug resistance and biofilm formation. The horizon of knowledge on S. aureus pathogenesis has expanded with the advancement of data-driven bioinformatics techniques. Mining information from sequenced genomes and their expression data is an economic approach that alleviates wastage of resources and redundancy in experiments. The current review covers how big data bioinformatics has been used in the analysis of S. aureus from publicly available -omics data to uncover mechanisms of infection and inhibition. Particularly, advances in the past two decades in biomarker discovery, host responses, phenotype identification, consolidation of information, and drug development are discussed highlighting the challenges and shortcomings. Overall, the review summarizes the diverse aspects of scrupulous re-analysis of S. aureus proteomic and transcriptomic expression datasets retrieved from public repositories in terms of the efforts taken, benefits offered, and follow-up actions. The detailed review thus serves as a reference and aid for (i) Computational biologists by briefing the approaches utilized for bacterial omics re-analysis concerning S. aureus and (ii) Experimental biologists by elucidating the potential of bioinformatics in biological research to generate reliable postulates in a prompt and economical manner.
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Affiliation(s)
- Devika Subramanian
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, India
| | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, India
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Sulaiman JE, Long L, Qian PY, Lam H. Proteomics and Transcriptomics Uncover Key Processes for Elasnin Tolerance in Methicillin-Resistant Staphylococcus aureus. mSystems 2022; 7:e0139321. [PMID: 35076266 PMCID: PMC8788329 DOI: 10.1128/msystems.01393-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/03/2022] [Indexed: 01/21/2023] Open
Abstract
Elasnin is a new antibiofilm compound that was recently reported to have excellent activity against methicillin-resistant Staphylococcus aureus (MRSA) biofilms. In this study, we established that elasnin also has antibacterial activity against growing S. aureus planktonic cells. To explore elasnin's potential as an antibiotic, we applied adaptive laboratory evolution (ALE) and produced evolved strains with elevated elasnin tolerance. Interestingly, they were more sensitive toward daptomycin and lysostaphin. Whole-genome sequencing revealed that all of the evolved strains possessed a single point mutation in a putative phosphate transport regulator. Subsequently, they exhibited increased intracellular phosphate (Pi) and polyphosphate levels. Inhibition of the phosphate transport regulator gene changed the phenotype of the wild type to one resembling those observed in the evolved strains. Proteomics and transcriptomics analyses showed that elasnin treatment resulted in the downregulation of many proteins related to cell division and cell wall synthesis, which is important for the survival of growing exponential-phase cells. Other downregulated processes and factors were fatty acid metabolism, glycolysis, the two-component system, RNA degradation, and ribosomal proteins. Most importantly, transport proteins and proteins involved in oxidative phosphorylation and the phosphotransferase system were more upregulated in the evolved strain than in the ancestral strain, indicating that they are important for elasnin tolerance. Overall, this study showed that elasnin has antibacterial activity against growing S. aureus cells and revealed the altered processes due to elasnin treatment and those associated with its tolerance. IMPORTANCE Besides the excellent antibiofilm properties of elasnin, we discovered that it can also kill growing methicillin-resistant Staphylococcus aureus (MRSA) planktonic cells. We subjected MRSA cells to an in vitro evolution experiment, and the resulting evolved strains exhibited increased elasnin tolerance, reduced growth rate, loss of pigmentation, and an increased proportion of small-colony formation, and they became more sensitive toward daptomycin and lysostaphin. Through multiomics analysis, we uncovered the affected processes in growing S. aureus planktonic cells following elasnin treatment, including the downregulation of cell wall synthesis, cell division, and some genes/proteins for the two-component system. These findings suggest that elasnin suppressed processes important for the cells' survival and adaptation to environmental stresses, making it an ideal drug adjuvant candidate. Overall, our study provides new insights into the mechanism of elasnin in S. aureus planktonic cells and pointed out the potential application of elasnin in clinics.
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Affiliation(s)
- Jordy Evan Sulaiman
- Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, People’s Republic of China
| | - Lexin Long
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, People’s Republic of China
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, People’s Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, People’s Republic of China
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, People’s Republic of China
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Chen Y, Moran JC, Campbell-Lee S, Horsburgh MJ. Transcriptomic Responses and Survival Mechanisms of Staphylococci to the Antimicrobial Skin Lipid Sphingosine. Antimicrob Agents Chemother 2022; 66:e0056921. [PMID: 34902269 PMCID: PMC8846397 DOI: 10.1128/aac.00569-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 11/17/2021] [Indexed: 11/20/2022] Open
Abstract
Sphingosines are antimicrobial lipids that form part of the innate barrier to skin colonization by microbes. Sphingosine deficiencies can result in increased epithelial infections by bacteria including Staphylococcus aureus. Recent studies have focused on the potential use of sphingosine resistance or its potential mechanisms. We used RNA-Seq to identify the common d-sphingosine transcriptomic response of the transient skin colonizer S. aureus and the dominant skin coloniser S. epidermidis. A common d-sphingosine stimulon was identified that included downregulation of the SaeSR two-component system (TCS) regulon and upregulation of both the VraSR TCS and CtsR stress regulons. We show that the PstSCAB phosphate transporter, and VraSR offer intrinsic resistance to d-sphingosine. Further, we demonstrate increased sphingosine resistance in these staphylococci evolves readily through mutations in genes encoding the FarE-FarR efflux/regulator proteins. The ease of selecting mutants with resistance to sphingosine may impact upon staphylococcal colonization of skin where the lipid is present and have implications with topical therapeutic applications.
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Affiliation(s)
- Yiyun Chen
- Staphylococcus Research Group, Institute of Infection Biology, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Josephine C. Moran
- Staphylococcus Research Group, Institute of Infection Biology, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Stuart Campbell-Lee
- Staphylococcus Research Group, Institute of Infection Biology, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Malcolm J. Horsburgh
- Staphylococcus Research Group, Institute of Infection Biology, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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Overton IM, Sims AH, Owen JA, Heale BSE, Ford MJ, Lubbock ALR, Pairo-Castineira E, Essafi A. Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling. Cancers (Basel) 2020; 12:cancers12102823. [PMID: 33007944 PMCID: PMC7652213 DOI: 10.3390/cancers12102823] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 09/16/2020] [Accepted: 09/24/2020] [Indexed: 12/15/2022] Open
Abstract
Cell identity is governed by gene expression, regulated by transcription factor (TF) binding at cis-regulatory modules. Decoding the relationship between TF binding patterns and gene regulation is nontrivial, remaining a fundamental limitation in understanding cell decision-making. We developed the NetNC software to predict functionally active regulation of TF targets; demonstrated on nine datasets for the TFs Snail, Twist, and modENCODE Highly Occupied Target (HOT) regions. Snail and Twist are canonical drivers of epithelial to mesenchymal transition (EMT), a cell programme important in development, tumour progression and fibrosis. Predicted "neutral" (non-functional) TF binding always accounted for the majority (50% to 95%) of candidate target genes from statistically significant peaks and HOT regions had higher functional binding than most of the Snail and Twist datasets examined. Our results illuminated conserved gene networks that control epithelial plasticity in development and disease. We identified new gene functions and network modules including crosstalk with notch signalling and regulation of chromatin organisation, evidencing networks that reshape Waddington's epigenetic landscape during epithelial remodelling. Expression of orthologous functional TF targets discriminated breast cancer molecular subtypes and predicted novel tumour biology, with implications for precision medicine. Predicted invasion roles were validated using a tractable cell model, supporting our approach.
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Affiliation(s)
- Ian M. Overton
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (A.H.S.); (B.S.E.H.); (M.J.F.); (A.L.R.L.); (E.P.-C.); (A.E.)
- Department of Systems Biology, Harvard University, Boston, MA 02115, USA;
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH9 3BF, UK
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK
- Correspondence:
| | - Andrew H. Sims
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (A.H.S.); (B.S.E.H.); (M.J.F.); (A.L.R.L.); (E.P.-C.); (A.E.)
| | - Jeremy A. Owen
- Department of Systems Biology, Harvard University, Boston, MA 02115, USA;
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bret S. E. Heale
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (A.H.S.); (B.S.E.H.); (M.J.F.); (A.L.R.L.); (E.P.-C.); (A.E.)
| | - Matthew J. Ford
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (A.H.S.); (B.S.E.H.); (M.J.F.); (A.L.R.L.); (E.P.-C.); (A.E.)
| | - Alexander L. R. Lubbock
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (A.H.S.); (B.S.E.H.); (M.J.F.); (A.L.R.L.); (E.P.-C.); (A.E.)
| | - Erola Pairo-Castineira
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (A.H.S.); (B.S.E.H.); (M.J.F.); (A.L.R.L.); (E.P.-C.); (A.E.)
| | - Abdelkader Essafi
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (A.H.S.); (B.S.E.H.); (M.J.F.); (A.L.R.L.); (E.P.-C.); (A.E.)
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Karatzas KAG, Lemmens-den Toom NA, Tassou CC, van Leeuwen W, van Belkum A. Molecular characterization of piezotolerant and stress-resistant mutants of Staphylococcus aureus. J Appl Microbiol 2020; 130:901-912. [PMID: 32871628 DOI: 10.1111/jam.14832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/08/2020] [Accepted: 08/04/2020] [Indexed: 11/29/2022]
Abstract
AIMS In the previous work, following a pressure treatment with wild-type Staphylococcus aureus, we obtained piezotolerant isolates showing altered phenotypic characteristics. This work focuses on understanding the genetic background of their altered phenotype. METHODS AND RESULTS AK23, a representative piezotolerant isolate was subjected to DNA microarrays, corroborated by PCR product sequencing and revealed 10-gene deletion. All other piezotolerant isolates possessed the mutation encompassing the region from SAR0665 to SAR0674 genes (9351 bp) which was most likely the result of recombination between two homologous loci (ATTGCGGGTG) present in both genes. RNA microarray transcriptomic analysis showed that due to partial deletion of the low-affinity phosphate transporter pitA, the high-affinity PhoU-PstABCS operon was upregulated in AK23 which could be the reason for piezotolerance. Furthermore, AK23 showed low levels of the virulence gene regulator rnaIII resulting in the downregulation of several agr system genes explaining the impaired virulence characteristics of the mutant. CONCLUSIONS Naturally occurring mutations can result in piezotolerance which can be of a concern for high hydrostatic pressure-treated foods. SIGNIFICANCE AND IMPACT OF THE STUDY A locus has been identified in piezotolerant S. aureus mutants providing insight into possible mechanisms associated with phenotypic characteristics of S. aureus. Further work should study each individual gene of the locus.
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Affiliation(s)
- K A G Karatzas
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | - N A Lemmens-den Toom
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, GD Rotterdam, The Netherlands
| | - C C Tassou
- Hellenic Agricultural Organisation 'DEMETER', Institute of Technology of Agricultural Products, Attikis, Greece
| | - W van Leeuwen
- Leiden Centre for Applied Bioscience, University of Applied Science Leiden, Leiden, The Netherlands
| | - A van Belkum
- BioMérieux, Open Innovation & Partnerships, La Balme Les Grottes, France
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Li J, Fernández-Millán P, Boix E. Synergism between Host Defence Peptides and Antibiotics Against Bacterial Infections. Curr Top Med Chem 2020; 20:1238-1263. [DOI: 10.2174/1568026620666200303122626] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/22/2020] [Accepted: 02/07/2020] [Indexed: 01/10/2023]
Abstract
Background:Antimicrobial resistance (AMR) to conventional antibiotics is becoming one of the main global health threats and novel alternative strategies are urging. Antimicrobial peptides (AMPs), once forgotten, are coming back into the scene as promising tools to overcome bacterial resistance. Recent findings have attracted attention to the potentiality of AMPs to work as antibiotic adjuvants.Methods:In this review, we have tried to collect the currently available information on the mechanism of action of AMPs in synergy with other antimicrobial agents. In particular, we have focused on the mechanisms of action that mediate the inhibition of the emergence of bacterial resistance by AMPs.Results and Conclusion:We find in the literature many examples where AMPs can significantly reduce the antibiotic effective concentration. Mainly, the peptides work at the bacterial cell wall and thereby facilitate the drug access to its intracellular target. Complementarily, AMPs can also contribute to permeate the exopolysaccharide layer of biofilm communities, or even prevent bacterial adhesion and biofilm growth. Secondly, we find other peptides that can directly block the emergence of bacterial resistance mechanisms or interfere with the community quorum-sensing systems. Interestingly, the effective peptide concentrations for adjuvant activity and inhibition of bacterial resistance are much lower than the required for direct antimicrobial action. Finally, many AMPs expressed by innate immune cells are endowed with immunomodulatory properties and can participate in the host response against infection. Recent studies in animal models confirm that AMPs work as adjuvants at non-toxic concentrations and can be safely administrated for novel combined chemotherapies.
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Affiliation(s)
- Jiarui Li
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autonoma de Barcelona, Cerdanyola del Valles, Spain
| | - Pablo Fernández-Millán
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autonoma de Barcelona, Cerdanyola del Valles, Spain
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autonoma de Barcelona, Cerdanyola del Valles, Spain
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Shang Y, Wang X, Chen Z, Lyu Z, Lin Z, Zheng J, Wu Y, Deng Q, Yu Z, Zhang Y, Qu D. Staphylococcus aureus PhoU Homologs Regulate Persister Formation and Virulence. Front Microbiol 2020; 11:865. [PMID: 32670206 PMCID: PMC7326077 DOI: 10.3389/fmicb.2020.00865] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/14/2020] [Indexed: 12/12/2022] Open
Abstract
PhoU homologs are one of the determinant factors in the regulation of persister formation and phosphate metabolism in many bacterial species; however, the functions of PhoU homologs exhibit species-specific characteristics. The pathogenesis of Staphylococcus aureus is closely correlated with persister formation and virulence factors. The functions of two PhoU homologs, PhoU1 and PhoU2, in S. aureus are unclear yet. In this study, single- and double-deletion mutants of phoU1 and phoU2 were generated in strain USA500 2395. The ΔphoU1 or ΔphoU2 mutants displayed a change in persister formation and virulence compared to the parent strain; the persisters to vancomycin and levofloxacin were decreased at least 1,000-fold, and the number of intracellular bacteria surviving in the A549 cells for 24 h decreased to 82 or 85%. The α-hemolysin expression and activity were increased in the ΔphoU2 mutants. Transcriptome analysis revealed that 573 or 285 genes were differentially expressed by at least 2.0-fold in the ΔphoU1 or ΔphoU2 mutant vs. the wild type. Genes involved in carbon and pyruvate metabolism were up-regulated, and virulence genes and virulence regulatory genes were down-regulated, including type VII secretion system, serine protease, leukocidin, global regulator (sarA, rot), and the two-component signal transduction system (saeS). Correspondingly, the deletion of the phoU1 or phoU2 resulted in increased levels of intracellular pyruvate and ATP. Deletion of the phoU2, but not the phoU1, resulted in the up-regulation of inorganic phosphate transport genes and increased levels of intracellular inorganic polyphosphate. In conclusion, both PhoU1 and PhoU2 in S. aureus regulate virulence by the down-regulation of multiple virulence factors (type VII secretion system, serine protease, and leucocidin) and the persister generation by hyperactive carbon metabolism accompanied by increasing intracellular ATP. The results in S. aureus are different from what we have previously found in Staphylococcus epidermis, where only PhoU2 regulates biofilm and persister formation. The different functions of PhoU homologs between the two species of Staphylococcus warrant further investigation.
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Affiliation(s)
- Yongpeng Shang
- Key Laboratory of Medical Molecular Virology of MOE and MOH, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiaofei Wang
- Key Laboratory of Medical Molecular Virology of MOE and MOH, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Zhong Chen
- Key Laboratory of Medical Molecular Virology of MOE and MOH, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Zhihui Lyu
- Key Laboratory of Medical Molecular Virology of MOE and MOH, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Zhiwei Lin
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Union Shenzhen Hospital, Huazhong University of Science and Technology, Shenzhen, China
| | - Jinxin Zheng
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Union Shenzhen Hospital, Huazhong University of Science and Technology, Shenzhen, China
| | - Yang Wu
- Key Laboratory of Medical Molecular Virology of MOE and MOH, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qiwen Deng
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Union Shenzhen Hospital, Huazhong University of Science and Technology, Shenzhen, China
| | - Zhijian Yu
- Department of Infectious Diseases and Shenzhen Key Lab for Endogenous Infection, Union Shenzhen Hospital, Huazhong University of Science and Technology, Shenzhen, China
| | - Ying Zhang
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Di Qu
- Key Laboratory of Medical Molecular Virology of MOE and MOH, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
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Zhao Y, Pang X, Nepal A, Jiang X, Xu X, Zhao D, Murtaza G, Ma Y. Caffeic Acid Phenethyl Ester Effects: In Silico Study of its Osteoimmunological Mechanisms. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180815666180803111902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Biological system complexity impedes the drug target identification by
biological experiments. Thus drugs, rather than acting on target site only, can interact with the entire
biological system. Study of this phenomenon, known as network pharmacology, provides
grounds for biological target identification of new drugs or acts as a foundation for the discovery of
new targets of present drugs. No publication is available on the interaction network of CAPE.
Aim:
This study was aimed at the investigation of the candidate targets and possible interactions of
caffeic acid phenethyl ester (CAPE) involved in its osteoimmunological effects.
Methods:
This study encompasses the investigation of candidate targets and possible interactions of
CAPE by analyzing through PASS Prediction and constructing a biological network of CAPE.
Results:
In response to input (CAPE), PASS Prediction generated a network of 1723 targets. While
selecting the probability to be active (Pa) value greater than 0.7 brought forth only 27 targets for
CAPE. Most of these targets predicted the therapeutic role of CAPE as an osteoimmunological
agent. Apart from this, this network pharmacology also identified 10 potential anti-cancer targets
for CAPE, out of which 7 targets have been used efficiently in developing potent osteoimmunological
drugs.
Conclusion:
This study provides scientific prediction of the mechanisms involved in osteoimmunological
effects of CAPE, presenting its promising use in the development of a natural therapeutic
agent for the pharmaceutical industry. CAPE targets identified by web-based online databases and
network pharmacology need additional in silico assessment such as docking and MD simulation
studies and experimental verification to authenticate these results.
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Affiliation(s)
- Yuhao Zhao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China
| | - Xiaokun Pang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China
| | - Akriti Nepal
- Department of Pharmacology, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Xincan Jiang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China
| | - Xiaoxin Xu
- Information center, Beijing University of Chinese Medicine, 100029 Beijing, China
| | - Dongbin Zhao
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Ghulam Murtaza
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Yanxu Ma
- Department of Orthopedics, Beijing Traditional Chinese Medicine Hospital, Capital Medical University, Beijing 100010, China
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11
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Ribič U, Jakše J, Toplak N, Koren S, Kovač M, Klančnik A, Jeršek B. Transporters and Efflux Pumps Are the Main Mechanisms Involved in Staphylococcus epidermidis Adaptation and Tolerance to Didecyldimethylammonium Chloride. Microorganisms 2020; 8:E344. [PMID: 32121333 PMCID: PMC7143832 DOI: 10.3390/microorganisms8030344] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 01/28/2023] Open
Abstract
Staphylococcus epidermidis cleanroom strains are often exposed to sub-inhibitory concentrations of disinfectants, including didecyldimethylammonium chloride (DDAC). Consequently, they can adapt or even become tolerant to them. RNA-sequencing was used to investigate adaptation and tolerance mechanisms of S. epidermidis cleanroom strains (SE11, SE18), with S. epidermidis SE11Ad adapted and S. epidermidis SE18To tolerant to DDAC. Adaptation to DDAC was identified with up-regulation of genes mainly involved in transport (thioredoxin reductase [pstS], the arsenic efflux pump [gene ID, SE0334], sugar phosphate antiporter [uhpT]), while down-regulation was seen for the Agr system (agrA, arC, agrD, psm, SE1543), for enhanced biofilm formation. Tolerance to DDAC revealed the up-regulation of genes associated with transporters (L-cysteine transport [tcyB]; uracil permease [SE0875]; multidrug transporter [lmrP]; arsenic efflux pump [arsB]); the down-regulation of genes involved in amino-acid biosynthesis (lysine [dapE]; histidine [hisA]; methionine [metC]), and an enzyme involved in peptidoglycan, and therefore cell wall modifications (alanine racemase [SE1079]). We show for the first time the differentially expressed genes in DDAC-adapted and DDAC-tolerant S. epidermidis strains, which highlight the complexity of the responses through the involvement of different mechanisms.
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Affiliation(s)
- Urška Ribič
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (U.R.); (A.K.)
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia;
| | - Nataša Toplak
- Omega d.o.o., Dolinškova 8, SI-1000 Ljubljana, Slovenia; (N.T.); (S.K.); (M.K.)
| | - Simon Koren
- Omega d.o.o., Dolinškova 8, SI-1000 Ljubljana, Slovenia; (N.T.); (S.K.); (M.K.)
| | - Minka Kovač
- Omega d.o.o., Dolinškova 8, SI-1000 Ljubljana, Slovenia; (N.T.); (S.K.); (M.K.)
| | - Anja Klančnik
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (U.R.); (A.K.)
| | - Barbara Jeršek
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (U.R.); (A.K.)
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12
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Subramanian D, Bhasuran B, Natarajan J. Genomic analysis of RNA-Seq and sRNA-Seq data identifies potential regulatory sRNAs and their functional roles in Staphylococcus aureus. Genomics 2019; 111:1431-1446. [DOI: 10.1016/j.ygeno.2018.09.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 09/21/2018] [Accepted: 09/26/2018] [Indexed: 12/17/2022]
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13
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FOXO Transcriptional Factors and Long-Term Living. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:3494289. [PMID: 28894507 PMCID: PMC5574317 DOI: 10.1155/2017/3494289] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 06/21/2017] [Indexed: 12/15/2022]
Abstract
Several pathologies such as neurodegeneration and cancer are associated with aging, which is affected by many genetic and environmental factors. Healthy aging conceives human longevity, possibly due to carrying the defensive genes. For instance, FOXO (forkhead box O) genes determine human longevity. FOXO transcription factors are involved in the regulation of longevity phenomenon via insulin and insulin-like growth factor signaling. Only one FOXO gene (FOXO DAF-16) exists in invertebrates, while four FOXO genes, that is, FOXO1, FOXO3, FOXO4, and FOXO6 are found in mammals. These four transcription factors are involved in the multiple cellular pathways, which regulate growth, stress resistance, metabolism, cellular differentiation, and apoptosis in mammals. However, the accurate mode of longevity by FOXO factors is unclear until now. This article describes briefly the existing knowledge that is related to the role of FOXO factors in human longevity.
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14
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Pando JM, Pfeltz RF, Cuaron JA, Nagarajan V, Mishra MN, Torres NJ, Elasri MO, Wilkinson BJ, Gustafson JE. Ethanol-induced stress response of Staphylococcus aureus. Can J Microbiol 2017; 63:745-757. [PMID: 28521110 DOI: 10.1139/cjm-2017-0221] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Transcriptional profiles of 2 unrelated clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates were analyzed following 10% (v/v) ethanol challenge (15 min), which arrested growth but did not reduce viability. Ethanol-induced stress (EIS) resulted in differential gene expression of 1091 genes, 600 common to both strains, of which 291 were upregulated. With the exception of the downregulation of genes involved with osmotic stress functions, EIS resulted in the upregulation of genes that contribute to stress response networks, notably those altered by oxidative stress, protein quality control in general, and heat shock in particular. In addition, genes involved with transcription, translation, and nucleotide biosynthesis were downregulated. relP, which encodes a small alarmone synthetase (RelP), was highly upregulated in both MRSA strains following ethanol challenge, and relP inactivation experiments indicated that this gene contributed to EIS growth arrest. A number of persistence-associated genes were also upregulated during EIS, including those that encode toxin-antitoxin systems. Overall, transcriptional profiling indicated that the MRSA investigated responded to EIS by entering a state of dormancy and by altering the expression of elements from cross protective stress response systems in an effort to protect preexisting proteins.
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Affiliation(s)
- Jasmine M Pando
- a Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
| | - Richard F Pfeltz
- b BD Diagnostic Systems, Microbiology R&D Department, Sparks, MD 21152, USA
| | - Jesus A Cuaron
- a Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
| | - Vijayaraj Nagarajan
- c Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Mukti N Mishra
- d Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Nathanial J Torres
- d Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Mohamed O Elasri
- c Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Brian J Wilkinson
- e Microbiology Group, School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - John E Gustafson
- a Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA.,d Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
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15
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Domínguez Á, Muñoz E, López MC, Cordero M, Martínez JP, Viñas M. Transcriptomics as a tool to discover new antibacterial targets. Biotechnol Lett 2017; 39:819-828. [PMID: 28289911 DOI: 10.1007/s10529-017-2319-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/07/2017] [Indexed: 12/20/2022]
Abstract
The emergence of antibiotic-resistant pathogens, multiple drug-resistance, and extremely drug-resistant strains demonstrates the need for improved strategies to discover new drug-based compounds. The development of transcriptomics, proteomics, and metabolomics has provided new tools for global studies of living organisms. However, the compendium of expression profiles produced by these methods has introduced new scientific challenges into antimicrobial research. In this review, we discuss the practical value of transcriptomic techniques as well as their difficulties and pitfalls. We advocate the construction of new databases of transcriptomic data, using standardized formats in addition to standardized models of bacterial and yeast similar to those used in systems biology. The inclusion of proteomic and metabolomic data is also essential, as the resulting networks can provide a landscape to rationally predict and exploit new drug targets and to understand drug synergies.
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Affiliation(s)
- Ángel Domínguez
- Department of Microbiology and Genetics, Universidad de Salamanca, Plaza de los Drs. de la Reina s/n, 37007, Salamanca, Spain.
| | - Elisa Muñoz
- Department of Cell Biology & Pathology, Universidad de Salamanca, Salamanca, Spain
| | - M Carmen López
- Department of Microbiology and Genetics, Universidad de Salamanca, Plaza de los Drs. de la Reina s/n, 37007, Salamanca, Spain
| | - Miguel Cordero
- Department of Medicine, Universidad de Salamanca, Salamanca, Spain
| | - José Pedro Martínez
- Department of Microbiology & Ecology, Universitat de Valencia/Estudi General (UVEG), Valencia, Spain
| | - Miguel Viñas
- Department of Pathology and Experimental Therapeutics, Universitat de Barcelona, Barcelona, Spain
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16
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Malin J, Shetty AC, Daugherty SC, de Leeuw EP. Effect of a small molecule Lipid II binder on bacterial cell wall stress. Infect Drug Resist 2017; 10:69-73. [PMID: 28280373 PMCID: PMC5338996 DOI: 10.2147/idr.s126254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We have recently identified small molecule compounds that act as binders of Lipid II, an essential precursor of bacterial cell wall biosynthesis. Lipid II comprised a hydrophilic head group that includes a peptidoglycan subunit composed of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) coupled to a short pentapeptide moiety. This headgroup is coupled to a long bactoprenol chain via a pyrophosphate group. Here, we report on the cell wall activity relationship of dimethyl-3-methyl(phenyl)amino-ethenylcyclohexylidene-propenyl-3-ethyl-1,3-benzothiazolium iodide (compound 5107930) obtained by functional and genetic analyses. Our results indicate that compounds bind to Lipid II and cause specific upregulation of the vancomycin-resistance associated gene vraX. vraX is implicated in the cell wall stress stimulon that confers glycopeptide resistance. Our small molecule Lipid II inhibitor retained activity against strains of Staphylococcus aureus mutated in genes encoding the cell wall stress stimulon. This suggests the feasibility of developing this new scaffold as a therapeutic agent in view of increasing glycopeptide resistance.
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Affiliation(s)
- Jakob Malin
- Institute of Human Virology; Department of Biochemistry and Molecular Biology
| | - Amol C Shetty
- Institute for Genome Sciences, University of Maryland Baltimore School of Medicine, Baltimore, MD, USA
| | - Sean C Daugherty
- Institute for Genome Sciences, University of Maryland Baltimore School of Medicine, Baltimore, MD, USA
| | - Erik Ph de Leeuw
- Institute of Human Virology; Department of Biochemistry and Molecular Biology
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17
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Côté-Gravel J, Brouillette E, Obradović N, Ster C, Talbot BG, Malouin F. Characterization of a vraG Mutant in a Genetically Stable Staphylococcus aureus Small-Colony Variant and Preliminary Assessment for Use as a Live-Attenuated Vaccine against Intrammamary Infections. PLoS One 2016; 11:e0166621. [PMID: 27855187 PMCID: PMC5113970 DOI: 10.1371/journal.pone.0166621] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 11/01/2016] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus aureus is a leading cause of bovine intramammary infections (IMIs) that can evolve into difficult-to-treat chronic mastitis. To date, no vaccine formulation has shown high protective efficacy against S. aureus IMI, partly because this bacterium can efficiently evade the immune system. For instance, S. aureus small colony variants (SCVs) have intracellular abilities and can persist without producing invasive infections. As a first step towards the development of a live vaccine, this study describes the elaboration of a novel attenuated mutant of S. aureus taking advantage of the SCV phenotype. A genetically stable SCV was created through the deletion of the hemB gene, impairing its ability to adapt and revert to the invasive phenotype. Further attenuation was obtained through inactivation of gene vraG (SACOL0720) which we previously showed to be important for full virulence during bovine IMIs. After infection of bovine mammary epithelial cells (MAC-T), the double mutant (ΔvraGΔhemB) was less internalized and caused less cell destruction than that seen with ΔhemB and ΔvraG, respectively. In a murine IMI model, the ΔvraGΔhemB mutant was strongly attenuated, with a reduction of viable counts of up to 5-log10 CFU/g of mammary gland when compared to the parental strain. A complete clearance of ΔvraGΔhemB from glands was observed whereas mortality rapidly (48h) occurred with the wild-type strain. Immunization of mice using subcutaneous injections of live ΔvraGΔhemB raised a strong immune response as judged by the high total IgG titers measured against bacterial cell extracts and by the high IgG2a/IgG1 ratio observed against the IsdH protein. Also, ΔvraGΔhemB had sufficient common features with bovine mastitis strains so that the antibody response also strongly recognized strains from a variety of mastitis associated spa types. This double mutant could serve as a live-attenuated component in vaccines to improve cell-mediated immune responses against S. aureus IMIs.
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Affiliation(s)
- Julie Côté-Gravel
- Centre d’Étude et de Valorisation de la Diversité Microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Eric Brouillette
- Centre d’Étude et de Valorisation de la Diversité Microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Nataša Obradović
- Centre d’Étude et de Valorisation de la Diversité Microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Céline Ster
- Centre d’Étude et de Valorisation de la Diversité Microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Brian G. Talbot
- Centre d’Étude et de Valorisation de la Diversité Microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - François Malouin
- Centre d’Étude et de Valorisation de la Diversité Microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
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18
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Broadbent JA, Broszczak DA, Tennakoon IUK, Huygens F. Pan-proteomics, a concept for unifying quantitative proteome measurements when comparing closely-related bacterial strains. Expert Rev Proteomics 2016; 13:355-65. [PMID: 26889693 DOI: 10.1586/14789450.2016.1155986] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The comparison of proteomes between genetically heterogeneous bacterial strains may offer valuable insights into physiological diversity and function, particularly where such variation aids in the survival and virulence of clinically-relevant strains. However, reports of such comparisons frequently fail to account for underlying genetic variance. As a consequence, the current knowledge regarding bacterial physiological diversity at the protein level may be incomplete or inaccurate. To address this, greater consideration must be given to the impact of genetic heterogeneity on proteome comparisons. This may be possible through the use of pan-proteomics, an analytical concept that permits the ability to qualitatively and quantitatively compare the proteomes of genetically heterogeneous organisms. Limited examples of this emerging technology highlight currently unmet analytical challenges. In this article we define pan-proteomics, where its value lies in microbiology, and discuss the technical considerations critical to its successful execution and potential future application.
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Affiliation(s)
- James A Broadbent
- a Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health , Queensland University of Technology , Brisbane , Australia.,b Molecular Microbiological Pathogenesis Group, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health , Queensland University of Technology , Brisbane , Australia
| | - Daniel A Broszczak
- a Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health , Queensland University of Technology , Brisbane , Australia
| | - Imalka U K Tennakoon
- b Molecular Microbiological Pathogenesis Group, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health , Queensland University of Technology , Brisbane , Australia
| | - Flavia Huygens
- b Molecular Microbiological Pathogenesis Group, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health , Queensland University of Technology , Brisbane , Australia
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19
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Agarwal S, Sharma G, Dang S, Gupta S, Gabrani R. Antimicrobial Peptides as Anti-Infectives against Staphylococcus epidermidis. Med Princ Pract 2016; 25:301-8. [PMID: 26684017 PMCID: PMC5588407 DOI: 10.1159/000443479] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 12/17/2015] [Indexed: 01/15/2023] Open
Abstract
Staphylococcus epidermidis has emerged as the main causative agent for graft-related and nosocomial infections. Rampant use of antibiotics and biofilm formed by the organism results in poor penetration of the drug and further aggravates the antibiotic resistance, emphasizing an urgent need to explore alternative treatment modalities. Antimicrobial peptides (AMPs), produced as effector molecules of the innate immunity of living organisms, have therapeutic potential that can be used to inhibit the growth of microbes. In addition, the susceptibility of a microbe to become resistant to an AMP is relatively low. The AMPs are amphipathic peptides of 12-100 residues, which have broad-spectrum activity against microbes. There are scattered reports of AMPs listed against S. epidermidis and there is an urgent need to systematically study the AMPs. Various natural AMPs as well as synthetic peptides have been investigated against S. epidermidis. These peptides have been shown to inhibit both planktonic culture and S. epidermidis biofilm effectively. The multiple modes of action in killing the organism minimize the chances for the development of resistance. This review focused on various natural and synthetic peptides that demonstrate activity against S. epidermidis.
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Affiliation(s)
| | | | | | | | - Reema Gabrani
- *Reema Gabrani, Department of Biotechnology, Jaypee Institute of Information Technology, Sector-62, Noida, UP-201307 (India), E-Mail
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20
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Subramanian D, Natarajan J. Network analysis of S. aureus response to ramoplanin reveals modules for virulence factors and resistance mechanisms and characteristic novel genes. Gene 2015; 574:149-62. [DOI: 10.1016/j.gene.2015.08.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/30/2015] [Accepted: 08/03/2015] [Indexed: 12/27/2022]
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21
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Gene network analysis reveals the association of important functional partners involved in antibiotic resistance: A report on an important pathogenic bacterium Staphylococcus aureus. Gene 2015; 575:253-63. [PMID: 26342962 DOI: 10.1016/j.gene.2015.08.068] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/30/2015] [Accepted: 08/31/2015] [Indexed: 12/27/2022]
Abstract
Staphylococcus aureus (S. aureus) is an emerging concern in hospital settings as it causes serious human infections. The multidrug resistance (MDR) in S. aureus is a complicated problem that is difficult to overcome due to the presence of numerous antibiotic resistance genes and it exhibit resistance to most of the currently available antibiotics. Presently, the resistance mechanisms of these genes/proteins are not completely understood. Therefore, identifying and understanding the functional relationship between the antibiotic resistant genes and their associated proteins might provide necessary information on resistance mechanisms and thereby help in designing successful drugs to combat the antibiotic resistance. In this study, we propose a model based on protein/gene network to identify genes/proteins associated with drug resistance in S. aureus. We filtered 50 functional partners in NorA, aacA-aphD (aac6ie), aad9ib (ant), aadd (knt), baca (uppP), bl2a_pc (blaZ), ble, ermA, SAV0052 (ermb), ermc, fosB, mecA (mecI), mecR (mecr1), mepA, msrA1, qacA, vraR (str), tet38 and tetM while 40 functional partners are identified in tet and aphA-3 (aph3iiia). The average shortest path length and betweenness centrality of functional partners in the clusters are calculated and they are functionally enriched with the Gene Ontology (GO) terms with a p-value cut-off ≤0.05. Interestingly, the constructed network reveals many associated antibiotic resistant genes and proteins and their role in resistance mechanisms. Thus, our results might provide a better understanding of the molecular mechanisms of action and their mode of drug resistance that will be useful for researchers exploring in the field of antibiotic resistance mechanisms.
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22
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A novel point mutation promotes growth phase-dependent daptomycin tolerance in Staphylococcus aureus. Antimicrob Agents Chemother 2015; 59:5366-76. [PMID: 26100694 DOI: 10.1128/aac.00643-15] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/11/2015] [Indexed: 12/30/2022] Open
Abstract
Recalcitrance of genetically susceptible bacteria to antibiotic killing is a hallmark of bacterial drug tolerance. This phenomenon is prevalent in biofilms, persisters, and also planktonic cells and is associated with chronic or relapsing infections with pathogens such as Staphylococcus aureus. Here we report the in vitro evolution of an S. aureus strain that exhibits a high degree of nonsusceptibility to daptomycin as a result of cyclic challenges with bactericidal concentrations of the drug. This phenotype was attributed to stationary growth phase-dependent drug tolerance and was clearly distinguished from resistance. The underlying genetic basis was revealed to be an adaptive point mutation in the putative inorganic phosphate (Pi) transporter gene pitA. Drug tolerance caused by this allele, termed pitA6, was abrogated when the upstream gene pitR was inactivated. Enhanced tolerance toward daptomycin, as well as the acyldepsipeptide antibiotic ADEP4 and various combinations of other drugs, was accompanied by elevated intracellular concentrations of Pi and polyphosphate, which may reversibly interfere with critical cellular functions. The evolved strain displayed increased rates of survival within human endothelial cells, demonstrating the correlation of intracellular persistence and drug tolerance. These findings will be useful for further investigations of S. aureus drug tolerance, toward the development of additional antipersister compounds and strategies.
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23
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Choose wisely: Network, ontology and annotation resources for the analysis of Staphylococcus aureus omics data. Int J Med Microbiol 2015; 305:339-47. [DOI: 10.1016/j.ijmm.2015.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 01/21/2015] [Accepted: 02/09/2015] [Indexed: 01/25/2023] Open
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Carbonell P, Trosset JY. Overcoming drug resistance through in silico prediction. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 11:101-7. [PMID: 24847659 DOI: 10.1016/j.ddtec.2014.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Prediction tools are commonly used in pre-clinical research to assist target selection, to optimize drug potency or to predict the pharmacological profile of drug candidates. In silico prediction and overcoming drug resistance is a new opportunity that creates a high interest in pharmaceutical research. This review presents two main in silico strategies to meet this challenge: a structure-based approach to study the influence of mutations on the drug-target interaction and a system-biology approach to identify resistance pathways for a given drug. In silico screening of synergies between therapeutic and resistant pathways through biological network analysis is an example of technique to escape drug resistance. Structure-based drug design and in silico system biology are complementary approaches to reach few objectives at once: increase efficiency, reduce toxicity and overcoming drug resistance.
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25
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Proctor RA, Kriegeskorte A, Kahl BC, Becker K, Löffler B, Peters G. Staphylococcus aureus Small Colony Variants (SCVs): a road map for the metabolic pathways involved in persistent infections. Front Cell Infect Microbiol 2014; 4:99. [PMID: 25120957 PMCID: PMC4112797 DOI: 10.3389/fcimb.2014.00099] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 07/07/2014] [Indexed: 12/31/2022] Open
Abstract
Persistent and relapsing infections, despite apparently adequate antibiotic therapy, occur frequently with many pathogens, but it is an especially prominent problem with Staphylococcus aureus infections. For the purposes of this review, persistence will encompass both of the concepts of long term survival within the host, including colonization, and the concept of resisting antibiotic therapy even when susceptible in the clinical microbiology laboratory. Over the past two decades, the mechanisms whereby bacteria achieve persistence are slowly being unraveled. S. aureus small colony variants (SCVs) are linked to chronic, recurrent, and antibiotic-resistant infections, and the study of SCVs has contributed significantly to understanding of persistence. In our earlier work, defects in electron transport and thymidylate biosynthesis were linked to the development of the SCV phenotype (reviewed in 2006), thus this work will be discussed only briefly. Since 2006, it has been found that persistent organisms including SCVs are part of the normal life cycle of bacteria, and often they arise in response to harsh conditions, e.g., antibiotics, starvation, host cationic peptides. Many of the changes found in these early SCVs have provided a map for the discovery mechanisms (pathways) for the development of persistent organisms. For example, changes in RNA processing, stringent response, toxin-antitoxin, ribosome protein L6 (RplF), and cold shock protein B (CspB) found in SCVs are also found in other persisters. In addition, many classic persister organisms also show slow growth, hence SCVs. Recent work on S. aureus USA300 has elucidated the impact of aerobic expression of arginine deiminase genes on its ability to chronically colonize the skin and survive in abscesses. S. aureus SCVs also express arginine deiminase genes aerobically as well. Thus, many pathways found activated in electron transport type of SCVs are also increased in persisters that have intact electron transport. Many of these changes in metabolism result in slow growth; hence, small colonies are formed. Another common theme is that slow growth is also associated with reduced expression of virulence factors and enhanced uptake/survival within host cells. These adaptations to survive within the host are rooted in responses that were required for organisms to survive in a harsh environment long before they were mammals on the earth.
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Affiliation(s)
- Richard A Proctor
- Departments of Medical Microbiology/Immunology and Medicine, University of Wisconsin School of Medicine and Public Health Madison, WI, USA
| | - André Kriegeskorte
- Institute of Medical Microbiology, University Hospital, Münster Münster, Germany
| | - Barbara C Kahl
- Institute of Medical Microbiology, University Hospital, Münster Münster, Germany
| | - Karsten Becker
- Institute of Medical Microbiology, University Hospital, Münster Münster, Germany
| | - Bettina Löffler
- Institute of Medical Microbiology, University Hospital, Münster Münster, Germany
| | - Georg Peters
- Institute of Medical Microbiology, University Hospital, Münster Münster, Germany
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Bäsell K, Otto A, Junker S, Zühlke D, Rappen GM, Schmidt S, Hentschker C, Macek B, Ohlsen K, Hecker M, Becher D. The phosphoproteome and its physiological dynamics in Staphylococcus aureus. Int J Med Microbiol 2014; 304:121-32. [DOI: 10.1016/j.ijmm.2013.11.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Castelhano Santos N, Pereira MO, Lourenço A. Pathogenicity phenomena in three model systems: from network mining to emerging system-level properties. Brief Bioinform 2013; 16:169-82. [PMID: 24106130 DOI: 10.1093/bib/bbt071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Understanding the interconnections of microbial pathogenicity phenomena, such as biofilm formation, quorum sensing and antimicrobial resistance, is a tremendous open challenge for biomedical research. Progress made by wet-lab researchers and bioinformaticians in understanding the underlying regulatory phenomena has been significant, with converging evidence from multiple high-throughput technologies. Notably, network reconstructions are already of considerable size and quality, tackling both intracellular regulation and signal mediation in microbial infection. Therefore, it stands to reason that in silico investigations would play a more active part in this research. Drug target identification and drug repurposing could take much advantage of the ability to simulate pathogen regulatory systems, host-pathogen interactions and pathogen cross-talking. Here, we review the bioinformatics resources and tools available for the study of the gram-negative bacterium Pseudomonas aeruginosa, the gram-positive bacterium Staphylococcus aureus and the fungal species Candida albicans. The choice of these three microorganisms fits the rationale of the review converging into pathogens of great clinical importance, which thrive in biofilm consortia and manifest growing antimicrobial resistance.
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Priest NK, Rudkin JK, Feil EJ, van den Elsen JMH, Cheung A, Peacock SJ, Laabei M, Lucks DA, Recker M, Massey RC. From genotype to phenotype: can systems biology be used to predict Staphylococcus aureus virulence? Nat Rev Microbiol 2012; 10:791-7. [PMID: 23070558 PMCID: PMC7097209 DOI: 10.1038/nrmicro2880] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
With the advent of high-throughput whole-genome sequencing, it is now possible to sequence a bacterial genome in a matter of hours. However, although the presence or absence of a particular gene can be determined, we do not yet have the tools to extract information about the true virulence potential of an organism from sequence data alone. Here, we focus on the important human pathogen Staphylococcus aureus and present a framework for the construction of a broad systems biology-based tool that could be used to predict virulence phenotypes from S. aureus genomic sequences using existing technology.
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Affiliation(s)
- Nicholas K. Priest
- Maisem Laabei and Ruth C. Massey are at the Department of Biology and Biochemistry, Nicholas K. Priest, Justine K. Rudkin, Edward J. Feil, Jean M. H. van den Elsen, University of Bath, Bath BA2 7AY, UK.,
| | - Justine K. Rudkin
- Maisem Laabei and Ruth C. Massey are at the Department of Biology and Biochemistry, Nicholas K. Priest, Justine K. Rudkin, Edward J. Feil, Jean M. H. van den Elsen, University of Bath, Bath BA2 7AY, UK.,
| | - Edward J. Feil
- Maisem Laabei and Ruth C. Massey are at the Department of Biology and Biochemistry, Nicholas K. Priest, Justine K. Rudkin, Edward J. Feil, Jean M. H. van den Elsen, University of Bath, Bath BA2 7AY, UK.,
| | - Jean M. H. van den Elsen
- Maisem Laabei and Ruth C. Massey are at the Department of Biology and Biochemistry, Nicholas K. Priest, Justine K. Rudkin, Edward J. Feil, Jean M. H. van den Elsen, University of Bath, Bath BA2 7AY, UK.,
| | - Ambrose Cheung
- Ambrose Cheung is at Dartmouth Medical School, Vail Building - HB 7550, Hanover, New Hampshire 03755, USA.,
| | - Sharon J. Peacock
- Sharon J. Peacock is at the Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.,
| | - Maisem Laabei
- Maisem Laabei and Ruth C. Massey are at the Department of Biology and Biochemistry, Nicholas K. Priest, Justine K. Rudkin, Edward J. Feil, Jean M. H. van den Elsen, University of Bath, Bath BA2 7AY, UK.,
| | - David A. Lucks
- David A. Lucks is at Western Infectious Disease Consultants, PC, 3885 Upham Street Suite 200, Wheat Ridge, Colorado 80033, USA.,
| | - Mario Recker
- Mario Recker is at the Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.,
| | - Ruth C. Massey
- Maisem Laabei and Ruth C. Massey are at the Department of Biology and Biochemistry, Nicholas K. Priest, Justine K. Rudkin, Edward J. Feil, Jean M. H. van den Elsen, University of Bath, Bath BA2 7AY, UK.,
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Aleinein RA, Hamoud R, Schäfer H, Wink M. Molecular cloning and expression of ranalexin, a bioactive antimicrobial peptide from Rana catesbeiana in Escherichia coli and assessments of its biological activities. Appl Microbiol Biotechnol 2012; 97:3535-43. [PMID: 23053091 DOI: 10.1007/s00253-012-4441-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 08/22/2012] [Accepted: 09/16/2012] [Indexed: 12/12/2022]
Abstract
The coding sequence, which corresponds to the mature antimicrobial peptide ranalexin from the frog Rana catesbeiana, was chemically synthesized with preferred codons for expression in Escherichia coli. It was cloned into the vector pET32c (+) to express a thioredoxin-ranalexin fusion protein which was produced in soluble form in E. coli BL21 (DE3) induced under optimized conditions. After two purification steps through affinity chromatography, about 1 mg of the recombinant ranalexin was obtained from 1 L of culture. Mass spectrometrical analysis of the purified recombinant ranalexin demonstrated its identity with ranalexin. The purified recombinant ranalexin is biologically active. It showed antibacterial activities similar to those of the native peptide against Staphylococcus aureus, Streptococcus pyogenes, E. coli, and multidrug-resistant strains of S. aureus with minimum inhibitory concentration values between 8 and 128 μg/ml. The recombinant ranalexin is also cytotoxic in HeLa and COS7 human cancer cells (IC50 = 13-15 μg/ml).
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Affiliation(s)
- Rasha Abou Aleinein
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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Cuaron JA, Dulal S, Song Y, Singh AK, Montelongo CE, Yu W, Nagarajan V, Jayaswal RK, Wilkinson BJ, Gustafson JE. Tea tree oil-induced transcriptional alterations in Staphylococcus aureus. Phytother Res 2012; 27:390-6. [PMID: 22619070 DOI: 10.1002/ptr.4738] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 04/18/2012] [Accepted: 04/22/2012] [Indexed: 11/09/2022]
Abstract
Tea tree oil (TTO) is a steam distillate of Melaleuca alternifolia that demonstrates broad-spectrum antibacterial activity. This study was designed to document how TTO challenge influences the Staphylococcus aureus transcriptome. Overall, bioinformatic analyses (S. aureus microarray meta-database) revealed that both ethanol and TTO induce related transcriptional alterations. TTO challenge led to the down-regulation of genes involved with energy-intensive transcription and translation, and altered the regulation of genes involved with heat shock (e.g. clpC, clpL, ctsR, dnaK, groES, groEL, grpE and hrcA) and cell wall metabolism (e.g. cwrA, isaA, sle1, vraSR and vraX). Inactivation of the heat shock gene dnaK or vraSR which encodes a two-component regulatory system that responds to peptidoglycan biosynthesis inhibition led to an increase in TTO susceptibility which demonstrates a protective role for these genes in the S. aureus TTO response. A gene (mmpL) encoding a putative resistance, nodulation and cell division efflux pump was also highly induced by TTO. The principal antimicrobial TTO terpene, terpinen-4-ol, altered ten genes in a transcriptional direction analogous to TTO. Collectively, this study provides additional insight into the response of a bacterial pathogen to the antimicrobial terpene mixture TTO.
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Affiliation(s)
- Jesus A Cuaron
- Microbiology Group, Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
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Zhang A, Sun H, Yang B, Wang X. Predicting new molecular targets for rhein using network pharmacology. BMC SYSTEMS BIOLOGY 2012; 6:20. [PMID: 22433437 PMCID: PMC3338090 DOI: 10.1186/1752-0509-6-20] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 03/21/2012] [Indexed: 11/21/2022]
Abstract
Background Drugs can influence the whole biological system by targeting interaction reactions. The existence of interactions between drugs and network reactions suggests a potential way to discover targets. The in silico prediction of potential interactions between drugs and target proteins is of core importance for the identification of new drugs or novel targets for existing drugs. However, only a tiny portion of drug-targets in current datasets are validated interactions. This motivates the need for developing computational methods that predict true interaction pairs with high accuracy. Currently, network pharmacology has used in identifying potential drug targets to predicting the spread of drug activity and greatly contributed toward the analysis of biological systems on a much larger scale than ever before. Methods In this article, we present a computational method to predict targets for rhein by exploring drug-reaction interactions. We have implemented a computational platform that integrates pathway, protein-protein interaction, differentially expressed genome and literature mining data to result in comprehensive networks for drug-target interaction. We used Cytoscape software for prediction rhein-target interactions, to facilitate the drug discovery pipeline. Results Results showed that 3 differentially expressed genes confirmed by Cytoscape as the central nodes of the complicated interaction network (99 nodes, 153 edges). Of note, we further observed that the identified targets were found to encompass a variety of biological processes related to immunity, cellular apoptosis, transport, signal transduction, cell growth and proliferation and metabolism. Conclusions Our findings demonstrate that network pharmacology can not only speed the wide identification of drug targets but also find new applications for the existing drugs. It also implies the significant contribution of network pharmacology to predict drug targets.
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Affiliation(s)
- Aihua Zhang
- National TCM Key Lab of Serum Pharmacochemistry, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin 150040, China
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Jorge P, Lourenço A, Pereira MO. New trends in peptide-based anti-biofilm strategies: a review of recent achievements and bioinformatic approaches. BIOFOULING 2012; 28:1033-1061. [PMID: 23016989 DOI: 10.1080/08927014.2012.728210] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Antimicrobial peptides (AMPs) have a broad spectrum of activity and unspecific mechanisms of action. Therefore, they are seen as valid alternatives to overcome clinically relevant biofilms and reduce the chance of acquired resistance. This paper reviews AMPs and anti-biofilm AMP-based strategies and discusses ongoing and future work. Recent studies report successful AMP-based prophylactic and therapeutic strategies, several databases catalogue AMP information and analysis tools, and novel bioinformatics tools are supporting AMP discovery and design. However, most AMP studies are performed with planktonic cultures, and most studies on sessile cells test AMPs on growing rather than mature biofilms. Promising preliminary synergistic studies have to be consubstantiated and the study of functionalized coatings with AMPs must be further explored. Standardized operating protocols, to enforce the repeatability and reproducibility of AMP anti-biofilm tests, and automated means of screening and processing the ever-expanding literature are still missing.
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Affiliation(s)
- Paula Jorge
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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