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Nazli A, Qiu J, Tang Z, He Y. Recent Advances and Techniques for Identifying Novel Antibacterial Targets. Curr Med Chem 2024; 31:464-501. [PMID: 36734893 DOI: 10.2174/0929867330666230123143458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/30/2022] [Accepted: 11/11/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND With the emergence of drug-resistant bacteria, the development of new antibiotics is urgently required. Target-based drug discovery is the most frequently employed approach for the drug development process. However, traditional drug target identification techniques are costly and time-consuming. As research continues, innovative approaches for antibacterial target identification have been developed which enabled us to discover drug targets more easily and quickly. METHODS In this review, methods for finding drug targets from omics databases have been discussed in detail including principles, procedures, advantages, and potential limitations. The role of phage-driven and bacterial cytological profiling approaches is also discussed. Moreover, current article demonstrates the advancements being made in the establishment of computational tools, machine learning algorithms, and databases for antibacterial target identification. RESULTS Bacterial drug targets successfully identified by employing these aforementioned techniques are described as well. CONCLUSION The goal of this review is to attract the interest of synthetic chemists, biologists, and computational researchers to discuss and improve these methods for easier and quicker development of new drugs.
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Affiliation(s)
- Adila Nazli
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Jingyi Qiu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Ziyi Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
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2
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Classification of antimicrobial mechanism of action using dynamic bacterial morphology imaging. Sci Rep 2022; 12:11162. [PMID: 35778598 PMCID: PMC9249789 DOI: 10.1038/s41598-022-15405-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022] Open
Abstract
Antimicrobial resistance is a major threat to human health. Basic knowledge of antimicrobial mechanism of action (MoA) is imperative for patient care and for identification of novel antimicrobials. However, the process of antimicrobial MoA identification is relatively laborious. Here, we developed a simple, quantitative time-lapse fluorescence imaging method, Dynamic Bacterial Morphology Imaging (DBMI), to facilitate this process. It uses a membrane dye and a nucleoid dye to track the morphological changes of single Bacillus subtilis cells in response to antimicrobials for up to 60 min. DBMI of bacterial cells facilitated assignment of the MoAs of 14 distinct, known antimicrobial compounds to the five main classes. We conclude that DBMI is a simple method, which facilitates rapid classification of the MoA of antimicrobials in functionally distinct classes.
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Miranda RR, Parthasarathy A, Hudson AO. Exploration of Chemical Biology Approaches to Facilitate the Discovery and Development of Novel Antibiotics. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.845469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Approximately 2.8 million people worldwide are infected with bacteria that are deemed resistant to clinically relevant antibiotics. This accounts for 700,000 deaths every year and represents a major public health threat that has been on the rise for the past two decades. In contrast, the pace of antibiotic discovery to treat these resistant pathogens has significantly decreased. Most antibiotics are complex natural products that were isolated from soil microorganisms during the golden era of antibiotic discovery (1940s to 1960s) employing the “Waksman platform”. After the collapse of this discovery platform, other strategies and approaches emerged, including phenotype- or target-based screenings of large synthetic compound libraries. However, these methods have not resulted in the discovery and/or development of new drugs for clinical use in over 30 years. A better understanding of the structure and function of the molecular components that constitute the bacterial system is of paramount importance to design new strategies to tackle drug-resistant pathogens. Herein, we review the traditional approaches as well as novel strategies to facilitate antibiotic discovery that are chemical biology-focused. These include the design and application of chemical probes that can undergo bioorthogonal reactions, such as copper (I)-catalyzed azide-alkyne cycloadditions (CuAAC). By specifically interacting with bacterial proteins or being incorporated in the microorganism’s metabolism, chemical probes are powerful tools in drug discovery that can help uncover new drug targets and investigate the mechanisms of action and resistance of new antibacterial leads.
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4
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Combining CRISPRi and metabolomics for functional annotation of compound libraries. Nat Chem Biol 2022; 18:482-491. [PMID: 35194207 PMCID: PMC7612681 DOI: 10.1038/s41589-022-00970-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023]
Abstract
Molecular profiling of small-molecules offers invaluable insights into the function of compounds and allows for hypothesis generation about small molecule direct targets and secondary effects. However, current profiling methods are either limited in the number of measurable parameters or throughput. Here, we developed a multiplexed, unbiased framework that, by linking genetic to drug-induced changes in nearly a thousand metabolites, allows for high-throughput functional annotation of compound libraries in Escherichia coli. First, we generated a reference map of metabolic changes from (CRISPR) interference with 352 genes in all major essential biological processes. Next, based on the comparison of genetic with 1342 drug-induced metabolic changes we made de novo predictions of compound functionality and revealed antibacterials with unconventional Modes of Action. We show that our framework, combining dynamic gene silencing with metabolomics, can be adapted as a general strategy for comprehensive high-throughput analysis of compound functionality, from bacteria to human cell lines.
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Bheemireddy S, Srinivasan N. Computational Study on the Dynamics of Mycobacterium Tuberculosis RNA Polymerase Assembly. Methods Mol Biol 2022; 2516:61-79. [PMID: 35922622 DOI: 10.1007/978-1-0716-2413-5_5] [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] [Indexed: 06/15/2023]
Abstract
Gene regulation is an intricate phenomenon involving precise function of many macromolecular complexes. Molecular basis of this phenomenon is highly complex and cannot be fully understood using a single technique. Computational approaches can play a crucial role in overall understanding of functional and mechanistic features of a protein or an assembly. Large amounts of structural data pertaining to these complexes are publicly available. In this project, we took advantage of the availability of the structural information to unravel functional intricacies of Mycobacterium tuberculosis RNA polymerase upon interaction with RbpA. In this article, we discuss how the knowledge on protein structure and dynamics can be exploited to study function using various computational tools and resources. Overall, this article provides an overview of various computational methods which can be efficiently used to understand the role of any protein. We hope especially the nonexperts in the field could benefit from our article.
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Affiliation(s)
- Sneha Bheemireddy
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka, India.
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6
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Dkhili S, Ribeiro M, Ghariani S, Yahia HB, Hillion M, Poeta P, Slama KB, Hébraud M, Igrejas G. Bacteriophages as Antimicrobial Agents? Proteomic Insights on Three Novel Lytic Bacteriophages Infecting ESBL-Producing Escherichia coli. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:626-640. [PMID: 34559008 DOI: 10.1089/omi.2021.0122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
With the emergence of multiresistant bacteria, the use of bacteriophages is gaining renewed interest as potential antimicrobial agents. The aim of this study was to analyze the structure of three lytic bacteriophages infecting Escherichia coli (SD1, SD2, and SD3) using a gel-based proteomics approach and the cellular response of this bacterium to phage SD1 infection at the proteome level. The combination of the results of 1-DE and 2-DE followed by mass spectrometry led to the identification of 3, 14, and 9 structure proteins for SD1, SD2, and SD3 phages, respectively. Different protein profiles with common proteins were noticed. We also analyzed phage-induced effects by comparing samples from infected cells to those of noninfected cells. We verified important changes in E. coli proteins expression during phage SD1 infection, where there was an overexpression of proteins involved in stress response. Our results indicated that viral infection caused bacterial oxidative stress and bacterial cells response to stress was orchestrated by antioxidant defense mechanisms. This article makes an empirical scientific contribution toward the concept of bacteriophages as potential antimicrobial agents. With converging ecological threats in the 21st century, novel approaches to address the innovation gaps in antimicrobial development are more essential than ever. Further research on bacteriophages is called for in this broader context of planetary health and integrative biology.
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Affiliation(s)
- Sadika Dkhili
- Laboratoire des Microorganismes et Biomolécules actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie.,Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Miguel Ribeiro
- Department of Genetics and Biotechnology and University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, Lisbon, Portugal
| | - Salma Ghariani
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Houssem Ben Yahia
- Laboratoire des Microorganismes et Biomolécules actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie.,Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Mélanie Hillion
- University Clermont Auvergne, INRAE, UMR0454 Microbiology Digestive Environment Health (MEDiS), Saint-Genès Champanelle, France.,INRAE, Metabolism Exploration Platform, Proteomic Component (PFEMcp), Saint-Genès Champanelle, France
| | - Patricia Poeta
- Department of Genetics and Biotechnology and University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Karim Ben Slama
- Laboratoire des Microorganismes et Biomolécules actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie.,Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Michel Hébraud
- University Clermont Auvergne, INRAE, UMR0454 Microbiology Digestive Environment Health (MEDiS), Saint-Genès Champanelle, France.,INRAE, Metabolism Exploration Platform, Proteomic Component (PFEMcp), Saint-Genès Champanelle, France
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology and University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, Lisbon, Portugal
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7
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da Cunha BR, Zoio P, Fonseca LP, Calado CRC. Technologies for High-Throughput Identification of Antibiotic Mechanism of Action. Antibiotics (Basel) 2021; 10:565. [PMID: 34065815 PMCID: PMC8151116 DOI: 10.3390/antibiotics10050565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 01/23/2023] Open
Abstract
There are two main strategies for antibiotic discovery: target-based and phenotypic screening. The latter has been much more successful in delivering first-in-class antibiotics, despite the major bottleneck of delayed Mechanism-of-Action (MOA) identification. Although finding new antimicrobial compounds is a very challenging task, identifying their MOA has proven equally challenging. MOA identification is important because it is a great facilitator of lead optimization and improves the chances of commercialization. Moreover, the ability to rapidly detect MOA could enable a shift from an activity-based discovery paradigm towards a mechanism-based approach. This would allow to probe the grey chemical matter, an underexplored source of structural novelty. In this study we review techniques with throughput suitable to screen large libraries and sufficient sensitivity to distinguish MOA. In particular, the techniques used in chemical genetics (e.g., based on overexpression and knockout/knockdown collections), promoter-reporter libraries, transcriptomics (e.g., using microarrays and RNA sequencing), proteomics (e.g., either gel-based or gel-free techniques), metabolomics (e.g., resourcing to nuclear magnetic resonance or mass spectrometry techniques), bacterial cytological profiling, and vibrational spectroscopy (e.g., Fourier-transform infrared or Raman scattering spectroscopy) were discussed. Ultimately, new and reinvigorated phenotypic assays bring renewed hope in the discovery of a new generation of antibiotics.
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Affiliation(s)
- Bernardo Ribeiro da Cunha
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (B.R.d.C.); (P.Z.); (L.P.F.)
| | - Paulo Zoio
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (B.R.d.C.); (P.Z.); (L.P.F.)
- CIMOSM—Centro de Investigação em Modelação e Optimização de Sistemas Multifuncionais, ISEL—Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - Luís P. Fonseca
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (B.R.d.C.); (P.Z.); (L.P.F.)
| | - Cecília R. C. Calado
- CIMOSM—Centro de Investigação em Modelação e Optimização de Sistemas Multifuncionais, ISEL—Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
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8
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Espinoza JL, Dupont CL, O’Rourke A, Beyhan S, Morales P, Spoering A, Meyer KJ, Chan AP, Choi Y, Nierman WC, Lewis K, Nelson KE. Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach. PLoS Comput Biol 2021; 17:e1008857. [PMID: 33780444 PMCID: PMC8031737 DOI: 10.1371/journal.pcbi.1008857] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 04/08/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
To better combat the expansion of antibiotic resistance in pathogens, new compounds, particularly those with novel mechanisms-of-action [MOA], represent a major research priority in biomedical science. However, rediscovery of known antibiotics demonstrates a need for approaches that accurately identify potential novelty with higher throughput and reduced labor. Here we describe an explainable artificial intelligence classification methodology that emphasizes prediction performance and human interpretability by using a Hierarchical Ensemble of Classifiers model optimized with a novel feature selection algorithm called Clairvoyance; collectively referred to as a CoHEC model. We evaluated our methods using whole transcriptome responses from Escherichia coli challenged with 41 known antibiotics and 9 crude extracts while depositing 122 transcriptomes unique to this study. Our CoHEC model can properly predict the primary MOA of previously unobserved compounds in both purified forms and crude extracts at an accuracy above 99%, while also correctly identifying darobactin, a newly discovered antibiotic, as having a novel MOA. In addition, we deploy our methods on a recent E. coli transcriptomics dataset from a different strain and a Mycobacterium smegmatis metabolomics timeseries dataset showcasing exceptionally high performance; improving upon the performance metrics of the original publications. We not only provide insight into the biological interpretation of our model but also that the concept of MOA is a non-discrete heuristic with diverse effects for different compounds within the same MOA, suggesting substantial antibiotic diversity awaiting discovery within existing MOA.
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Affiliation(s)
- Josh L. Espinoza
- J. Craig Venter Institute, La Jolla, CA, United States of America
- Department of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Chris L. Dupont
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Aubrie O’Rourke
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Sinem Beyhan
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Pavel Morales
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Amy Spoering
- NovoBiotic Pharmaceuticals, Cambridge, MA, United States of America
| | - Kirsten J. Meyer
- Department of Biology, Northeastern University, Boston, MA, United States of America
| | - Agnes P. Chan
- J. Craig Venter Institute, Rockville, MD, United States of America
| | - Yongwook Choi
- J. Craig Venter Institute, Rockville, MD, United States of America
| | | | - Kim Lewis
- Department of Biology, Northeastern University, Boston, MA, United States of America
| | - Karen E. Nelson
- J. Craig Venter Institute, La Jolla, CA, United States of America
- Department of Applied Sciences, Durban University of Technology, Durban, South Africa
- J. Craig Venter Institute, Rockville, MD, United States of America
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9
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Wareth G, Pletz MW, Neubauer H, Murugaiyan J. Proteomics of Brucella: Technologies and Their Applications for Basic Research and Medical Microbiology. Microorganisms 2020; 8:microorganisms8050766. [PMID: 32443785 PMCID: PMC7285364 DOI: 10.3390/microorganisms8050766] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/26/2022] Open
Abstract
Brucellosis is a global zoonosis caused by Gram-negative, facultative intracellular bacteria of the genus Brucella (B.). Proteomics has been used to investigate a few B. melitensis and B. abortus strains, but data for other species and biovars are limited. Hence, a comprehensive analysis of proteomes will significantly contribute to understanding the enigmatic biology of brucellae. For direct identification and typing of Brucella, matrix-assisted laser desorption ionization - time of flight mass spectrometry (MALDI - TOF MS) has become a reliable tool for routine diagnosis due to its ease of handling, price and sensitivity highlighting the potential of proteome-based techniques. Proteome analysis will also help to overcome the historic but still notorious Brucella obstacles of infection medicine, the lack of safe and protective vaccines and sensitive serologic diagnostic tools by identifying the most efficient protein antigens. This perspective summarizes past and recent developments in Brucella proteomics with a focus on species identification and serodiagnosis. Future applications of proteomics in these fields are discussed.
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Affiliation(s)
- Gamal Wareth
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany;
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany;
- Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh 13736, Egypt
- Correspondence: ; Tel.: +49-364-1804-2296
| | - Mathias W. Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany;
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany;
| | - Jayaseelan Murugaiyan
- Institute of Animal Hygiene and Environmental Health, Centre for Infectious Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany;
- Department of Biotechnology, SRM University AP, Neerukonda, Mangalagiri, Andhra Pradesh 522502, India
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10
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Valliammai A, Sethupathy S, Ananthi S, Priya A, Selvaraj A, Nivetha V, Aravindraja C, Mahalingam S, Pandian SK. Proteomic profiling unveils citral modulating expression of IsaA, CodY and SaeS to inhibit biofilm and virulence in methicillin-resistant Staphylococcus aureus. Int J Biol Macromol 2020; 158:S0141-8130(20)33095-6. [PMID: 32360467 DOI: 10.1016/j.ijbiomac.2020.04.231] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/15/2020] [Accepted: 04/26/2020] [Indexed: 12/17/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the dangerous human pathogens and it is categorized as a high priority multi-drug resistant bacterium by WHO. Biofilm forming ability of MRSA is responsible for persistent infections and also difficult to eradicate using antibiotic therapy as biofilm is much more resistant to antibiotics. Thus, targeting biofilm and virulence has become an alternative approach to attenuate the pathogenicity of bacterium without affecting the growth. Hence, the present study was aimed at evaluation of antibiofilm potential of citral against MRSA and to decode the possible mode of action. Citral inhibited biofilm formation by MRSA without affecting growth at 100 μg/mL. Microscopic analyses evidenced that citral greatly hampered the surface adherence of MRSA. Effect of citral on cellular proteome of MRSA was studied using two-dimensional gel electrophoresis (2DGE) and differentially regulated proteins were identified using nano LC-MS/MS and MALDI-TOF/TOF analysis. Gene ontology and STRING analysis revealed that citral differentially regulated the proteins involved in pleotropic transcriptional repression (CodY), cell wall homeostasis (IsaA), regulation of exotoxin secretion (SaeS), cell adhesion, hemolysis, capsular polysaccharide biosynthesis and pathogenesis. Gene expression analysis and in vitro assays further validated the alteration in synthesis of slime, hemolysin, lipase, staphyloxanthin and oxidant susceptibility. Thus, the present study unveiled the multiple protein targeted antibiofilm potential of citral and portrays citral as a promising therapeutic agent to combat biofilm mediated MRSA infections with less possibility of resistance development.
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Affiliation(s)
- Alaguvel Valliammai
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi 630 003, Tamil Nadu, India
| | - Sivasamy Sethupathy
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi 630 003, Tamil Nadu, India; Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Sivagnanam Ananthi
- Laboratory of Molecular Virology and Cell Biology, Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, Tamil Nadu, India; Department of Preventive Oncology Research, Cancer Institute (WIA), Adyar, Chennai 600 036, Tamil Nadu, India
| | - Arumugam Priya
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi 630 003, Tamil Nadu, India
| | - Anthonymuthu Selvaraj
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi 630 003, Tamil Nadu, India
| | - Venkatesan Nivetha
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi 630 003, Tamil Nadu, India
| | - Chairmandurai Aravindraja
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi 630 003, Tamil Nadu, India; Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Sundarasamy Mahalingam
- Laboratory of Molecular Virology and Cell Biology, Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, Tamil Nadu, India
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Liu X, Wang J, Chen M, Che R, Ding W, Yu F, Zhou Y, Cui W, Xiaoxu X, God'spower BO, Li Y. Comparative proteomic analysis reveals drug resistance of Staphylococcus xylosus ATCC700404 under tylosin stress. BMC Vet Res 2019; 15:224. [PMID: 31266490 PMCID: PMC6604186 DOI: 10.1186/s12917-019-1959-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 06/13/2019] [Indexed: 12/13/2022] Open
Abstract
Background As a kind of opportunist pathogen, Staphylococcus xylosus (S. xylosus) can cause mastitis. Antibiotics are widely used for treating infected animals and tylosin is a member of such group. Thus, the continuous use of antibiotics in dairy livestock enterprise will go a long way in increasing tylosin resistance. However, the mechanism of tylosin-resistant S. xylosus is not clear. Here, isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomics methods was used to find resistance-related proteins. Results We compared the differential expression of S. xylosus in response to tylosin stress by iTRAQ. A total of 155 proteins (59 up-regulated, 96 down-regulated) with the fold-change of >1.2 or <0.8 (p value ≤0.05) were observed between the S. xylosus treated with 1/2 MIC (0.25 μg/mL) tylosin and the untreated S. xylosus. Bioinformatic analysis revealed that these proteins play important roles in stress-response and transcription. Then, in order to verify the relationship between the above changed proteins and mechanism of tylosin-resistant S. xylosus, we induced the tylosin-resistant S. xylosus, and performed quantitative PCR analysis to verify the changes in the transcription proteins and the stress-response proteins in tylosin-resistant S. xylosus at the mRNA level. The data displayed that ribosomal protein L23 (rplw), thioredoxin(trxA) and Aldehyde dehydrogenase A(aldA-1) are up-regulated in the tylosin-resistant S. xylosus, compared with the tylosin-sensitive strains. Conclusion Our findings demonstrate the important of stress-response and transcription in the tylosin resistance of S. xylosus and provide an insight into the prevention of this resistance, which would aid in finding new medicines . Electronic supplementary material The online version of this article (10.1186/s12917-019-1959-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xin Liu
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Jinpeng Wang
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Mo Chen
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Ruixiang Che
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Wenya Ding
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Fei Yu
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Yonghui Zhou
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Wenqiang Cui
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Xing Xiaoxu
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Bello-Onaghise God'spower
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Yanhua Li
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China.
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Chernov VM, Chernova OA, Mouzykantov AA, Lopukhov LL, Aminov RI. Omics of antimicrobials and antimicrobial resistance. Expert Opin Drug Discov 2019; 14:455-468. [DOI: 10.1080/17460441.2019.1588880] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Vladislav M. Chernov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russian Federation
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russian Federation
| | - Olga A. Chernova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russian Federation
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russian Federation
| | - Alexey A. Mouzykantov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russian Federation
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russian Federation
| | - Leonid L. Lopukhov
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russian Federation
| | - Rustam I. Aminov
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russian Federation
- Applied Health Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
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Božik M, Cejnar P, Šašková M, Nový P, Maršík P, Klouček P. Stress response of Escherichia coli to essential oil components - insights on low-molecular-weight proteins from MALDI-TOF. Sci Rep 2018; 8:13042. [PMID: 30158663 PMCID: PMC6115441 DOI: 10.1038/s41598-018-31255-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 08/15/2018] [Indexed: 01/21/2023] Open
Abstract
The antibacterial effects of essential oils and their components (EOCs) are usually attributed to effects on membranes and metabolism. Studies of the effects of EOCs on protein expression have primarily analysed proteins larger than 10 kDa using gel electrophoresis. In the present study, we used MALDI-TOF-MS to investigate the effects of EOCs on low-molecular-weight proteins. From 297 m/z features, we identified 94 proteins with important differences in expression among untreated samples, samples treated with EOCs, and samples treated with antibiotics, peroxide, or chlorine. The targets of these treatments obviously differ, even among EOCs. In addition to ribosomal proteins, stress-, membrane- and biofilm-related proteins were affected. These findings may provide a basis for identifying new targets of essential oils and synergies with other antibiotics.
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Affiliation(s)
- Matěj Božik
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Quality of Agricultural Products, Prague, Czech Republic
| | - Pavel Cejnar
- University of Chemistry and Technology, Department of Computing and Control Engineering, Prague, Czech Republic.,Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Plant Protection, Prague, Czech Republic
| | - Martina Šašková
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Quality of Agricultural Products, Prague, Czech Republic
| | - Pavel Nový
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Quality of Agricultural Products, Prague, Czech Republic
| | - Petr Maršík
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Quality of Agricultural Products, Prague, Czech Republic
| | - Pavel Klouček
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Quality of Agricultural Products, Prague, Czech Republic.
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Abstract
Despite all its apparent limitations proteome analysis based on two-dimensional protein gels combined with mass spectrometry is still the method of choice to study global protein synthesis activity in bacterial cells. Alterations in global protein synthesis play an important role during adaptation of bacteria to changing environmental conditions which are rather the role than the exception in their natural habitats. The protein synthesis pattern in response to a certain stimulus is highly specific and reflects the new challenges the bacterium has to meet. Here we present the techniques to analyze global protein synthesis in bacteria as exemplified by Staphylococcus aureus which is an important human pathogen and one main cause of nosocomial infections with severe outcome.
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Preclinical Assessment of a 68Ga-DOTA-Functionalized Depsipeptide as a Radiodiagnostic Infection Imaging Agent. Molecules 2017; 22:molecules22091403. [PMID: 28837117 PMCID: PMC6151697 DOI: 10.3390/molecules22091403] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/18/2017] [Indexed: 11/16/2022] Open
Abstract
The study assessed a radiolabeled depsipeptide conjugate (68Ga-DOTA-TBIA101) for its potential as an imaging agent targeting infection or infection-associated inflammation. 68Ga-labeled DOTA-TBIA101 imaging was performed in (NZR1) healthy rabbits; (NZR2) rabbits bearing muscular sterile inflammation and Staphylococcus aureus (SA) infection; and (NZR3) rabbits infected with Mycobacterium tuberculosis (MTB) combined with a subcutaneous scruff infection of SA in the same animal. All animals were imaged using a PET/CT scanner at 5 and 60 min post injection. Images showed elevated accumulation of 68Ga-DOTA-TBIA101 in the sterile muscular inflammation site (T/NT ratio = 2.6 ± 0.37 (5 min) and 2.8 ± 2.3 (60 min)) and muscles infected with MTB (T/NT ratio = 2.6 ± 0.35 (5 min) and 2.8 ± 0.16 (60 min)). The findings suggest that 68Ga-DOTA-TBIA101-PET/CT may detect MTB-associated inflammation, although more foundational studies need to be performed to rationalize the diagnostic value of this technique.
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Li L, Tian Y, Yu J, Song X, Jia R, Cui Q, Tong W, Zou Y, Li L, Yin L, Liang X, He C, Yue G, Ye G, Zhao L, Shi F, Lv C, Cao S, Yin Z. iTRAQ-based quantitative proteomic analysis reveals multiple effects of Emodin to Haemophilus parasuis. J Proteomics 2017; 166:39-47. [DOI: 10.1016/j.jprot.2017.06.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 06/09/2017] [Accepted: 06/21/2017] [Indexed: 12/20/2022]
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17
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Brucella abortus: Current Research and Future Trends. CURRENT CLINICAL MICROBIOLOGY REPORTS 2017. [DOI: 10.1007/s40588-017-0052-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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18
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Thai VC, Lim TK, Le KPU, Lin Q, Nguyen TTH. iTRAQ-based proteome analysis of fluoroquinolone-resistant Staphylococcus aureus. J Glob Antimicrob Resist 2017; 8:82-89. [DOI: 10.1016/j.jgar.2016.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/25/2016] [Accepted: 11/05/2016] [Indexed: 12/12/2022] Open
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19
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Gokgoz NB, Akbulut BS. Proteomics Evidence for the Activity of the Putative Antibacterial Plant Alkaloid (-)-Roemerine: Mainstreaming Omics-Guided Drug Discovery. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 19:478-89. [PMID: 26230533 DOI: 10.1089/omi.2015.0056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Discovery of new antibacterials with novel mechanisms is important to counteract the ingenious resistance mechanisms of bacteria. In this connection, omics-guided drug discovery offers a rigorous method in the quest of new antibacterials. (-)-Roemerine is a plant alkaloid that has been reported to possess putative antibacterial activity against Escherichia coli, Bacillus subtilis, and Salmonella typhimurium. The aim of the present study was to characterize the activity of (-)-roemerine in Escherichia coli TB1 using proteomics tools. With (-)-roemerine treatment, we found limited permeability through the outer membrane and repression of transport proteins involved in carbohydrate metabolism, resulting in poor carbon source availability. The shortfall of intracellular carbon sources in turn led to impaired cell growth. The reduction in the abundance of proteins related to translational machinery, amino acid biosynthesis, and metabolism was accompanied by a nutrient-limited state. The latter finding could suggest a metabolic shutdown in E. coli cells. High osmolarity was clearly not one of the reasons of bacterial death by (-)-roemerine. These observations collectively attest to the promise of plant omics and profiling of putative drug candidates using proteomics tools. Omics-guided drug discovery deserves greater attention in mainstream pharmacology so as to better understand the plants' medicinal potentials.
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20
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Khan SN, Khan AU. Breaking the Spell: Combating Multidrug Resistant 'Superbugs'. Front Microbiol 2016; 7:174. [PMID: 26925046 PMCID: PMC4757689 DOI: 10.3389/fmicb.2016.00174] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/01/2016] [Indexed: 12/15/2022] Open
Abstract
Multidrug-resistant (MDR) bacteria have become a severe threat to community wellbeing. Conventional antibiotics are getting progressively more ineffective as a consequence of resistance, making it imperative to realize improved antimicrobial options. In this review we emphasized the microorganisms primarily reported of being resistance, referred as ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacteriaceae) accentuating their capacity to "escape" from routine antimicrobial regimes. The upcoming antimicrobial agents showing great potential and can serve as alternative therapeutic options are discussed. We also provided succinct overview of two evolving technologies; specifically network pharmacology and functional genomics profiling. Furthermore, In vivo imaging techniques can provide novel targets and a real time tool for potential lead molecule assessment. The employment of such approaches at prelude of a drug development process, will enables more informed decisions on candidate drug selection and will maximize or predict therapeutic potential before clinical testing.
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Affiliation(s)
| | - Asad U. Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim UniversityAligarh, India
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21
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Otto A, Becher D, Schmidt F. Quantitative proteomics in the field of microbiology. Proteomics 2014; 14:547-65. [PMID: 24376008 DOI: 10.1002/pmic.201300403] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 11/15/2013] [Accepted: 12/06/2013] [Indexed: 12/11/2022]
Abstract
Quantitative proteomics has become an indispensable analytical tool for microbial research. Modern microbial proteomics covers a wide range of topics in basic and applied research from in vitro characterization of single organisms to unravel the physiological implications of stress/starvation to description of the proteome content of a cell at a given time. With the techniques available, ranging from classical gel-based procedures to modern MS-based quantitative techniques, including metabolic and chemical labeling, as well as label-free techniques, quantitative proteomics is today highly successful in sophisticated settings of high complexity such as host-pathogen interactions, mixed microbial communities, and microbial metaproteomics. In this review, we will focus on the vast range of techniques practically applied in current research with an introduction of the workflows used for quantitative comparisons, a description of the advantages/disadvantages of the various methods, reference to hallmark publications and presentation of applications in current microbial research.
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Affiliation(s)
- Andreas Otto
- Institute for Microbiology, Ernst Moritz Arndt University Greifswald, Germany
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Bednarz-Misa I, Serek P, Dudek B, Pawlak A, Bugla-Płoskońska G, Gamian A. Application of zwitterionic detergent to the solubilization of Klebsiella pneumoniae outer membrane proteins for two-dimensional gel electrophoresis. J Microbiol Methods 2014; 107:74-9. [PMID: 25261774 DOI: 10.1016/j.mimet.2014.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/17/2014] [Accepted: 09/17/2014] [Indexed: 01/09/2023]
Abstract
Klebsiella pneumoniae is a frequent cause of nosocomial respiratory, urinary and gastrointestinal tract infections and septicemia with the multidrug-resistant K. pneumoniae being a major public health concern. Outer membrane proteins (OMPs) are important virulence factors responsible for the appropriate adaptation to the host environment. They constitute of the antigens being the first in contact with infected organism. However, K. pneumoniae strains are heavily capsulated and it is important to establish the OMPs isolation procedure prior to proteomics extensive studies. In this study we used Zwittergent Z 3-14® as a detergent to isolate the OMPs from K. pneumoniae cells and resolve them using two-dimensional electrophoresis (2-DE). As a result we identified 134 protein spots. The OMPs identified in this study are possible candidates for the development of a protein-based vaccine against K. pneumoniae infections.
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Affiliation(s)
- I Bednarz-Misa
- Department of Medical Biochemistry, Wroclaw Medical University, Chałubińskiego 10, 50-368 Wrocalaw, Poland.
| | - P Serek
- Department of Medical Biochemistry, Wroclaw Medical University, Chałubińskiego 10, 50-368 Wrocalaw, Poland
| | - B Dudek
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - A Pawlak
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - G Bugla-Płoskońska
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - A Gamian
- Department of Medical Biochemistry, Wroclaw Medical University, Chałubińskiego 10, 50-368 Wrocalaw, Poland; Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
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23
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24
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Antelmann H, Hecker M, Zuber P. Proteomic signatures uncover thiol-specific electrophile resistance mechanisms inBacillus subtilis. Expert Rev Proteomics 2014; 5:77-90. [DOI: 10.1586/14789450.5.1.77] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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25
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Thongboonkerd V. Proteomics in leptospirosis research: towards molecular diagnostics and vaccine development. Expert Rev Mol Diagn 2014; 8:53-61. [DOI: 10.1586/14737159.8.1.53] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Raatschen N, Elisabeth Bandow J. 2‐D Gel‐Based Proteomic Approaches to Antibiotic Drug Discovery. ACTA ACUST UNITED AC 2012; Chapter 1:Unit1F.2. [DOI: 10.1002/9780471729259.mc01f02s26] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Evaluating the suitability of essential genes as targets for antibiotic screening assays using proteomics. Protein Cell 2012; 3:5-7. [PMID: 22246580 DOI: 10.1007/s13238-011-1135-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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28
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Van Oudenhove L, De Vriendt K, Van Beeumen J, Mercuri PS, Devreese B. Differential proteomic analysis of the response of Stenotrophomonas maltophilia to imipenem. Appl Microbiol Biotechnol 2012; 95:717-33. [DOI: 10.1007/s00253-012-4167-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 05/09/2012] [Accepted: 05/10/2012] [Indexed: 11/28/2022]
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After genomics, what proteomics tools could help us understand the antimicrobial resistance of Escherichia coli? J Proteomics 2012; 75:2773-89. [PMID: 22245553 DOI: 10.1016/j.jprot.2011.12.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 12/21/2011] [Accepted: 12/23/2011] [Indexed: 12/30/2022]
Abstract
Proteomic approaches have been considerably improved during the past decade and have been used to investigate the differences in protein expression profiles of cells grown under a broad spectrum of growth conditions and with different stress factors including antibiotics. In Europe, the most significant disease threat remains the presence of microorganisms that have become resistant to antimicrobials and so it is important that different scientific tools are combined to achieve the largest amount of knowledge in this area of expertise. The emergence and spread of the antibiotic-resistant Gram-negative pathogens, such as Escherichia coli, can lead to serious problem public health in humans. E. coli, a very well described prokaryote, has served as a model organism for several biological and biotechnological studies increasingly so since the completion of the E. coli genome-sequencing project. The purpose of this review is to present an overview of the different proteomic approaches to antimicrobial-resistant E. coli that will be helpful to obtain a better knowledge of the antibiotic-resistant mechanism(s). This can also aid to understand the molecular determinants involved with pathogenesis, which is essential for the development of effective strategies to combat infection and to reveal new therapeutic targets. This article is part of a Special Issue entitled: Proteomics: The clinical link.
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Wecke T, Mascher T. Antibiotic research in the age of omics: from expression profiles to interspecies communication. J Antimicrob Chemother 2011; 66:2689-704. [DOI: 10.1093/jac/dkr373] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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31
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Wenzel M, Bandow JE. Proteomic signatures in antibiotic research. Proteomics 2011; 11:3256-68. [DOI: 10.1002/pmic.201100046] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 03/13/2011] [Accepted: 03/22/2011] [Indexed: 11/06/2022]
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Proteomic signature of fatty acid biosynthesis inhibition available for in vivo mechanism-of-action studies. Antimicrob Agents Chemother 2011; 55:2590-6. [PMID: 21383089 DOI: 10.1128/aac.00078-11] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fatty acid biosynthesis is a promising novel antibiotic target. Two inhibitors of fatty acid biosynthesis, platencin and platensimycin, were recently discovered and their molecular targets identified. Numerous structure-activity relationship studies for both platencin and platensimycin are currently being undertaken. We established a proteomic signature for fatty acid biosynthesis inhibition in Bacillus subtilis using platencin, platensimycin, cerulenin, and triclosan. The induced proteins, FabHA, FabHB, FabF, FabI, PlsX, and PanB, are enzymes involved in fatty acid biosynthesis and thus linked directly to the target pathway. The proteomic signature can now be used to assess the in vivo mechanisms of action of compounds derived from structure-activity relationship programs, as demonstrated for the platensimycin-inspired chromium bioorganometallic PM47. It will further serve as a reference signature for structurally novel natural and synthetic antimicrobial compounds with unknown mechanisms of action. In summary, we described a proteomic signature in B. subtilis consisting of six upregulated proteins that is diagnostic of fatty acid biosynthesis inhibition and thus can be applied to advance antibacterial drug discovery programs.
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Abstract
The discovery of novel small-molecule antibacterial drugs has been stalled for many years. The purpose of this review is to underscore and illustrate those scientific problems unique to the discovery and optimization of novel antibacterial agents that have adversely affected the output of the effort. The major challenges fall into two areas: (i) proper target selection, particularly the necessity of pursuing molecular targets that are not prone to rapid resistance development, and (ii) improvement of chemical libraries to overcome limitations of diversity, especially that which is necessary to overcome barriers to bacterial entry and proclivity to be effluxed, especially in Gram-negative organisms. Failure to address these problems has led to a great deal of misdirected effort.
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Affiliation(s)
- Lynn L Silver
- LL Silver Consulting, LLC, 955 S. Springfield Ave., Unit C403, Springfield, NJ 07081, USA.
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Brötz-Oesterhelt H, Sass P. Postgenomic strategies in antibacterial drug discovery. Future Microbiol 2010; 5:1553-79. [DOI: 10.2217/fmb.10.119] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
During the last decade the field of antibacterial drug discovery has changed in many aspects including bacterial organisms of primary interest, discovery strategies applied and pharmaceutical companies involved. Target-based high-throughput screening had been disappointingly unsuccessful for antibiotic research. Understanding of this lack of success has increased substantially and the lessons learned refer to characteristics of targets, screening libraries and screening strategies. The ‘genomics’ approach was replaced by a diverse array of discovery strategies, for example, searching for new natural product leads among previously abandoned compounds or new microbial sources, screening for synthetic inhibitors by targeted approaches including structure-based design and analyses of focused libraries and designing resistance-breaking properties into antibiotics of established classes. Furthermore, alternative treatment options are being pursued including anti-virulence strategies and immunotherapeutic approaches. This article summarizes the lessons learned from the genomics era and describes discovery strategies resulting from that knowledge.
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Affiliation(s)
- Heike Brötz-Oesterhelt
- AiCuris, Wuppertal, Germany, Institute for Pharmaceutical Biology, University of Duesseldorf, Universitätsstrasse 1, Building 26.23.U1, Germany
| | - Peter Sass
- Institute of Medical Microbiology, Immunology & Parasitology, Pharmaceutical Microbiology Section, University of Bonn, Germany
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35
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Ho MY, Chiou ML, Chang RC, Chen YH, Cheng CC. Outer membrane protein OmpF involved in the transportation of polypyridyl ruthenium complexes into Escherichia coli. J Inorg Biochem 2010; 104:614-7. [DOI: 10.1016/j.jinorgbio.2010.01.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 01/28/2010] [Accepted: 01/28/2010] [Indexed: 10/19/2022]
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36
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Witzmann FA, Richardson MR. Two-dimensional gels for toxicological drug discovery applications. Expert Opin Drug Metab Toxicol 2009; 2:103-11. [PMID: 16863472 DOI: 10.1517/17425255.2.1.103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Two-dimensional gel electrophoresis (2DGE) continues to be a useful approach to study protein expression. Although liquid chromatographic and mass spectrometric approaches that overcome some of the limitations and labour intensity of 2DGE are increasingly popular, this electrophoretic approach still has exceptional relevance in toxicology. Despite the technical challenges, pharmacologists/toxicologists continue to use gel-based proteomics to assess the biological and health effects of chemical treatment and exposure. This brief review addresses the use of 2DGE-based proteomics in drug development and toxicology, emphasising its unique strengths and weaknesses, and considers recent developments in this strategy that have evolved to directly confront the issues of dynamic range and reproducibility that have previously limited the overall use of 2D electrophoresis.
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Affiliation(s)
- Frank A Witzmann
- Indiana University School of Medicine, Department of Cellular & Integrative Physiology, Biotechnology & Research Training Center, Indianapolis, IN 46202, USA.
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37
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Soares NC, Cabral MP, Parreira JR, Gayoso C, Barba MJ, Bou G. 2-DE analysis indicates that Acinetobacter baumannii displays a robust and versatile metabolism. Proteome Sci 2009; 7:37. [PMID: 19785748 PMCID: PMC2761859 DOI: 10.1186/1477-5956-7-37] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 09/28/2009] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Acinetobacter baumannii is a nosocomial pathogen that has been associated with outbreak infections in hospitals. Despite increasing awareness about this bacterium, its proteome remains poorly characterised, however recently the complete genome of A. baumannii reference strain ATCC 17978 has been sequenced. Here, we have used 2-DE and MALDI-TOF/TOF approach to characterise the proteome of this strain. RESULTS The membrane and cytoplasmatic protein extracts were analysed separately, these analyses revealed the reproducible presence of 239 and 511 membrane and cytoplamatic protein spots, respectively. MALDI-TOF/TOF characterisation identified a total of 192 protein spots (37 membrane and 155 cytoplasmatic) and revealed that the identified membrane proteins were mainly transport-related proteins, whereas the cytoplasmatic proteins were of diverse nature, although mainly related to metabolic processes. CONCLUSION This work indicates that A. baumannii has a versatile and robust metabolism and also reveal a number of proteins that may play a key role in the mechanism of drug resistance and virulence. The data obtained complements earlier reports of A. baumannii proteome and provides new tools to increase our knowledge on the protein expression profile of this pathogen.
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38
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Hecker M, Antelmann H, Büttner K, Bernhardt J. Gel-based proteomics of Gram-positive bacteria: A powerful tool to address physiological questions. Proteomics 2008; 8:4958-75. [DOI: 10.1002/pmic.200800278] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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39
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Wase NV, Wright PC. Systems biology of cyanobacterial secondary metabolite production and its role in drug discovery. Expert Opin Drug Discov 2008; 3:903-29. [DOI: 10.1517/17460441.3.8.903] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Nishikant V Wase
- The University of Sheffield, Biological and Environmental Systems Group, Department of Chemical and Process Engineering, Mappin St., Sheffield, S1 3JD, UK ;
| | - Phillip C Wright
- The University of Sheffield, Biological and Environmental Systems Group, Department of Chemical and Process Engineering, Mappin St., Sheffield, S1 3JD, UK ;
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40
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Böttcher T, Sieber SA. Beta-lactones as privileged structures for the active-site labeling of versatile bacterial enzyme classes. Angew Chem Int Ed Engl 2008; 47:4600-3. [PMID: 18383487 DOI: 10.1002/anie.200705768] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Thomas Böttcher
- Center for integrated Protein Science Munich, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 Munich, Germany
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Shao C, Zhang Q, Tang W, Qu W, Zhou Y, Sun Y, Yu H, Jia J. The changes of proteomes components of Helicobacter pylori in response to acid stress without urea. J Microbiol 2008; 46:331-7. [DOI: 10.1007/s12275-008-0062-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Accepted: 04/13/2008] [Indexed: 10/21/2022]
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42
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Böttcher T, Sieber S. β-Lactone als privilegierte Strukturen für die Markierung des aktiven Zentrums vielfältiger bakterieller Enzymklassen. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705768] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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43
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Nie L, Wu G, Culley DE, Scholten JCM, Zhang W. Integrative analysis of transcriptomic and proteomic data: challenges, solutions and applications. Crit Rev Biotechnol 2007; 27:63-75. [PMID: 17578703 DOI: 10.1080/07388550701334212] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Recent advances in high-throughput technologies enable quantitative monitoring of the abundance of various biological molecules and allow determination of their variation between biological states on a genomic scale. Two popular platforms are DNA microarrays that measure messenger RNA transcript levels, and gel-free proteomic analyses that quantify protein abundance. Obviously, no single approach can fully unravel the complexities of fundamental biology and it is equally clear that integrative analysis of multiple levels of gene expression would be valuable in this endeavor. However, most integrative transcriptomic and proteomic studies have thus far either failed to find a correlation or only observed a weak correlation. In addition to various biological factors, it is suggested that the poor correlation could be quite possibly due to the inadequacy of available statistical tools to compensate for biases in the data collection methodologies. To address this issue, attempts have recently been made to systematically investigate the correlation patterns between transcriptomic and proteomic datasets, and to develop sophisticated statistical tools to improve the chances of capturing a relationship. The goal of these efforts is to enhance understanding of the relationship between transcriptomes and proteomes so that integrative analyses may be utilized to reveal new biological insights that are not accessible through one-dimensional datasets. In this review, we outline some of the challenges associated with integrative analyses and present some preliminary statistical solutions. In addition, some new applications of integrated transcriptomic and proteomic analysis to the investigation of post-transcriptional regulation are also discussed.
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Affiliation(s)
- Lei Nie
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University. Washington, DC, USA
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44
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Affiliation(s)
- Michael F Loughlin
- The University of Nottingham, Division of Food Sciences, School of Biosciences, Sutton Bonnington Campus, Loughborough, Leicestershire, LE12 5RD, UK ;
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45
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Nguyen VD, Wolf C, Mäder U, Lalk M, Langer P, Lindequist U, Hecker M, Antelmann H. Transcriptome and proteome analyses in response to 2-methylhydroquinone and 6-brom-2-vinyl-chroman-4-on reveal different degradation systems involved in the catabolism of aromatic compounds inBacillus subtilis. Proteomics 2007; 7:1391-408. [PMID: 17407181 DOI: 10.1002/pmic.200700008] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Bacillus subtilis is exposed to a variety of antimicrobial compounds in the soil. In this paper, we report on the response of B. subtilis to the fungal-related antimicrobials 6-brom-2-vinyl-chroman-4-on (chromanon) and 2-methylhydroquinone (2-MHQ) using proteome and transcriptome analyses. Chromanon, a derivative of aposphaerins from Aposphaeria species caused predominant protein damage in B. subtilis as indicated by the induction of the HrcA, CtsR, and Spx regulons. The expression profile of the ganomycin-related substance 2-MHQ was similar to that of catechol as reflected by the common induction of the thiol-specific oxidative stress response. Several putative ring-cleavage dioxygenases and oxidoreductases were differentially up-regulated by 2-MHQ, catechol, and chromanon including yfiDE, ydfNOP, yodED, ycnDE, yodC, and ykcA. The nitroreductase encoding yodC gene is induced in response to catechol, 2-MHQ, and chromanon, which depend on the MarR-type repressor YodB. The yfiDE (catDE) operon encodes a catechol-2,3-dioxygenase which is most strongly induced by catechol. The yodED (mhqED), ydfNOP (mhqNOP) operons, and ykcA (mhqA) respond most strongly to 2-MHQ and encode putative hydroquinone-specific extradiol dioxygenases. The ycnDE operon was most strongly induced by chromanon. Mutational analyses revealed that the putative hydroquinone-specific dioxygenases MhqO and MhqA confer resistance to 2-MHQ in B. subtilis.
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Affiliation(s)
- Van Duy Nguyen
- Institute for Microbiology, Ernst-Moritz-Arndt University of Greifswald, Greifswald, Germany
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46
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Bandow JE, Hecker M. Proteomic profiling of cellular stresses in Bacillus subtilis reveals cellular networks and assists in elucidating antibiotic mechanisms of action. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2007; 64:79, 81-101. [PMID: 17195472 DOI: 10.1007/978-3-7643-7567-6_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Proteomic profiling provides a global view of the protein composition of the cell. In contrast to the static nature of the genome sequence, which provides the blueprint for all protein-based cellular building blocks, the proteome is highly dynamic. The protein composition is constantly adjusting to facilitate survival, growth, and reproduction in an ever-changing environment. In a quest to understand the regulation of cellular networks in bacteria and the role of individual proteins in the adaptation process, the proteomic response to stress and starvation was analyzed in wild-type and mutant strains. The knowledge derived from these proteomic studies was applied to investigating the bacterial response to antibiotics. It was found that proteomics presents a powerful tool for hypothesis generation regarding antibiotic mechanism of action.
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Affiliation(s)
- Julia E Bandow
- Pfizer Global Research and Development, Pfizer Inc., Ann Arbor, Michigan, USA.
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47
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Li DA, He Y, Guo YJ, Wang F, Song SX, Wang Y, Yang F, He XW, Sun SH. Comparative proteomics analysis to annexin B1 DNA and protein vaccination in mice. Vaccine 2007; 25:932-8. [PMID: 17027125 DOI: 10.1016/j.vaccine.2006.08.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Revised: 08/27/2006] [Accepted: 08/29/2006] [Indexed: 11/21/2022]
Abstract
DNA vaccines have been widely reported to elicit both effective humoral and cellular immune responses, but the mechanisms of antigen processing and presentation in DNA immunization is still ambiguous. Aiming to molecular mechanisms involved in DNA immunization, comparative serum proteomics was introduced to discover differentially expressed proteins after different immunizations. Using two-dimensional electrophoresis and matrix-assisted laser desorption ionisation-time-of-flight mass spectrometry, 23 three-fold or greater up-regulated proteins were separated and identified, including 14 from ANXB1 DNA immunized mice and 9 from annexin B1 protein immunized mice. The histocompatibility class I molecule H2-Q10 (HA10_MOUSE) and proteasome activator PA28 alpha-subunit (PSME1_MOUSE) were found up-regulated in ANXB1 DNA immunized mice, which may contribute to the augmented activation of T lymphocytes. These proteins may serve as potential surrogate markers of successful vaccination and provide research targets for molecular mechanisms of vaccinology.
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Affiliation(s)
- De-An Li
- Department of Medical Genetics, Second Military Medical University, 800 Xiang-Yin Road, Yangpu District, Shanghai 200433, China
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48
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Cordwell SJ. Technologies for bacterial surface proteomics. Curr Opin Microbiol 2006; 9:320-9. [PMID: 16679049 DOI: 10.1016/j.mib.2006.04.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Accepted: 04/27/2006] [Indexed: 01/11/2023]
Abstract
Proteins from bacterial membranes are notoriously difficult to analyze using the traditional technologies encompassed under the term 'proteomics'. This is because of several factors, including the comparatively low abundance of most membrane proteins within a complex mixture containing cytoplasmic metabolic enzymes, the poor solubility of membrane components such as phospholipids, lipopolysaccharides and peptidoglycans, and the inherent hydrophobicity of many integral membrane proteins that contain up to 15 transmembrane-spanning regions. Recent advances in gel-based and chromatographic separations, coupled with protein and peptide labelling and the exquisite sensitivity of mass spectrometry, are finally beginning to overcome these problems. New technologies in membrane proteomics enable comparative analysis of these recalcitrant proteins from bacteria under a variety of biological conditions.
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Affiliation(s)
- Stuart J Cordwell
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia.
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Abstract
Proteomics was established 10 years ago by the analysis of microbial genomes via their protein complement or proteome. Bionics is an ancient art, which converts structures optimized by nature into advanced technical products. Previously, we analyzed survival modalities in nanobacteria and converted the interplay between survival-oriented protein functions and nanoscale mineral shells into models for advanced drug delivery. Exploiting protein functions observed in nature to design biomedical products and therapies could be named proteobionics. Here, we present examples for this new branch of nanoproteomics.
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Affiliation(s)
- Andrei P Sommer
- Central Institute of Biomedical Engineering, University of Ulm, 89081 Ulm, Germany.
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50
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Phillips CI, Bogyo M. Proteomics meets microbiology: technical advances in the global mapping of protein expression and function. Cell Microbiol 2005; 7:1061-76. [PMID: 16008574 DOI: 10.1111/j.1462-5822.2005.00554.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The availability of complete genome sequences for a large number of pathogenic organisms has opened the door for large-scale proteomic studies to dissect both protein expression/regulation and function. This review highlights key proteomic methods including two-dimensional gel electrophoresis, reference mapping, protein expression profiling and recent advances in gel-free separation techniques that have made a significant impact on the resolution of complex proteomes. In addition, we highlight recent developments in the field of chemical proteomics, a branch of proteomics aimed at functionally profiling a proteome. These techniques include the development of activity-based probes and activity-based protein profiling methods as well as the use of synthetic small molecule libraries to screen for pharmacological tools to perturb basic biological processes. This review will focus on the applications of these technologies to the field of microbiology.
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Affiliation(s)
- Carolyn I Phillips
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5324, USA
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