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Niu H, Gu J, Zhang Y. Bacterial persisters: molecular mechanisms and therapeutic development. Signal Transduct Target Ther 2024; 9:174. [PMID: 39013893 PMCID: PMC11252167 DOI: 10.1038/s41392-024-01866-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 07/18/2024] Open
Abstract
Persisters refer to genetically drug susceptible quiescent (non-growing or slow growing) bacteria that survive in stress environments such as antibiotic exposure, acidic and starvation conditions. These cells can regrow after stress removal and remain susceptible to the same stress. Persisters are underlying the problems of treating chronic and persistent infections and relapse infections after treatment, drug resistance development, and biofilm infections, and pose significant challenges for effective treatments. Understanding the characteristics and the exact mechanisms of persister formation, especially the key molecules that affect the formation and survival of the persisters is critical to more effective treatment of chronic and persistent infections. Currently, genes related to persister formation and survival are being discovered and confirmed, but the mechanisms by which bacteria form persisters are very complex, and there are still many unanswered questions. This article comprehensively summarizes the historical background of bacterial persisters, details their complex characteristics and their relationship with antibiotic tolerant and resistant bacteria, systematically elucidates the interplay between various bacterial biological processes and the formation of persister cells, as well as consolidates the diverse anti-persister compounds and treatments. We hope to provide theoretical background for in-depth research on mechanisms of persisters and suggest new ideas for choosing strategies for more effective treatment of persistent infections.
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Affiliation(s)
- Hongxia Niu
- School of Basic Medical Science and Key Laboratory of Blood-stasis-toxin Syndrome of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Jiaying Gu
- School of Basic Medical Science and Key Laboratory of Blood-stasis-toxin Syndrome of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Ying Zhang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250022, Shandong, China.
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Shabbir S, Wang W, Nawaz M, Boruah P, Kulyar MFEA, Chen M, Wu B, Liu P, Dai Y, Sun L, Gou Q, Liu R, Hu G, Younis T, He M. Molecular mechanism of engineered Zymomonas mobilis to furfural and acetic acid stress. Microb Cell Fact 2023; 22:88. [PMID: 37127628 PMCID: PMC10152622 DOI: 10.1186/s12934-023-02095-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023] Open
Abstract
Acetic acid and furfural (AF) are two major inhibitors of microorganisms during lignocellulosic ethanol production. In our previous study, we successfully engineered Zymomonas mobilis 532 (ZM532) strain by genome shuffling, but the molecular mechanisms of tolerance to inhibitors were still unknown. Therefore, this study investigated the responses of ZM532 and its wild-type Z. mobilis (ZM4) to AF using multi-omics approaches (transcriptomics, genomics, and label free quantitative proteomics). Based on RNA-Seq data, two differentially expressed genes, ZMO_RS02740 (up-regulated) and ZMO_RS06525 (down-regulated) were knocked out and over-expressed through CRISPR-Cas technology to investigate their roles in AF tolerance. Overall, we identified 1865 and 14 novel DEGs in ZM532 and wild-type ZM4. In contrast, 1532 proteins were identified in ZM532 and wild-type ZM4. Among these, we found 96 important genes in ZM532 involving acid resistance mechanisms and survival rates against stressors. Furthermore, our knockout results demonstrated that growth activity and glucose consumption of mutant strains ZM532∆ZMO_RS02740 and ZM4∆ZMO_RS02740 decreased with increased fermentation time from 42 to 55 h and ethanol production up to 58% in ZM532 than that in ZM532∆ZMO_RS02740. Hence, these findings suggest ZMO_RS02740 as a protective strategy for ZM ethanol production under stressful conditions.
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Affiliation(s)
- Samina Shabbir
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Department of Chemistry, The Women University Multan, Multan, Pakistan
| | - Weiting Wang
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Mohsin Nawaz
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Prerona Boruah
- School of Biotechnology and Bioinformatics, DY PATIL Deemed to Be University, Navi Mumbai, India
| | | | - Mao Chen
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Bo Wu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Panting Liu
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Yonghua Dai
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Lingling Sun
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Qiyu Gou
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Renbin Liu
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Guoquan Hu
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Tahira Younis
- Department of Biochemistry and Biotechnology, The Women University Multan, Multan, Pakistan
| | - Mingxiong He
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China.
- Chengdu National Agricultural Science and Technology Center, Chengdu, People's Republic of China.
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Wang C, Chen R, Xu J, Jin L. Single-cell Raman spectroscopy identifies Escherichia coli persisters and reveals their enhanced metabolic activities. Front Microbiol 2022; 13:936726. [PMID: 35992656 PMCID: PMC9386477 DOI: 10.3389/fmicb.2022.936726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/05/2022] [Indexed: 01/14/2023] Open
Abstract
Microbial persisters are the featured tiny sub-population of microorganisms that are highly tolerant to multiple antimicrobials. Currently, studies on persisters remain a considerable challenge owing to technical limitations. Here, we explored the application of single-cell Raman spectroscopy (SCRS) in the investigation of persisters. Escherichia coli (ATCC 25922) cells were treated with a lethal dosage of ampicillin (100 μg/mL, 32 × MIC, 4 h) for the formation of persisters. The biochemical characters of E. coli and its persisters were assessed by SCRS, and their metabolic activities were labeled and measured with D2O-based single-cell Raman spectroscopy (D2O-Ramanometry). Notable differences in the intensity of Raman bands related to major cellular components and metabolites were observed between E. coli and its ampicillin-treated persisters. Based on their distinct Raman spectra, E. coli and its persister cells were classified into different projective zones through the principal component analysis and t-distributed stochastic neighbor embedding. According to the D2O absorption rate, E. coli persisters exhibited higher metabolic activities than those of untreated E. coli. Importantly, after the termination of ampicillin exposure, these persister cells showed a temporal pattern of D2O intake that was distinct from non-persister cells. To our knowledge, this is the first report on identifying E. coli persisters and assessing their metabolic activities through the integrated SCRS and D2O-Ramanometry approach. These novel findings enhance our understanding of the phenotypes and functionalities of microbial persister cells. Further investigations could be extended to other pathogens by disclosing microbial pathogenicity mechanisms for developing novel therapeutic strategies and approaches.
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Affiliation(s)
- Chuan Wang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Rongze Chen
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Jian Xu
| | - Lijian Jin
- Faculty of Dentistry, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- *Correspondence: Lijian Jin
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Chebotar' IV, Emelyanova MA, Bocharova JA, Mayansky NA, Kopantseva EE, Mikhailovich VM. The classification of bacterial survival strategies in the presence of antimicrobials. Microb Pathog 2021; 155:104901. [PMID: 33930413 DOI: 10.1016/j.micpath.2021.104901] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 01/14/2023]
Abstract
The survival of bacteria under antibiotic therapy varies in nature and is based on the bacterial ability to employ a wide range of fundamentally different resistance mechanisms. This great diversity requires a disambiguation of the term 'resistance' and the development of a more precise classification of bacterial survival strategies during contact with antibiotics. The absence of a unified definition for the terms 'resistance', 'tolerance' and 'persistence' further aggravates the imperfections of the current classification system. This review suggests a number of original classification criteria that will take into account (1) the bacterial ability to replicate in the presence of antimicrobial agents, (2) existing evolutionary stability of a trait within a species, and (3) the presence or absence of specialized genes that determine the ability of a microorganism to decrease its own metabolism or switch it completely off. This review describes potential advantages of the suggested classification system, which include a better understanding of the relationship between bacterial survival in the presence of antibiotics and molecular mechanisms of cellular metabolism suppression, the opportunity to pinpoint targets to identify a true bacterial resistance profile. The true resistance profile in turn, could be used to develop effective diagnostic and antimicrobial therapy methods, while taking into consideration specific bacterial survival mechanisms.
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Affiliation(s)
- Igor V Chebotar'
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova St., Moscow, 119991, Russian Federation; Pirogov Russian National Research Medical University, 1 Ostrovitianov St., Moscow, 117997, Russian Federation
| | - Marina A Emelyanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova St., Moscow, 119991, Russian Federation
| | - Julia A Bocharova
- Pirogov Russian National Research Medical University, 1 Ostrovitianov St., Moscow, 117997, Russian Federation
| | - Nikolay A Mayansky
- Pirogov Russian National Research Medical University, 1 Ostrovitianov St., Moscow, 117997, Russian Federation
| | - Elena E Kopantseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova St., Moscow, 119991, Russian Federation
| | - Vladimir M Mikhailovich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova St., Moscow, 119991, Russian Federation.
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