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Ousalem F, Ngo S, Oïffer T, Omairi-Nasser A, Hamon M, Monlezun L, Boël G. Global regulation via modulation of ribosome pausing by the ABC-F protein EttA. Nat Commun 2024; 15:6314. [PMID: 39060293 PMCID: PMC11282234 DOI: 10.1038/s41467-024-50627-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Having multiple rounds of translation of the same mRNA creates dynamic complexities along with opportunities for regulation related to ribosome pausing and stalling at specific sequences. Yet, mechanisms controlling these critical processes and the principles guiding their evolution remain poorly understood. Through genetic, genomic, physiological, and biochemical approaches, we demonstrate that regulating ribosome pausing at specific amino acid sequences can produce ~2-fold changes in protein expression levels which strongly influence cell growth and therefore evolutionary fitness. We demonstrate, both in vivo and in vitro, that the ABC-F protein EttA directly controls the translation of mRNAs coding for a subset of enzymes in the tricarboxylic acid (TCA) cycle and its glyoxylate shunt, which modulates growth in some chemical environments. EttA also modulates expression of specific proteins involved in metabolically related physiological and stress-response pathways. These regulatory activities are mediated by EttA rescuing ribosomes paused at specific patterns of negatively charged residues within the first 30 amino acids of nascent proteins. We thus establish a unique global regulatory paradigm based on sequence-specific modulation of translational pausing.
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Affiliation(s)
- Farès Ousalem
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
- Biomarqueurs et nouvelles cibles thérapeutiques en oncologie, INSERM U981, Université Paris Saclay, Institut de Cancérologie Gustave Roussy, Villejuif Cedex, France
| | - Saravuth Ngo
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Thomas Oïffer
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Amin Omairi-Nasser
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Marion Hamon
- CNRS, Institut de Biologie Physico-Chimique, Plateforme de Protéomique, FR550, Paris, France
| | - Laura Monlezun
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Grégory Boël
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France.
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2
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Pourciau C, Yakhnin H, Pannuri A, Gorelik MG, Lai YJ, Romeo T, Babitzke P. CsrA coordinates the expression of ribosome hibernation and anti-σ factor proteins. mBio 2023; 14:e0258523. [PMID: 37943032 PMCID: PMC10746276 DOI: 10.1128/mbio.02585-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE The Csr/Rsm system (carbon storage regulator or repressor of stationary phase metabolites) is a global post-transcriptional regulatory system that coordinates and responds to environmental cues and signals, facilitating the transition between active growth and stationary phase. Another key determinant of bacterial lifestyle decisions is the management of the cellular gene expression machinery. Here, we investigate the connection between these two processes in Escherichia coli. Disrupted regulation of the transcription and translation machinery impacts many cellular functions, including gene expression, growth, fitness, and stress resistance. Elucidating the role of the Csr system in controlling the activity of RNAP and ribosomes advances our understanding of mechanisms controlling bacterial growth. A more complete understanding of these processes could lead to the improvement of therapeutic strategies for recalcitrant infections.
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Affiliation(s)
- Christine Pourciau
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Helen Yakhnin
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Archanna Pannuri
- Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Mark G. Gorelik
- Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Ying-Jung Lai
- Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Tony Romeo
- Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
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3
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Wang Y, Liang B, Song Z, Chen W, Niu H, Xing D, Zhang Y. High antipersister activity of a promising new quinolone drug candidate in eradicating uropathogenic Escherichia coli persisters and persistent infection in mice. J Appl Microbiol 2023; 134:lxad193. [PMID: 37667517 DOI: 10.1093/jambio/lxad193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/29/2023] [Accepted: 08/25/2023] [Indexed: 09/06/2023]
Abstract
AIMS To develop more potent drugs that eradicate persister bacteria and cure persistent urinary tract infections (rUTIs). METHODS AND RESULTS We synthesized eight novel clinifloxacin analogs and measured minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), the time-kill curves in uropathogenic Escherichia coli (UPEC) UTI89, and applied the candidate drugs and combinations against biofilm bacteria in vitro and in mice. Transcriptomic analysis was performed for UPEC after candidate drug treatment to shed light on potential mechanism of action. We identified Compound 2, named Qingdafloxacin (QDF), which was more potent than clinafloxacin and clinically used levofloxacin and moxifloxacin, with an MIC of < 0.04 μg ml-1 and an MBC of 0.08∼0.16 μg ml-1. In drug combination studies, QDF + gentamicin + nitrofuran combination but not single drugs completely eradicated all stationary phase bacteria containing persisters and biofilm bacteria, and all bacteria in a persistent UTI mouse model. Transcriptome analysis revealed that the unique antipersister activity of QDF was associated with downregulation of genes involved in bacterial stress response, DNA repair, protein misfolding repair, pyrimidine metabolism, glutamate, and glutathione metabolism, and efflux. CONCLUSIONS QDF has high antipersister activity and its drug combinations proved highly effective against biofilm bacteria in vitro and persistent UTIs in mice, which may have implications for treating rUTIs.
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Affiliation(s)
- Yanyan Wang
- Qingdao Cancer Institute, The Affiliated Hospital of Qingdao University, School of Basic Medicine of Qingdao University, Qingdao 266071, China
| | - Bing Liang
- Qingdao Cancer Institute, The Affiliated Hospital of Qingdao University, School of Basic Medicine of Qingdao University, Qingdao 266071, China
| | - Zhengming Song
- Qingdao Cancer Institute, The Affiliated Hospital of Qingdao University, School of Basic Medicine of Qingdao University, Qingdao 266071, China
| | - Wujun Chen
- Qingdao Cancer Institute, The Affiliated Hospital of Qingdao University, School of Basic Medicine of Qingdao University, Qingdao 266071, China
| | - Hongxia Niu
- Institute of Pathogenic Biology, School of Basic Medicine, Lanzhou University, Lanzhou 730000, China
| | - Dongming Xing
- Qingdao Cancer Institute, The Affiliated Hospital of Qingdao University, School of Basic Medicine of Qingdao University, Qingdao 266071, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ying Zhang
- Qingdao Cancer Institute, The Affiliated Hospital of Qingdao University, School of Basic Medicine of Qingdao University, Qingdao 266071, China
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China
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4
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Goldberger O, Szoke T, Nussbaum-Shochat A, Amster-Choder O. Heterotypic phase separation of Hfq is linked to its roles as an RNA chaperone. Cell Rep 2022; 41:111881. [PMID: 36577380 DOI: 10.1016/j.celrep.2022.111881] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 11/25/2022] [Accepted: 12/03/2022] [Indexed: 12/29/2022] Open
Abstract
Hfq, an Sm-like protein and the major RNA chaperone in E. coli, has been shown to distribute non-uniformly along a helical path under normal growth conditions and to relocate to the cell poles under certain stress conditions. We have previously shown that Hfq relocation to the poles is accompanied by polar accumulation of most small RNAs (sRNAs). Here, we show that Hfq undergoes RNA-dependent phase separation to form cytoplasmic or polar condensates of different density under normal and stress conditions, respectively. Purified Hfq forms droplets in the presence of crowding agents or RNA, indicating that its condensation is via heterotypic interactions. Stress-induced relocation of Hfq condensates and sRNAs to the poles depends on the pole-localizer TmaR. Phase separation of Hfq correlates with its ability to perform its posttranscriptional roles as sRNA-stabilizer and sRNA-mRNA matchmaker. Our study offers a spatiotemporal mechanism for sRNA-mediated regulation in response to environmental changes.
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Affiliation(s)
- Omer Goldberger
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O. Box 12272, Jerusalem 91120, Israel
| | - Tamar Szoke
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O. Box 12272, Jerusalem 91120, Israel
| | - Anat Nussbaum-Shochat
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O. Box 12272, Jerusalem 91120, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, P.O. Box 12272, Jerusalem 91120, Israel.
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5
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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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Sulaima JE, Lam H. Proteomics in antibiotic resistance and tolerance research: Mapping the resistome and the tolerome of bacterial pathogens. Proteomics 2022; 22:e2100409. [PMID: 35143120 DOI: 10.1002/pmic.202100409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 11/12/2022]
Abstract
Antibiotic resistance, the ability of a microbial pathogen to evade the effects of antibiotics thereby allowing them to grow under elevated drug concentrations, is an alarming health problem worldwide and has attracted the attention of scientists for decades. On the other hand, the clinical importance of persistence and tolerance as alternative mechanisms for pathogens to survive prolonged lethal antibiotic doses has recently become increasingly appreciated. Persisters and high-tolerance populations are thought to cause the relapse of infectious diseases, and provide opportunities for the pathogens to evolve resistance during the course of antibiotic therapy. Although proteomics and other omics methodology have long been employed to study resistance, its applications in studying persistence and tolerance are still limited. However, due to the growing interest in the topic and recent progress in method developments to study them, there have been some proteomic studies that yield fresh insights into the phenomenon of persistence and tolerance. Combined with the studies on resistance, these collectively guide us to novel molecular targets for the potential drugs for the control of these dangerous pathogens. In this review, we surveyed previous proteomic studies to investigate resistance, persistence, and tolerance mechanisms, and discussed emerging experimental strategies for studying these phenotypes with a combination of adaptive laboratory evolution and high-throughput proteomics. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jordy Evan Sulaima
- Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
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7
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Cell Envelope Stress Response in Pseudomonas aeruginosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:147-184. [DOI: 10.1007/978-3-031-08491-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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8
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Szoke T, Nussbaum-Shochat A, Amster-Choder O. Evolutionarily conserved mechanism for membrane recognition from bacteria to mitochondria. FEBS Lett 2021; 595:2805-2815. [PMID: 34644400 DOI: 10.1002/1873-3468.14203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/13/2021] [Accepted: 09/28/2021] [Indexed: 11/09/2022]
Abstract
The mechanisms controlling membrane recognition by proteins with one hydrophobic stretch at their carboxyl terminus (tail anchor, TA) are poorly defined. The Escherichia coli TAs of ElaB and YqjD, which share sequential and structural similarity with the Saccharomyces cerevisiae TA of Fis1, were shown to localize to mitochondria. We show that YqjD and ElaB are directed by their TAs to bacterial cell poles. Fis1(TA) expressed in E. coli localizes like the endogenous TAs. The yeast and bacterial TAs are inserted in the E. coli inner membrane, and they all show affiliation to phosphatidic acid (PA), found in the membrane of the bacterial cell poles and of the yeast mitochondria. Our results suggest a mechanism for TA membrane recognition conserved from bacteria to mitochondria and raise the possibility that through their interaction with PA, and TAs play a role across prokaryotes and eukaryotes in controlling cell/organelle fate.
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Affiliation(s)
- Tamar Szoke
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Anat Nussbaum-Shochat
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem, Israel
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9
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Salcedo-Sora JE, Kell DB. A Quantitative Survey of Bacterial Persistence in the Presence of Antibiotics: Towards Antipersister Antimicrobial Discovery. Antibiotics (Basel) 2020; 9:E508. [PMID: 32823501 PMCID: PMC7460088 DOI: 10.3390/antibiotics9080508] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
Background: Bacterial persistence to antibiotics relates to the phenotypic ability to survive lethal concentrations of otherwise bactericidal antibiotics. The quantitative nature of the time-kill assay, which is the sector's standard for the study of antibiotic bacterial persistence, is an invaluable asset for global, unbiased, and cross-species analyses. Methods: We compiled the results of antibiotic persistence from antibiotic-sensitive bacteria during planktonic growth. The data were extracted from a sample of 187 publications over the last 50 years. The antibiotics used in this compilation were also compared in terms of structural similarity to fluorescent molecules known to accumulate in Escherichia coli. Results: We reviewed in detail data from 54 antibiotics and 36 bacterial species. Persistence varies widely as a function of the type of antibiotic (membrane-active antibiotics admit the fewest), the nature of the growth phase and medium (persistence is less common in exponential phase and rich media), and the Gram staining of the target organism (persistence is more common in Gram positives). Some antibiotics bear strong structural similarity to fluorophores known to be taken up by E. coli, potentially allowing competitive assays. Some antibiotics also, paradoxically, seem to allow more persisters at higher antibiotic concentrations. Conclusions: We consolidated an actionable knowledge base to support a rational development of antipersister antimicrobials. Persistence is seen as a step on the pathway to antimicrobial resistance, and we found no organisms that failed to exhibit it. Novel antibiotics need to have antipersister activity. Discovery strategies should include persister-specific approaches that could find antibiotics that preferably target the membrane structure and permeability of slow-growing cells.
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Affiliation(s)
- Jesus Enrique Salcedo-Sora
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK;
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
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10
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Proteomic Study of the Survival and Resuscitation Mechanisms of Filamentous Persisters in an Evolved Escherichia coli Population from Cyclic Ampicillin Treatment. mSystems 2020; 5:5/4/e00462-20. [PMID: 32723793 PMCID: PMC7394356 DOI: 10.1128/msystems.00462-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Through adaptive laboratory evolution (ALE) experiments, it was recently found that when a bacterial population was repetitively treated with antibiotics, they will adapt to the treatment conditions and become tolerant to the drug. In this study, we utilized an ampicillin-tolerant Escherichia coli population isolated from an ALE experiment to study the mechanisms of persistence during ampicillin treatment and resuscitation. Interestingly, the persisters of this population exhibit filamentous morphology upon ampicillin treatment, and the filaments are getting longer over time. Proteomics analysis showed that proteins involved in carbohydrate metabolism are upregulated during antibiotic treatment, in addition to those involved in the oxidative stress response. Bacterial SOS response, which is associated with filamentation, was found to be induced on account of the increasing expression of RecA. Measurement of endogenous reactive oxygen species (ROS) revealed that the population have ∼100-fold less ROS generation under ampicillin treatment than the wild type, leading to a lower mutagenesis rate. Single-cell observations through time-lapse microscopy show that resuscitation of the filaments is stochastic. During resuscitation, proteins involved in the tricarboxylic acid (TCA) cycle, glyoxylate cycle and glycolytic processes, and ATP generation are downregulated, while ribosomal proteins and porins are upregulated in the filaments. One particular protein, ElaB, was upregulated by over 7-fold in the filaments after 3 h of resuspension in fresh medium, but its expression went down after the filaments divided. Knockout of elaB increased persistence on wild-type E. coli, and upon resumption of growth, mutants lacking elaB have a higher fraction of small colony variants (SCVs) than the wild type.IMPORTANCE Persisters are a subpopulation of cells with enhanced survival toward antibiotic treatment and have the ability to resume normal growth when the antibiotic stress is lifted. Although proteomics is the most suitable tool to study them from a system-level perspective, the number of persisters that present naturally is too few for proteomics analysis, and thus the complex mechanisms through which they are able to survive antibiotic stresses and resuscitate in fresh medium remain poorly understood. To overcome that challenge, we studied an evolved Escherichia coli population with elevated persister fraction under ampicillin treatment and obtained its proteome profiles during antibiotic treatment and resuscitation. We discovered that during treatment with ampicillin, this tolerant population employs an active oxidative stress response and exhibits lower ROS levels than the wild type. Moreover, an inner membrane protein which has implications in various stress responses, ElaB, was found to be highly upregulated in the persisters during resuscitation, and its knockout caused increased formation of small colony variants after ampicillin treatment, suggesting that ElaB is important for persisters to resume normal growth.
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Li B, Yin F, Zhao X, Guo Y, Wang W, Wang P, Zhu H, Yin Y, Wang X. Colistin Resistance Gene mcr-1 Mediates Cell Permeability and Resistance to Hydrophobic Antibiotics. Front Microbiol 2020; 10:3015. [PMID: 31998280 PMCID: PMC6966882 DOI: 10.3389/fmicb.2019.03015] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/16/2019] [Indexed: 11/13/2022] Open
Abstract
Colistin is considered the last-resort antibiotic used to treat multidrug resistant bacteria-related infections. However, the discovery of the plasmid-mediated colistin resistance gene, mcr-1, threatens the clinical utility of colistin antibiotics. In this study, the physiological function of MCR-1, which encodes an LPS-modifying enzyme, was investigated in E. coli K-12. Specifically, the impact of mcr-1 on membrane permeability and antibiotic resistance of E. coli was assessed by constructing an mcr-1 deletion mutant and by a complementation study. The removal of the mcr-1 gene from plasmid pHNSHP45 not only led to reduced resistance to colistin but also resulted in a significant change in the membrane permeability of E. coli. Unexpectedly, the removal of the mcr-1 gene increased cell viability under high osmotic stress conditions (e.g., 7.0% NaCl) and led to increased resistance to hydrophobic antibiotics. Increased expression of mcr-1 also resulted in decreased growth rate and changed the cellular morphology of E. coli. Collectively, our results revealed that the spread of mcr-1-carrying plasmids alters other physiological functions in addition to conferring colistin resistance.
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Affiliation(s)
- Baiyuan Li
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, China
| | - Fang Yin
- Department of Breast and Thyroid Surgery, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Xuanyu Zhao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Yunxue Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Weiquan Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Pengxia Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangzhou, China
| | - Yeshi Yin
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of the Chinese Academy of Sciences, Beijing, China
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12
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Tyagi D, Kraft AL, Levadney Smith S, Roof SE, Sherwood JS, Wiedmann M, Bergholz TM. Pre-Harvest Survival and Post-Harvest Chlorine Tolerance of Enterohemorrhagic Escherichia coli on Lettuce. Toxins (Basel) 2019; 11:E675. [PMID: 31752303 PMCID: PMC6891304 DOI: 10.3390/toxins11110675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/06/2019] [Accepted: 11/13/2019] [Indexed: 11/16/2022] Open
Abstract
In the field, foodborne pathogens such as enterohemorrhagic Escherichia coli (EHEC) are capable of surviving on produce over time, yet little is known about how these pathogens adapt to this environment. To assess the impact of pre-harvest environmental conditions on EHEC survival, we quantified survival on romaine lettuce under two relative humidity (75% and 45%) and seasonal conditions (March and June). Greenhouse-grown lettuce was spray-inoculated with EHEC and placed in a growth chamber, mimicking conditions typical for June and March in Salinas Valley, California. Bacteria were enumerated on days 0, 1, 3, and 5 post-inoculation. Overall, we found that the effect of relative humidity on EHEC survival depended on the seasonal conditions. Under June seasonal conditions, higher relative humidity led to lower survival, and lower relative humidity led to greater survival, five days post-inoculation. Under March seasonal conditions, the impact of relative humidity on EHEC survival was minimal over the five days. The bacteria were also tested for their ability to survive a chlorine decontamination wash. Inoculated lettuce was incubated under the June 75% relative humidity conditions and then washed with a 50 ppm sodium hypochlorite solution (40 ppm free chlorine). When incubated under June seasonal conditions for three to five days, EHEC strains showed increased tolerance to chlorine (adj. p < 0.05) compared to chlorine tolerance upon inoculation onto lettuce. This indicated that longer incubation on lettuce led to greater EHEC survival upon exposure to chlorine. Subsequent transcriptome analysis identified the upregulation of osmotic and oxidative stress response genes by EHEC after three and five days of incubation on pre-harvest lettuce. Assessing the physiological changes in EHEC that occur during association with pre-harvest lettuce is important for understanding how changing tolerance to post-harvest control measures may occur.
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Affiliation(s)
- Deepti Tyagi
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Autumn L Kraft
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Sara Levadney Smith
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Sherry E Roof
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Julie S Sherwood
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Teresa M Bergholz
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58102, USA
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13
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Abstract
Protein synthesis consumes a large fraction of available resources in the cell. When bacteria encounter unfavorable conditions and cease to grow, specialized mechanisms are in place to ensure the overall reduction of costly protein synthesis while maintaining a basal level of translation. A number of ribosome-associated factors are involved in this regulation; some confer an inactive, hibernating state of the ribosome in the form of 70S monomers (RaiA; this and the following are based on Escherichia coli nomenclature) or 100S dimers (RMF and HPF homologs), and others inhibit translation at different stages in the translation cycle (RsfS, YqjD and paralogs, SRA, and EttA). Stationary phase cells therefore exhibit a complex array of different ribosome subpopulations that adjusts the translational capacity of the cell to the encountered conditions and ensures efficient reactivation of translation when conditions improve. Here, we review the current state of research regarding stationary phase-specific translation factors, in particular ribosome hibernation factors and other forms of translational regulation in response to stress conditions.
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Affiliation(s)
- Thomas Prossliner
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
| | | | | | - Kenn Gerdes
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
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Noster J, Persicke M, Chao TC, Krone L, Heppner B, Hensel M, Hansmeier N. Impact of ROS-Induced Damage of TCA Cycle Enzymes on Metabolism and Virulence of Salmonella enterica serovar Typhimurium. Front Microbiol 2019; 10:762. [PMID: 31105651 PMCID: PMC6491894 DOI: 10.3389/fmicb.2019.00762] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 03/26/2019] [Indexed: 01/10/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (STM) is exposed to reactive oxygen species (ROS) originating from aerobic respiration, antibiotic treatment, and the oxidative burst occurring inside the Salmonella-containing vacuole (SCV) within host cells. ROS damage cellular compounds, thereby impairing bacterial viability and inducing cell death. Proteins containing iron–sulfur (Fe–S) clusters are particularly sensitive and become non-functional upon oxidation. Comprising five enzymes with Fe–S clusters, the TCA cycle is a pathway most sensitive toward ROS. To test the impact of ROS-mediated metabolic perturbations on bacterial physiology, we analyzed the proteomic and metabolic profile of STM deficient in both cytosolic superoxide dismutases (ΔsodAB). Incapable of detoxifying superoxide anions (SOA), endogenously generated SOA accumulate during growth. ΔsodAB showed reduced abundance of aconitases, leading to a metabolic profile similar to that of an aconitase-deficient strain (ΔacnAB). Furthermore, we determined a decreased expression of acnA in STM ΔsodAB. While intracellular proliferation in RAW264.7 macrophages and survival of methyl viologen treatment were not reduced for STM ΔacnAB, proteomic profiling revealed enhanced stress response. We conclude that ROS-mediated reduced expression and damage of aconitase does not impair bacterial viability or virulence, but might increase ROS amounts in STM, which reinforces the bactericidal effects of antibiotic treatment and immune responses of the host.
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Affiliation(s)
- Janina Noster
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Marcus Persicke
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Tzu-Chiao Chao
- Institute of Environmental Change and Society, University of Regina, Regina, SK, Canada
| | - Lena Krone
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Bianca Heppner
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Michael Hensel
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Nicole Hansmeier
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany.,Institute of Environmental Change and Society, University of Regina, Regina, SK, Canada.,Luther College, University of Regina, Regina, SK, Canada
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15
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Guo Y, Li Y, Zhan W, Wood TK, Wang X. Resistance to oxidative stress by inner membrane protein ElaB is regulated by OxyR and RpoS. Microb Biotechnol 2019; 12:392-404. [PMID: 30656833 PMCID: PMC6389858 DOI: 10.1111/1751-7915.13369] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/18/2018] [Indexed: 02/06/2023] Open
Abstract
C-tail anchored inner membrane proteins are a family of proteins that contain a C-terminal transmembrane domain but lack an N-terminal signal sequence for membrane targeting. They are widespread in eukaryotes and prokaryotes and play critical roles in membrane traffic, apoptosis and protein translocation in eukaryotes. Recently, we identified and characterized in Escherichia coli a new C-tail anchored inner membrane, ElaB, which is regulated by the stationary phase sigma factor RpoS. ElaB is important for resistance to oxidative stress but the exact mechanism is unclear. Here, we show that ElaB functions as part of the adaptive oxidative stress response by maintaining membrane integrity. Production of ElaB is induced by oxidative stress at the transcriptional level. Moreover, elaB expression is also regulated by the key regulator OxyR via an OxyR binding site in the promoter of elaB. OxyR induces the expression of elaB in the exponential growth phase, while excess OxyR reduces elaB expression in an RpoS-dependent way in the stationary phase. In addition, deletion of elaB reduced fitness compared to wild-type cells after prolonged incubation. Therefore, we determined how ElaB is regulated under oxidative stress: RpoS and OxyR coordinately control the expression of inner membrane protein ElaB.
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Affiliation(s)
- Yunxue Guo
- CAS Key Laboratory of Tropical Marine Bio‐resources and EcologyGuangdong Key Laboratory of Marine Materia MedicaRNAM Center for Marine MicrobiologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou510301China
| | - Yangmei Li
- CAS Key Laboratory of Tropical Marine Bio‐resources and EcologyGuangdong Key Laboratory of Marine Materia MedicaRNAM Center for Marine MicrobiologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou510301China
- University of Chinese Academy of SciencesBeijing100049China
| | - Waner Zhan
- CAS Key Laboratory of Tropical Marine Bio‐resources and EcologyGuangdong Key Laboratory of Marine Materia MedicaRNAM Center for Marine MicrobiologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou510301China
- University of Chinese Academy of SciencesBeijing100049China
| | - Thomas K. Wood
- Department of Chemical EngineeringPennsylvania State University, University ParkPA16802‐4400USA
- Department of Biochemistry and Molecular BiologyPennsylvania State UniversityUniversity ParkPA16802‐4400USA
| | - Xiaoxue Wang
- CAS Key Laboratory of Tropical Marine Bio‐resources and EcologyGuangdong Key Laboratory of Marine Materia MedicaRNAM Center for Marine MicrobiologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou510301China
- University of Chinese Academy of SciencesBeijing100049China
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16
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Raman spectral signature reflects transcriptomic features of antibiotic resistance in Escherichia coli. Commun Biol 2018; 1:85. [PMID: 30271966 PMCID: PMC6123714 DOI: 10.1038/s42003-018-0093-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 06/07/2018] [Indexed: 12/23/2022] Open
Abstract
To be able to predict antibiotic resistance in bacteria from fast label-free microscopic observations would benefit a broad range of applications in the biological and biomedical fields. Here, we demonstrate the utility of label-free Raman spectroscopy in monitoring the type of resistance and the mode of action of acquired resistance in a bacterial population of Escherichia coli, in the absence of antibiotics. Our findings are reproducible. Moreover, we identified spectral regions that best predicted the modes of action and explored whether the Raman signatures could be linked to the genetic basis of acquired resistance. Spectral peak intensities significantly correlated (False Discovery Rate, p < 0.05) with the gene expression of some genes contributing to antibiotic resistance genes. These results suggest that the acquisition of antibiotic resistance leads to broad metabolic effects reflected through Raman spectral signatures and gene expression changes, hinting at a possible relation between these two layers of complementary information. Techniques for characterizing the mode of action of antibiotic resistance are crucial for developing new antimicrobial drugs. Arno Germond et al. have used Raman spectroscopy combined with gene expression to investigate large metabolic changes that occur when bacteria acquire antibiotic resistance.
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17
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Satheeshkumar PK, Anu PV, Junaida MI, Madanan MG, Jebasingh T, Nair AJ, Nair GA, Nair GPM, Sudhakaran PR. Expression of Leptospira membrane proteins Signal Peptidase (SP) and Leptospira Endostatin like A (Len A) in BL-21(DE3) is toxic to the host cells. J Genet Eng Biotechnol 2018; 16:393-398. [PMID: 30733752 PMCID: PMC6353657 DOI: 10.1016/j.jgeb.2018.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/18/2018] [Accepted: 01/24/2018] [Indexed: 02/06/2023]
Abstract
Heterologous expression of Integral Membrane Proteins (IMPs) is reported to be toxic to the host system in many studies. Even though there are reports on various concerns like transformation efficiency, growth properties, protein toxicity, inefficient expression and protein degradation in IMP overexpression, no studies so far addressed these issues in a comprehensive way. In the present study, two transmembrane proteins of the pathogen Leptospira interrogans, namely Signal peptidase (SP), and Leptospira Endostatin like A (Len-A) were taken along with a cytosolic protein Hydrolase (HYD) to assess the differences in transformation efficiency, protein toxicity, and protein stability when over expressed in Escherichia coli (E. coli). Bioinformatics analysis to predict the transmembrane localization indicated that both SP and Len are targeted to the membrane. The three proteins were expressed in full length in the E. coli expression strain, BL 21 (DE3). Significant changes were observed for the strains transformed with IMP genes under the parameters analysed such as, the transformation efficiency, survival of colonies on IPTG-plate, culture growth kinetics and protein expression compared to the strain harbouring the cytosolic protein gene.
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Affiliation(s)
- Padikara K Satheeshkumar
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | - Prasannan V Anu
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | - Mohmed I Junaida
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | | | | | - Ananthakrishnan J Nair
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | - Gangaprasad A Nair
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | - Govinda Pillai M Nair
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | - Perumana R Sudhakaran
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
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18
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Zhang GB, Maddili SK, Tangadanchu VKR, Gopala L, Gao WW, Cai GX, Zhou CH. Discovery of natural berberine-derived nitroimidazoles as potentially multi-targeting agents against drug-resistant Escherichia coli. Sci China Chem 2017. [DOI: 10.1007/s11426-017-9169-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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