1
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Wang F, Sun H, Kang C, Yan J, Chen J, Feng X, Yang B. Genomic island-encoded regulatory proteins in enterohemorrhagic Escherichia coli O157:H7. Virulence 2024; 15:2313407. [PMID: 38357901 PMCID: PMC10877973 DOI: 10.1080/21505594.2024.2313407] [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: 10/24/2023] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) is an important zoonotic pathogen that is a major cause of foodborne diseases in most developed and developing countries and can cause uncomplicated diarrhoea, haemorrhagic colitis, and haemolytic uraemic syndrome. O islands (OIs), which are unique genomic islands in EHEC O157:H7, are composed of 177 isolated genomic features and harbour 26% of the total genes that are absent in the non-pathogenic E. coli K-12 genome. In the last twenty years, many OI-encoded proteins have been characterized, including proteins regulating virulence, motility, and acid resistance. Given the critical role of regulatory proteins in the systematic and hierarchical regulation of bacterial biological processes, this review summarizes the OI-encoded regulatory proteins in EHEC O157:H7 characterized to date, emphasizing OI-encoded regulatory proteins for bacterial virulence, motility, and acid resistance. This summary will be significant for further exploration and understanding of the virulence and pathogenesis of EHEC O157:H7.
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Affiliation(s)
- Fang Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- Intensive Care Unit, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Hongmin Sun
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Chenbo Kang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Jun Yan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Jingnan Chen
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Xuequan Feng
- Tianjin First Central Hospital, Nankai University, Tianjin, China
| | - Bin Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
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2
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Wu Z, Li J, Chen W. Biological characterization of lipoic acid- and heme-dependent Escherichia coli small colony variants isolated from sheep in Xinjiang, China. Vet Res Commun 2024:10.1007/s11259-024-10554-2. [PMID: 39325108 DOI: 10.1007/s11259-024-10554-2] [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: 07/20/2024] [Accepted: 09/19/2024] [Indexed: 09/27/2024]
Abstract
Escherichia coli (E. coli) small colony variants (SCVs) have garnered attention due to their heightened antibiotic resistance and enhanced cell retention, posing significant risks to public health and food safety. However, understanding of SCVs derived from sheep remains limited. This study aimed to detect the biological characterization of sheep-derived E. coli SCVs and investigate the factors contributing to SCV development with preliminary genomic data. In this study, a lipoic acid-dependent SCV (LA-SCV) and a wild-type (WT) strain were isolated from sheep bile. Then, a heme-dependent SCV (HD-SCV) was induced from WT using amikacin. Initially, we examined factors contributing to SCV formation via comparative genomics. Subsequent comparisons between WT and two SCV strains encompassed antibiotic resistance, hemolytic activity, biofilm formation, motility, and metabolism. Genomic analyses identified a frameshift deletion mutation in the lipA gene in LA-SCV and a stopgain mutation in the hemG gene in HD-SCV, hypothesized as potential triggers for lipoic acid- and heme-dependent SCV development, respectively. Physiological, biochemical, and cultural traits exhibited notable differences between WT and SCVs, including increased antibiotic resistance, hemolytic activity, and biofilm formation, but alongside non-fermentative acetate utilization, slow growth, reduced intracellular ATP, and decreased motility (P < 0.01). The energy and amino acid metabolism were suppressed during the logarithmic phase in LA-SCV, while both logarithmic and stable phases in HD-SCV. These alterations in biological characteristics present significant challenges in managing E. coli pathogenicity and antibiotic resistance.
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Affiliation(s)
- Zihao Wu
- College of Life Sciences and Technology, State Key Laboratory Breeding Base for The Protection and Utilization of Biological Resources in Tarim Basin Co-funded by Xinjiang Production & Construction Corps, Tarim University, The Ministry of Science & Technology, Alar, 86-843300, China
| | - Jing Li
- College of Animal Sciences and Technology, Engineering Laboratory of Tarim Animal Diseases Diagnosis and Control, Tarim University, Xinjiang Production & Construction Corps, Alar, 86-843300, China.
| | - Wei Chen
- College of Life Sciences and Technology, State Key Laboratory Breeding Base for The Protection and Utilization of Biological Resources in Tarim Basin Co-funded by Xinjiang Production & Construction Corps, Tarim University, The Ministry of Science & Technology, Alar, 86-843300, China.
- College of Animal Sciences and Technology, Engineering Laboratory of Tarim Animal Diseases Diagnosis and Control, Tarim University, Xinjiang Production & Construction Corps, Alar, 86-843300, China.
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3
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Hwang D, Kim HJ. Increased antimicrobial resistance of acid-adapted pathogenic Escherichia coli, and transcriptomic analysis of polymyxin-resistant strain. Microb Pathog 2024; 196:106974. [PMID: 39307200 DOI: 10.1016/j.micpath.2024.106974] [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: 05/16/2024] [Revised: 09/11/2024] [Accepted: 09/20/2024] [Indexed: 09/27/2024]
Abstract
This study investigated the acid adaptation and antimicrobial resistance of seven pathogenic Escherichia coli strains and one commensal strain under nutrient-rich acidic conditions. After acid adaptation, three pathogenic E. coli survived during 100 h incubation in tryptic soy broth at pH 3.25. Acid-adapted (AA) strains showed increased resistance to antimicrobials including ampicillin, ciprofloxacin and especially polymyxins (colistin and polymyxin B), the last resort antimicrobial for multidrug-resistant Gram-negative bacteria. Enterotoxigenic E. coli strain (NCCP 13717) showed significantly increased resistance to acids and polymyxins. Transcriptome analysis of the AA NCCP 13717 revealed upregulation of genes related to the acid fitness island and the arn operon, which reduces lipopolysaccharide binding affinity at the polymyxin site of action. Genes such as eptA, tolC, and ompCF were also upregulated to alter the structure of the cell membrane, reducing the outer membrane permeability compared to the control, which is likely to be another mechanism for polymyxin resistance. This study highlights the emergence of antimicrobial resistance in AA pathogenic E. coli strains, particularly polymyxin resistance, and the mechanisms behind the increased antimicrobial resistance, providing important insights for the development of risk management strategies to effectively control the antimicrobial resistant foodborne pathogens.
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Affiliation(s)
- Daekeun Hwang
- Korea Food Research Institute, Wanju, Jeolla-buk, 55365, South Korea; Department of Food Biotechnology, University of Science and Technology, Daejeon, 34113, South Korea
| | - Hyun Jung Kim
- Korea Food Research Institute, Wanju, Jeolla-buk, 55365, South Korea; Department of Food Biotechnology, University of Science and Technology, Daejeon, 34113, South Korea.
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Atasoy M, Bartkova S, Çetecioğlu-Gürol Z, P Mira N, O'Byrne C, Pérez-Rodríguez F, Possas A, Scheler O, Sedláková-Kaduková J, Sinčák M, Steiger M, Ziv C, Lund PA. Methods for studying microbial acid stress responses: from molecules to populations. FEMS Microbiol Rev 2024; 48:fuae015. [PMID: 38760882 PMCID: PMC11418653 DOI: 10.1093/femsre/fuae015] [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: 07/04/2023] [Revised: 03/27/2024] [Accepted: 05/16/2024] [Indexed: 05/20/2024] Open
Abstract
The study of how micro-organisms detect and respond to different stresses has a long history of producing fundamental biological insights while being simultaneously of significance in many applied microbiological fields including infection, food and drink manufacture, and industrial and environmental biotechnology. This is well-illustrated by the large body of work on acid stress. Numerous different methods have been used to understand the impacts of low pH on growth and survival of micro-organisms, ranging from studies of single cells to large and heterogeneous populations, from the molecular or biophysical to the computational, and from well-understood model organisms to poorly defined and complex microbial consortia. Much is to be gained from an increased general awareness of these methods, and so the present review looks at examples of the different methods that have been used to study acid resistance, acid tolerance, and acid stress responses, and the insights they can lead to, as well as some of the problems involved in using them. We hope this will be of interest both within and well beyond the acid stress research community.
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Affiliation(s)
- Merve Atasoy
- UNLOCK, Wageningen University and Research, PO Box 9101, 6700 HB, the Netherlands
| | - Simona Bartkova
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia
| | - Zeynep Çetecioğlu-Gürol
- Department of Industrial Biotechnology, KTH Royal Institute of Technology, Roslagstullsbacken 21 106 91 Stockholm, Stockholm, Sweden
| | - Nuno P Mira
- iBB, Institute for Bioengineering and Biosciences, Department of Bioengineering, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Conor O'Byrne
- Microbiology, School of Biological and Chemical Sciences, University of Galway, University Road, Galway, H91 TK33, Ireland
| | - Fernando Pérez-Rodríguez
- Department of Food Science and Tehcnology, UIC Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, 14014 Córdoba, Spain
| | - Aricia Possas
- Department of Food Science and Tehcnology, UIC Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, 14014 Córdoba, Spain
| | - Ott Scheler
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia
| | - Jana Sedláková-Kaduková
- Institute of Chemistry and Environmental Sciences, University of Ss. Cyril and Methodius, 91701 Trnava, Republic of Slovakia
| | - Mirka Sinčák
- Institute of Chemistry and Environmental Sciences, University of Ss. Cyril and Methodius, 91701 Trnava, Republic of Slovakia
| | - Matthias Steiger
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Carmit Ziv
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, 7505101 Rishon LeZion, Israel
| | - Peter A Lund
- School of Biosciences and Institute of Microbiology of Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
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Livne N, Koler M, Vaknin A. Collective condensation and auto-aggregation of Escherichia coli in uniform acidic environments. Commun Biol 2024; 7:1028. [PMID: 39169072 PMCID: PMC11339372 DOI: 10.1038/s42003-024-06698-1] [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: 04/10/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024] Open
Abstract
Chemotaxis-the movement of cells along chemical gradients-leads to collective behaviors when cells coordinate their movements. Here, using Escherichia coli as a model, we demonstrate a distinct type of bacterial collective response in acidic environments containing organic acids. Bacterial populations immersed in such environments collectively condensed into millimeter-sized focal points. Furthermore, this bacterial condensation fostered the formation of small, tightly packed cell aggregates, resembling non-surface-attached biofilms. These cell aggregates were physically displaced by the free-swimming condensing cells, leading to the segregation of the two cell populations. Bacterial condensation relied on feedback between the tendency of these bacteria to neutralize the pH and their chemotactic repulsion from low pH. Sustained cell condensation occurred when the bacteria occupied only part of the acidic environment, either dynamically or due to physical constraints. Such condensed bacterial populations can mitigate acid stress more efficiently, a principle that may be applicable to other stress conditions.
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Affiliation(s)
- Nir Livne
- The Racah Institute of Physics, The Hebrew University, Jerusalem, Israel
| | - Moriah Koler
- The Racah Institute of Physics, The Hebrew University, Jerusalem, Israel
| | - Ady Vaknin
- The Racah Institute of Physics, The Hebrew University, Jerusalem, Israel.
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6
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Wang YJ, Zhou X, Zhang MM, Liu MH, Ding N, Wu QF, Lei CR, Dong ZY, Ren JL, Zhao JR, Jia CL, Liu J, Zhou B, Lu D. Physiological and biochemical characteristics of the carbon ion beam irradiation-generated mutant strain Clostridium butyricum FZM 240 in vitro and in vivo. Enzyme Microb Technol 2024; 178:110447. [PMID: 38626534 DOI: 10.1016/j.enzmictec.2024.110447] [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: 12/12/2023] [Revised: 03/08/2024] [Accepted: 04/12/2024] [Indexed: 04/18/2024]
Abstract
Clostridium butyricum (C. butyricum) represents a new generation of probiotics, which is beneficial because of its good tolerance and ability to produce beneficial metabolites, such as short-chain fatty acids and enzymes; however, its low enzyme activity limits its probiotic efficacy. In this study, a mutant strain, C. butyricum FZM 240 was obtained using carbon ion beam irradiation, which exhibited greatly improved enzyme production and tolerance. The highest filter paper, endoglucanase, and amylase activities produced by C. butyricum FZM 240 were 125.69 U/mL, 225.82 U/ mL, and 252.28 U/mL, which were 2.58, 1.95, and 2.21-fold higher, respectively, than those of the original strain. The survival rate of the strain increased by 11.40 % and 5.60 % after incubation at 90 °C for 5 min and with simulated gastric fluid at pH 2.5 for 2 h, respectively, compared with that of the original strain. Whole-genome resequencing and quantitative real-time PCR(qRT-PCR) analysis showed that the expression of genes related to enzyme synthesis (GE000348, GE001963 and GE003123) and tolerance (GE001114) was significantly up-regulated, while that of genes related to acid metabolism (GE003450) was significantly down-regulated. On this basis, homology modeling and functional prediction of the proteins encoded by the mutated genes were performed. According to the results, the properties related to the efficacy of C. butyricum as a probiotic were significantly enhanced by carbon ion beam irradiation, which is a novel strategy for the application of Clostridium spp. as feed additives.
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Affiliation(s)
- Ya-Juan Wang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China
| | - Xiang Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China; Kejin Innovation Institute of Heavy Ion Beam Biological Industry, Baiyin 730900, China.
| | - Miao-Miao Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China; Gansu Key Laboratory of Microbial Resources Exploitation and Application, Lanzhou 730070, China
| | - Mei-Han Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410000, China
| | - Nan Ding
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China
| | - Qing-Feng Wu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Cai-Rong Lei
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China
| | - Zi-Yi Dong
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China
| | - Jun-Le Ren
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China
| | - Jing-Ru Zhao
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China
| | - Cheng-Lin Jia
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China
| | - Jun Liu
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410000, China
| | - Bo Zhou
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410000, China
| | - Dong Lu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing 100049, China; Kejin Innovation Institute of Heavy Ion Beam Biological Industry, Baiyin 730900, China; Gansu Key Laboratory of Microbial Resources Exploitation and Application, Lanzhou 730070, China.
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7
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Qin J, Guo H, Wu X, Ma S, Zhang X, Yang X, Liu B, Feng L, Liu H, Huang D. Characterization of Mild Acid Stress Response in an Engineered Acid-Tolerant Escherichia coli Strain. Microorganisms 2024; 12:1565. [PMID: 39203406 PMCID: PMC11356199 DOI: 10.3390/microorganisms12081565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/23/2024] [Accepted: 07/23/2024] [Indexed: 09/03/2024] Open
Abstract
Engineering acid-tolerant microbial strains is a cost-effective approach to overcoming acid stress during industrial fermentation. We previously constructed an acid-tolerant strain (Escherichia coli SC3124) with enhanced growth robustness and productivity under mildly acidic conditions by fine-tuning the expression of synthetic acid-tolerance module genes consisting of a proton-consuming acid resistance system (gadE), a periplasmic chaperone (hdeB), and ROS scavengers (sodB, katE). However, the precise acid-tolerance mechanism of E. coli SC3124 remained unclear. In this study, the growth of E. coli SC3124 under mild acid stress (pH 6.0) was determined. The final OD600 of E. coli SC3124 at pH 6.0 was 131% and 124% of that of the parent E. coli MG1655 at pH 6.8 and pH 6.0, respectively. Transcriptome analysis revealed the significant upregulation of the genes involved in oxidative phosphorylation, the tricarboxylic acid (TCA) cycle, and lysine-dependent acid-resistance system in E. coli SC3124 at pH 6.0. Subsequently, a weighted gene coexpression network analysis was performed to systematically determine the metabolic perturbations of E. coli SC3124 with mild acid treatment, and we extracted the gene modules highly associated with different acid traits. The results showed two biologically significant coexpression modules, and 263 hub genes were identified. Specifically, the genes involved in ATP-binding cassette (ABC) transporters, oxidative phosphorylation, the TCA cycle, amino acid metabolism, and purine metabolism were highly positively associated with mild acid stress responses. We propose that the overexpression of synthetic acid-tolerance genes leads to metabolic changes that confer mild acid stress resistance in E. coli. Integrated omics platforms provide valuable information for understanding the regulatory mechanisms of mild acid tolerance in E. coli and highlight the important roles of oxidative phosphorylation and ABC transporters in mild acid stress regulation. These findings offer novel insights to better the design of acid-tolerant chasses to synthesize value-added chemicals in a green and sustainable manner.
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Affiliation(s)
- Jingliang Qin
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China; (J.Q.); (B.L.)
| | - Han Guo
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China; (J.Q.); (B.L.)
| | - Xiaoxue Wu
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China; (J.Q.); (B.L.)
| | - Shuai Ma
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China; (J.Q.); (B.L.)
| | - Xin Zhang
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou 510006, China; (X.Z.); (X.Y.)
| | - Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou 510006, China; (X.Z.); (X.Y.)
| | - Bin Liu
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China; (J.Q.); (B.L.)
- Nankai International Advanced Research Institute, Nankai University, Shenzhen 518000, China
| | - Lu Feng
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China; (J.Q.); (B.L.)
| | - Huanhuan Liu
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Di Huang
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China; (J.Q.); (B.L.)
- Nankai International Advanced Research Institute, Nankai University, Shenzhen 518000, China
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8
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Wen Y, Tang C, Shen Q, Dong S, Wang Y, Li Y, Shao S. An efficient ratiometric fluorescence and colorimetric dual-mode probe for convenient determination of nitrite in real samples and E. coli. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4865-4872. [PMID: 38973349 DOI: 10.1039/d4ay00417e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Developing an effective and convenient nitrite detection method is indispensable in food safety, environmental monitoring, clinical diagnosis of diseases, and many other areas. Herein, a dicyanoisophorone derivative, TMN-NH2 with large Stokes shift and near-infrared (NIR) emission, was proposed as a ratiometric fluorescence and colorimetric dual-mode probe for the rapid determination of NO2- in acidic media, showing excellent selectivity and high sensitivity. The sensing mechanism is based on the diazotization of TMN-NH2 with NO2- and subsequent diazonium salt hydrolysis to form a hydroxyl-substituted product (TMN-OH). Under the optimized conditions of reaction and detection, a new quantitative analysis method based on TMN-NH2 was established for NO2- detection, exhibiting good linear relationships to NO2- in the range of 0.5 to 15 μM with practical detection limits of 26.6 nM and 17.6 nM for the colorimetric and fluorescent readout, respectively. The quantitative detection of NO2- in real samples demonstrated satisfactory recoveries and repeatability. Moreover, TMN-NH2 was successfully applied for monitoring NO2- in Escherichia coli by confocal fluorescence imaging.
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Affiliation(s)
- Yujie Wen
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China.
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, PR China
| | - Cong Tang
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, PR China
| | - Qing Shen
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, PR China
| | - Shuqing Dong
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China.
| | - Yaya Wang
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China.
| | - Yunchun Li
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China.
| | - Shijun Shao
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China.
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9
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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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10
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Davis NK, Chionh YH, McBee ME, Hia F, Ma D, Cui L, Sharaf ML, Cai WM, Jumpathong W, Levine SS, Alonso S, Dedon PC. Facile metabolic reprogramming distinguishes mycobacterial adaptation to hypoxia and starvation: ketosis drives starvation-induced persistence in M. bovis BCG. Commun Biol 2024; 7:866. [PMID: 39009734 PMCID: PMC11250799 DOI: 10.1038/s42003-024-06562-2] [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: 01/08/2024] [Accepted: 07/05/2024] [Indexed: 07/17/2024] Open
Abstract
Mycobacteria adapt to infection stresses by entering a reversible non-replicating persistence (NRP) with slow or no cell growth and broad antimicrobial tolerance. Hypoxia and nutrient deprivation are two well-studied stresses commonly used to model the NRP, yet little is known about the molecular differences in mycobacterial adaptation to these distinct stresses that lead to a comparable NRP phenotype. Here we performed a multisystem interrogation of the Mycobacterium bovis BCG (BCG) starvation response, which revealed a coordinated metabolic shift away from the glycolysis of nutrient-replete growth to depletion of lipid stores, lipolysis, and fatty acid ß-oxidation in NRP. This contrasts with BCG's NRP hypoxia response involving a shift to cholesterol metabolism and triglyceride storage. Our analysis reveals cryptic metabolic vulnerabilities of the starvation-induced NRP state, such as their newfound hypersensitivity to H2O2. These observations pave the way for developing precision therapeutics against these otherwise drug refractory pathogens.
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Affiliation(s)
- Nick K Davis
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yok Hian Chionh
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- GenScript Biotech (Singapore) Pte. Ltd, Singapore, Singapore
| | - Megan E McBee
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Fabian Hia
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Duanduan Ma
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Liang Cui
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Mariam Lucila Sharaf
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- BioNTech SE An der Goldgrube, Mainz, Germany
| | - Weiling Maggie Cai
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- British High Commission, Singapore, Singapore
| | - Watthanachai Jumpathong
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Chemical Biology Program, Chulabhorn Graduate Institute, Bangkok, Thailand
| | - Stuart S Levine
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sylvie Alonso
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.
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11
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Gavriil A, Giannenas I, Skandamis PN. A current insight into Salmonella's inducible acid resistance. Crit Rev Food Sci Nutr 2024:1-21. [PMID: 39014992 DOI: 10.1080/10408398.2024.2373387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Salmonella is a diverse and ubiquitous group of bacteria and a major zoonotic pathogen implicated in several foodborne disease outbreaks worldwide. With more than 2500 distinct serotypes, this pathogen has evolved to survive in a wide spectrum of environments and across multiple hosts. The primary and most common source of transmission is through contaminated food or water. Although the main sources have been primarily linked to animal-related food products, outbreaks due to the consumption of contaminated plant-related food products have increased in the last few years. The perceived ability of Salmonella to trigger defensive mechanisms following pre-exposure to sublethal acid conditions, namely acid adaptation, has renewed a decade-long attention. The impact of acid adaptation on the subsequent resistance against lethal factors of the same or multiple stresses has been underscored by multiple studies. Α plethora of studies have been published, aiming to outline the factors that- alone or in combination- can impact this phenomenon and to unravel the complex networking mechanisms underlying its induction. This review aims to provide a current and updated insight into the factors and mechanisms that rule this phenomenon.
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Affiliation(s)
- Alkmini Gavriil
- Department of Natural Resources Management and Agricultural Engineering, Agricultural University of Athens, Athens, Greece
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Ilias Giannenas
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Panagiotis N Skandamis
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
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12
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Reeder BJ, Svistunenko DA, Wilson MT. Hell's Gate Globin-I from Methylacidiphilum infernorum Displays a Unique Temperature-Independent pH Sensing Mechanism Utililized a Lipid-Induced Conformational Change. Int J Mol Sci 2024; 25:6794. [PMID: 38928500 PMCID: PMC11203436 DOI: 10.3390/ijms25126794] [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: 04/26/2024] [Revised: 06/05/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Hell's Gate globin-I (HGb-I) is a thermally stable globin from the aerobic methanotroph Methylacidiphilium infernorum. Here we report that HGb-I interacts with lipids stoichiometrically to induce structural changes in the heme pocket, changing the heme iron distal ligation coordination from hexacoordinate to pentacoordinate. Such changes in heme geometry have only been previously reported for cytochrome c and cytoglobin, linked to apoptosis regulation and enhanced lipid peroxidation activity, respectively. However, unlike cytoglobin and cytochrome c, the heme iron of HGb-I is altered by lipids in ferrous as well as ferric oxidation states. The apparent affinity for lipids in this thermally stable globin is highly pH-dependent but essentially temperature-independent within the range of 20-60 °C. We propose a mechanism to explain these observations, in which lipid binding and stability of the distal endogenous ligand are juxtaposed as a function of temperature. Additionally, we propose that these coupled equilibria may constitute a mechanism through which this acidophilic thermophile senses the pH of its environment.
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Affiliation(s)
- Brandon J. Reeder
- School of Biological Sciences, University of Essex, Wivenhoe Park Colchester, Essex CO4 3SQ, UK; (D.A.S.); (M.T.W.)
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13
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Sharma D, Chetri PB, Ranga V, Sen S, Sarmah BK, Barooah M. Genomic analysis of acid tolerance genes and deciphering the function of ydaG gene in mitigating acid tolerance in Priestia megaterium. Front Microbiol 2024; 15:1414777. [PMID: 38966390 PMCID: PMC11222612 DOI: 10.3389/fmicb.2024.1414777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024] Open
Abstract
Adverse environmental conditions, such as acid stress, induce bacteria to employ several strategies to overcome these stressors. These strategies include forming biofilms and activating specific molecular pathways, such as the general stress response (GSR). The genome of Priestia megaterium strain G18 was sequenced using the Illumina NextSeq 500 system, resulting in a de novo assembly of 80 scaffolds. The scaffolded genome comprises 5,367,956 bp with a GC content of 37.89%, and was compared to related strains using the MiGA web server, revealing high similarity to P. megaterium NBRC 15308 and P. aryabhattai B8W22 with ANI scores of 95.4%. Phylogenetic and ribosomal multilocus sequence typing (rMLST) analyses, based on the 16S rRNA and ribosomal protein-encoding alleles, confirmed close relationships within the P. megaterium species. Functional annotation identified 5,484 protein-coding genes, with 72.31% classified into 22 COG categories, highlighting roles in amino acid transport, transcription, carbohydrate metabolism, and ribosomal structure. An in-depth genome analysis of P. megaterium G18 revealed several key genes associated with acid tolerance. Targeted inactivation of the ydaG gene from SigB regulon, a general stress response gene, significantly reduced growth under acidic conditions compared to the wild type. qRT-PCR analysis showed increased ydaG expression in acidic conditions, further supporting its role in acid stress response. Microscopic analysis revealed no morphological differences between wild-type and mutant cells, suggesting that ydaG is not involved in maintaining cellular morphology but in facilitating acid tolerance through stress protein production. This research contributes to understanding the molecular mechanisms underlying acid tolerance in soil bacteria, P. megaterium, shedding light on potential applications in agriculture and industry.
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Affiliation(s)
- Darshana Sharma
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Purna Bahadur Chetri
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Vipin Ranga
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Subhajit Sen
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Bidyut Kumar Sarmah
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Madhumita Barooah
- DBT—North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
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14
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Schumacher K, Braun D, Kleigrewe K, Jung K. Motility-activating mutations upstream of flhDC reduce acid shock survival of Escherichia coli. Microbiol Spectr 2024; 12:e0054424. [PMID: 38651876 PMCID: PMC11237407 DOI: 10.1128/spectrum.00544-24] [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: 02/28/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Many neutralophilic bacterial species try to evade acid stress with an escape strategy, which is reflected in the increased expression of genes coding for flagellar components. Extremely acid-tolerant bacteria, such as Escherichia coli, survive the strong acid stress, e.g., in the stomach of vertebrates. Recently, we were able to show that the induction of motility genes in E. coli is strictly dependent on the degree of acid stress, i.e., they are induced under mild acid stress but not under severe acid stress. However, it was not known to what extent fine-tuned expression of motility genes is related to fitness and the ability to survive periods of acid shock. In this study, we demonstrate that the expression of FlhDC, the master regulator of flagellation, is inversely correlated with the acid shock survival of E. coli. We encountered this phenomenon when analyzing mutants from the Keio collection, in which the expression of flhDC was altered by an insertion sequence element. These results suggest a fitness trade-off between acid tolerance and motility.IMPORTANCEEscherichia coli is extremely acid-resistant, which is crucial for survival in the gastrointestinal tract of vertebrates. Recently, we systematically studied the response of E. coli to mild and severe acidic conditions using Ribo-Seq and RNA-Seq. We found that motility genes are induced at pH 5.8 but not at pH 4.4, indicating stress-dependent synthesis of flagellar components. In this study, we demonstrate that motility-activating mutations upstream of flhDC, encoding the master regulator of flagella genes, reduce the ability of E. coli to survive periods of acid shock. Furthermore, we show an inverse correlation between motility and acid survival using a chromosomal isopropyl β-D-thio-galactopyranoside (IPTG)-inducible flhDC promoter and by sampling differentially motile subpopulations from swim agar plates. These results reveal a previously undiscovered trade-off between motility and acid tolerance and suggest a differentiation of E. coli into motile and acid-tolerant subpopulations, driven by the integration of insertion sequence elements.
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Affiliation(s)
- Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Djanna Braun
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
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15
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Se J, Xie Y, Ma Q, Zhu L, Fu Y, Xu X, Shen C, Nannipieri P. Drying-wetting cycle enhances stress resistance of Escherichia coli O157:H7 in a model soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 350:123988. [PMID: 38648967 DOI: 10.1016/j.envpol.2024.123988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/13/2024] [Accepted: 04/13/2024] [Indexed: 04/25/2024]
Abstract
Outbreaks of Escherichia coli (E. coli) O157:H7 in farms are often triggered by heavy rains and flooding. Most cells die with the decreasing of soil moisture, while few cells enter a dormant state and then resuscitate after rewetting. The resistance of dormant cells to stress has been extensively studied, whereas the molecular mechanisms of the cross-resistance development of the resuscitated cells are poorly known. We performed a comparative proteomic analysis on O157:H7 before and after undergoing soil dry-wet alternation. A differential expression of 820 proteins was identified in resuscitated cells compared to exponential-phase cells, as determined by proteomics analysis. The GO and KEGG pathway enrichment analyses revealed that up-regulated proteins were associated with oxidative phosphorylation, glycolysis/gluconeogenesis, the citrate cycle (TCA cycle), aminoacyl-tRNA biosynthesis, ribosome activity, and transmembrane transporters, indicating increased energy production and protein synthesis in resuscitated O157:H7. Moreover, proteins related to acid, osmotic, heat, oxidative, antibiotic stress and horizontal gene transfer efficiency were up-regulated, suggesting a potential improvement in stress resistance. Subsequent validation experiments demonstrated that the survival rates of the resuscitated cells were 476.54 and 7786.34 times higher than the exponential-phase cells, with pH levels of 1.5 and 2.5, respectively. Similarly, resuscitated cells showed higher survival rates under osmotic stress, with 7.5%, 15%, and 30% NaCl resulting in survival rates that were 460.58, 1974.55, and 3475.31 times higher. Resuscitated cells also exhibited increased resistance to heat stress, with survival rates 69.64 and 139.72 times higher at 55 °C and 90 °C, respectively. Furthermore, the horizontal gene transfer (HGT) efficiency of resuscitated cells was significantly higher (153.12-fold) compared to exponential phase cells. This study provides new insights into bacteria behavior under changing soil moisture and this may explain O157:H7 outbreaks following rainfall and flooding, as the dry-wet cycle promotes stress cross-resistance development.
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Affiliation(s)
- Jing Se
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, 310058, China
| | - Yinan Xie
- Ministry of Education Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qingxu Ma
- Ministry of Education Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lin Zhu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Yulong Fu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, 310058, China
| | - Xin Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, 310058, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, 310058, China.
| | - Paolo Nannipieri
- Emeritus Professor, University of Firenze, Firenze, 50144, Italy
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16
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Guragain M, Schmidt JW, Bagi LK, Paoli GC, Kalchayanand N, Bosilevac JM. Antibiotic Resistance and Disinfectant Resistance Among Escherichia coli Isolated During Red Meat Production. J Food Prot 2024; 87:100288. [PMID: 38697484 DOI: 10.1016/j.jfp.2024.100288] [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: 10/13/2023] [Revised: 04/19/2024] [Accepted: 04/25/2024] [Indexed: 05/05/2024]
Abstract
Escherichia coli commonly found in the gastrointestinal tracts of food animals include Shiga toxin-producing E. coli (STEC, stx+, eae-), Enterohemorrhagic E. coli (EHEC, stx+, eae+), Enteropathogenic E. coli (EPEC, stx-, eae+), and "nondiarrheagenic" E. coli (NDEC, stx-, eae-). EHEC, EPEC, and STEC are associated with foodborne disease outbreaks. During meat processing, disinfectants are employed to control various bacteria, including human pathogens. Concerns exist that E. coli resistant to antibiotics are less susceptible to disinfectants used during meat processing. Since EHEC, EPEC, and STEC with reduced susceptibility to disinfectants are potential public health risks, the goal of this study was to evaluate the association of antibiotic resistant (ABR) E. coli with increased tolerance to 4% lactic acid (LA) and 150 ppm quaternary ammonium compounds (QACs). A pool of 3,367 E. coli isolated from beef cattle, veal calves, swine, and sheep at various processing stages was screened to identify ABR E. coli. Resistance to ≥1 of the six antibiotics examined was identified in 27.9%, 36.1%, 54.5%, and 28.7% among the NDEC (n = 579), EHEC (n = 693), EPEC (n = 787), and STEC (n = 1308) isolates evaluated, respectively. Disinfectant tolerance did not differ (P > 0.05) between ABR and antibiotic susceptible EHEC isolates. Comparable frequencies (P > 0.05) of biofilm formation or congo red binding were observed between ABR and antibiotic susceptible strains of E. coli. Understanding the frequencies of ABR and disinfectant tolerance among E. coli present in food-animal is a critically important component of meat safety.
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Affiliation(s)
- Manita Guragain
- Characterization and Interventions for Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, PA, USA.
| | - John W Schmidt
- Meat Safety and Quality Research Unit, Meat Animal Research Center, Agricultural Research Service, US Department of Agriculture, Clay Center, NE, USA
| | - Lori K Bagi
- Characterization and Interventions for Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, PA, USA
| | - George C Paoli
- Characterization and Interventions for Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, PA, USA
| | - Norasak Kalchayanand
- Meat Safety and Quality Research Unit, Meat Animal Research Center, Agricultural Research Service, US Department of Agriculture, Clay Center, NE, USA
| | - Joseph M Bosilevac
- Meat Safety and Quality Research Unit, Meat Animal Research Center, Agricultural Research Service, US Department of Agriculture, Clay Center, NE, USA
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17
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Van Looveren N, IJdema F, van der Heijden N, Van Der Borght M, Vandeweyer D. Microbial dynamics and vertical transmission of Escherichia coli across consecutive life stages of the black soldier fly (Hermetia illucens). Anim Microbiome 2024; 6:29. [PMID: 38797818 PMCID: PMC11129375 DOI: 10.1186/s42523-024-00317-4] [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: 01/26/2024] [Accepted: 05/22/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND The black soldier fly (BSF, Hermetia illucens L.) is one of the most promising insects for bioconversion of organic waste, which often carry a high microbial load with potential foodborne pathogens. Although horizontal transmission (from rearing substrate to larvae) has been extensively studied, less is known about vertical transmission of microorganisms, and particularly of foodborne pathogens, across different BSF life stages. RESULTS This study investigated the microbial dynamics and vertical transmission of Escherichia coli across different life stages (larvae, prepupae, pupae and adults) of one BSF life cycle and its associated substrate (chicken feed) and frass, based on a combination of general microbial counts (based on culture-dependent techniques) and the bacterial community composition (based on 16S rRNA gene sequencing). Multiple interactions between the microbiota of the substrate, frass and BSF larvae were affirmed. The larvae showed relative consistency among both the microbial counts and bacterial community composition. Diversification of the bacterial communities started during the pupal stage, while most notable changes of the microbial counts and bacterial community compositions occurred during metamorphosis to adults. Furthermore, vertical transmission of E. coli was investigated after substrate inoculation with approximately 7.0 log cfu/g of kanamycin-resistant E. coli, and monitoring E. coli counts from larval to adult stage. Although the frass still contained substantial levels of E. coli (> 4.5 log cfu/g) and E. coli was taken up by the larvae, limited vertical transmission of E. coli was observed with a decreasing trend until the prepupal stage. E. coli counts were below the detection limit (1.0 log cfu/g) for all BSF samples from the end of the pupal stage and the adult stage. Additionally, substrate inoculation of E. coli did not have a substantial impact on the bacterial community composition of the substrate, frass or different BSF life stages. CONCLUSIONS The fluctuating microbial counts and bacterial community composition underscored the dynamic character of the microbiota of BSF life stages. Additionally, vertical transmission throughout one BSF life cycle was not observed for E. coli. Hence, these findings paved the way for future case studies on vertical transmission of foodborne pathogens across consecutive BSF life stages or other insect species.
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Affiliation(s)
- Noor Van Looveren
- KU Leuven, Geel Campus, Department of Microbial and Molecular Systems (M2S), Research Group for Insect Production and Processing, Kleinhoefstraat 4, Geel, 2440, Belgium
| | - Freek IJdema
- KU Leuven, Geel Campus, Department of Microbial and Molecular Systems (M2S), Research Group for Insect Production and Processing, Kleinhoefstraat 4, Geel, 2440, Belgium
| | - Niels van der Heijden
- KU Leuven, Geel Campus, Department of Microbial and Molecular Systems (M2S), Research Group for Insect Production and Processing, Kleinhoefstraat 4, Geel, 2440, Belgium
| | - Mik Van Der Borght
- KU Leuven, Geel Campus, Department of Microbial and Molecular Systems (M2S), Research Group for Insect Production and Processing, Kleinhoefstraat 4, Geel, 2440, Belgium
| | - Dries Vandeweyer
- KU Leuven, Geel Campus, Department of Microbial and Molecular Systems (M2S), Research Group for Insect Production and Processing, Kleinhoefstraat 4, Geel, 2440, Belgium.
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18
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Qi YL, Chen YT, Xie YG, Li YX, Rao YZ, Li MM, Xie QJ, Cao XR, Chen L, Qu YN, Yuan ZX, Xiao ZC, Lu L, Jiao JY, Shu WS, Li WJ, Hedlund BP, Hua ZS. Analysis of nearly 3000 archaeal genomes from terrestrial geothermal springs sheds light on interconnected biogeochemical processes. Nat Commun 2024; 15:4066. [PMID: 38744885 PMCID: PMC11094006 DOI: 10.1038/s41467-024-48498-5] [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: 09/07/2023] [Accepted: 05/02/2024] [Indexed: 05/16/2024] Open
Abstract
Terrestrial geothermal springs are physicochemically diverse and host abundant populations of Archaea. However, the diversity, functionality, and geological influences of these Archaea are not well understood. Here we explore the genomic diversity of Archaea in 152 metagenomes from 48 geothermal springs in Tengchong, China, collected from 2016 to 2021. Our dataset is comprised of 2949 archaeal metagenome-assembled genomes spanning 12 phyla and 392 newly identified species, which increases the known species diversity of Archaea by ~48.6%. The structures and potential functions of the archaeal communities are strongly influenced by temperature and pH, with high-temperature acidic and alkaline springs favoring archaeal abundance over Bacteria. Genome-resolved metagenomics and metatranscriptomics provide insights into the potential ecological niches of these Archaea and their potential roles in carbon, sulfur, nitrogen, and hydrogen metabolism. Furthermore, our findings illustrate the interplay of competition and cooperation among Archaea in biogeochemical cycles, possibly arising from overlapping functional niches and metabolic handoffs. Taken together, our study expands the genomic diversity of Archaea inhabiting geothermal springs and provides a foundation for more incisive study of biogeochemical processes mediated by Archaea in geothermal ecosystems.
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Affiliation(s)
- Yan-Ling Qi
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Ya-Ting Chen
- Institute for Disaster Management and Reconstruction, Sichuan University-Hong Kong Polytechnic University, Chengdu, 610207, China
| | - Yuan-Guo Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yu-Xian Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yang-Zhi Rao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Qi-Jun Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Xing-Ru Cao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Lei Chen
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yan-Ni Qu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Zhen-Xuan Yuan
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Zhi-Chao Xiao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China.
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China.
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19
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Fang X, Yang Y, Guo Q, Zhang Y, Yuan M, Liang X, Liu J, Fang S, Fang C. Two-component system LiaSR negatively regulated the acid resistance and pathogenicity of Listeria monocytogenes 10403S. Food Microbiol 2024; 119:104428. [PMID: 38225058 DOI: 10.1016/j.fm.2023.104428] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 11/10/2023] [Accepted: 11/17/2023] [Indexed: 01/17/2024]
Abstract
The glutamate decarboxylase (GAD) system is one of the acid-resistant systems of Listeria monocytogenes (L. monocytogenes), while the regulatory mechanism of GadT2/GadD2, which plays the major role in the GAD system for acid resistance, is not clear. The two-component system (TCS) is a signal transduction system that is also involved in regulating acid resistance in bacteria. By screening the TCSs of L. monocytogenes 10403S, we found that knocking out the TCS LisSR (encoded by lmo1021/lmo1022) led to a significant increase in the transcription and expression of the gadT2/gadD2 cluster. Subsequently, we constructed a complemental strain CΔliaSR. and a complemental strain with LiaS His157 to Ala, which was designated as CΔliaSRH157A. Survival assay, transcriptional and expression analysis and pathogenicity assay revealed that liaSR deletion significantly enhanced the acid resistance and pathogenicity of 10403S and significantly increased the gadT2/gadD2 transcription and expression. Mutating LiaS His157 to Ala significantly enhanced the acid resistance and pathogenicity of CΔliaSR and significantly increased the gadT2/gadD2 transcription and expression. The results suggest that the two-component system LiaSR mediates the acid resistance and pathogenicity in 10403S by inhibiting the gadT2/gadD2 cluster, and the key activation site of LiaS is His157. This study provides novel knowledge on the regulation of GAD system and the control of this foodborne pathogen.
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Affiliation(s)
- Xiaowei Fang
- College of Animal Science, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China; College of Agriculture, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China
| | - Yuying Yang
- College of Animal Science, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China
| | - Qian Guo
- College of Animal Science, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China
| | - Yu Zhang
- College of Animal Science, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China
| | - Mei Yuan
- College of Animal Science, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China
| | - Xiongyan Liang
- College of Animal Science, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China
| | - Jing Liu
- College of Animal Science, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China
| | - Shouguo Fang
- College of Agriculture, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China.
| | - Chun Fang
- College of Animal Science, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China.
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20
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Gorelik MG, Yakhnin H, Pannuri A, Walker AC, Pourciau C, Czyz D, Romeo T, Babitzke P. Multitier regulation of the E. coli extreme acid stress response by CsrA. J Bacteriol 2024; 206:e0035423. [PMID: 38319100 PMCID: PMC11210196 DOI: 10.1128/jb.00354-23] [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: 10/26/2023] [Accepted: 01/15/2024] [Indexed: 02/07/2024] Open
Abstract
CsrA is an RNA-binding protein that regulates processes critical for growth and survival, including central carbon metabolism, motility, biofilm formation, stress responses, and expression of virulence factors in pathogens. Transcriptomics studies in Escherichia coli suggested that CsrA repressed genes involved in surviving extremely acidic conditions. Here, we examine the effects of disrupting CsrA-dependent regulation on the expression of genes and circuitry for acid stress survival and demonstrate CsrA-mediated repression at multiple levels. We show that this repression is critical for managing the trade-off between growth and survival; overexpression of acid stress genes caused by csrA disruption enhances survival under extreme acidity but is detrimental for growth under mildly acidic conditions. In vitro studies confirmed that CsrA binds specifically to mRNAs of structural and regulatory genes for acid stress survival, causing translational repression. We also found that translation of the top-tier acid stress regulator, evgA, is coupled to that of a small leader peptide, evgL, which is repressed by CsrA. Unlike dedicated acid stress response genes, csrA and its sRNA antagonists, csrB and csrC, did not exhibit a substantial response to acid shock. Furthermore, disruption of CsrA regulation of acid stress genes impacted host-microbe interactions in Caenorhabditis elegans, alleviating GABA deficiencies. This study expands the known regulon of CsrA to genes of the extreme acid stress response of E. coli and highlights a new facet of the global role played by CsrA in balancing the opposing physiological demands of stress resistance with the capacity for growth and modulating host interactions.IMPORTANCETo colonize/infect the mammalian intestinal tract, bacteria must survive exposure to the extreme acidity of the stomach. E. coli does this by expressing proteins that neutralize cytoplasmic acidity and cope with molecular damage caused by low pH. Because of the metabolic cost of these processes, genes for surviving acid stress are tightly regulated. Here, we show that CsrA negatively regulates the cascade of expression responsible for the acid stress response. Increased expression of acid response genes due to csrA disruption improved survival at extremely low pH but inhibited growth under mildly acidic conditions. Our findings define a new layer of regulation in the acid stress response of E. coli and a novel physiological function for CsrA.
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Affiliation(s)
- Mark G. Gorelik
- Department of 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
| | - Archana Pannuri
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Alyssa C. Walker
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Christine Pourciau
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Daniel Czyz
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Tony Romeo
- Department of 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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21
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Liu Y, Van Horn AM, Pham MTN, Dinh BNN, Chen R, Raphael SDR, Paulino A, Thaker K, Somadder A, Frost DJ, Menke CC, Slimak ZC, Slonczewski JL. Fitness trade-offs of multidrug efflux pumps in Escherichia coli K-12 in acid or base, and with aromatic phytochemicals. Appl Environ Microbiol 2024; 90:e0209623. [PMID: 38289137 PMCID: PMC10880634 DOI: 10.1128/aem.02096-23] [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: 11/20/2023] [Accepted: 12/14/2023] [Indexed: 02/22/2024] Open
Abstract
Multidrug efflux pumps are the frontline defense mechanisms of Gram-negative bacteria, yet little is known of their relative fitness trade-offs under gut conditions such as low pH and the presence of antimicrobial food molecules. Low pH contributes to the proton-motive force (PMF) that drives most efflux pumps. We show how the PMF-dependent pumps AcrAB-TolC, MdtEF-TolC, and EmrAB-TolC undergo selection at low pH and in the presence of membrane-permeant phytochemicals. Competition assays were performed by flow cytometry of co-cultured Escherichia coli K-12 strains possessing or lacking a given pump complex. All three pumps showed negative selection under conditions that deplete PMF (pH 5.5 with carbonyl cyanide 3-chlorophenylhydrazone or at pH 8.0). At pH 5.5, selection against AcrAB-TolC was increased by aromatic acids, alcohols, and related phytochemicals such as methyl salicylate. The degree of fitness cost for AcrA was correlated with the phytochemical's lipophilicity (logP). Methyl salicylate and salicylamide selected strongly against AcrA, without genetic induction of drug resistance regulons. MdtEF-TolC and EmrAB-TolC each had a fitness cost at pH 5.5, but salicylate or benzoate made the fitness contribution positive. Pump fitness effects were not explained by gene expression (measured by digital PCR). Between pH 5.5 and 8.0, acrA and emrA were upregulated in the log phase, whereas mdtE expression was upregulated in the transition-to-stationary phase and at pH 5.5 in the log phase. Methyl salicylate did not affect pump gene expression. Our results suggest that lipophilic non-acidic molecules select against a major efflux pump without inducing antibiotic resistance regulons.IMPORTANCEFor drugs that are administered orally, we need to understand how ingested phytochemicals modulate drug resistance in our gut microbiome. Bacteria maintain low-level resistance by proton-motive force (PMF)-driven pumps that efflux many different antibiotics and cell waste products. These pumps play a key role in bacterial defense by conferring resistance to antimicrobial agents at first exposure while providing time for a pathogen to evolve resistance to higher levels of the antibiotic exposed. Nevertheless, efflux pumps confer energetic costs due to gene expression and pump energy expense. The bacterial PMF includes the transmembrane pH difference (ΔpH), which may be depleted by permeant acids and membrane disruptors. Understanding the fitness costs of efflux pumps may enable us to develop resistance breakers, that is, molecules that work together with antibiotics to potentiate their effect. Non-acidic aromatic molecules have the advantage that they avoid the Mar-dependent induction of regulons conferring other forms of drug resistance. We show that different pumps have distinct selection criteria, and we identified non-acidic aromatic molecules as promising candidates for drug resistance breakers.
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Affiliation(s)
- Yangyang Liu
- Department of Biology, Kenyon College, Gambier, Ohio, USA
| | | | | | | | - Rachel Chen
- Department of Biology, Kenyon College, Gambier, Ohio, USA
| | | | | | - Kavya Thaker
- Department of Biology, Kenyon College, Gambier, Ohio, USA
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22
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Baquero F, Rodríguez-Beltrán J, Coque TM, del Campo R. Boosting Fitness Costs Associated with Antibiotic Resistance in the Gut: On the Way to Biorestoration of Susceptible Populations. Biomolecules 2024; 14:76. [PMID: 38254676 PMCID: PMC10812938 DOI: 10.3390/biom14010076] [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: 11/25/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
The acquisition and expression of antibiotic resistance implies changes in bacterial cell physiology, imposing fitness costs. Many human opportunistic pathogenic bacteria, such as those causing urinary tract or bloodstream infections, colonize the gut. In this opinionated review, we will examine the various types of stress that these bacteria might suffer during their intestinal stay. These stresses, and their compensatory responses, probably have a fitness cost, which might be additive to the cost of expressing antibiotic resistance. Such an effect could result in a disadvantage relative to antibiotic susceptible populations that might replace the resistant ones. The opinion proposed in this paper is that the effect of these combinations of fitness costs should be tested in antibiotic resistant bacteria with susceptible ones as controls. This testing might provide opportunities to increase the bacterial gut stress boosting physiological biomolecules or using dietary interventions. This approach to reduce the burden of antibiotic-resistant populations certainly must be answered empirically. In the end, the battle against antibiotic resistance should be won by antibiotic-susceptible organisms. Let us help them prevail.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- Network Center for Biomedical Research in Epidemiology and Public Health (CIBER-ESP), 28029 Madrid, Spain
| | - Jerónimo Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- Network Center for Biomedical Research in Infectious Diseases (CIBER-INFEC), 28034 Madrid, Spain
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- Network Center for Biomedical Research in Infectious Diseases (CIBER-INFEC), 28034 Madrid, Spain
| | - Rosa del Campo
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- Network Center for Biomedical Research in Infectious Diseases (CIBER-INFEC), 28034 Madrid, Spain
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23
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Schumacher K, Gelhausen R, Kion-Crosby W, Barquist L, Backofen R, Jung K. Ribosome profiling reveals the fine-tuned response of Escherichia coli to mild and severe acid stress. mSystems 2023; 8:e0103723. [PMID: 37909716 PMCID: PMC10746267 DOI: 10.1128/msystems.01037-23] [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: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Bacteria react very differently to survive in acidic environments, such as the human gastrointestinal tract. Escherichia coli is one of the extremely acid-resistant bacteria and has a variety of acid-defense mechanisms. Here, we provide the first genome-wide overview of the adaptations of E. coli K-12 to mild and severe acid stress at both the transcriptional and translational levels. Using ribosome profiling and RNA sequencing, we uncover novel adaptations to different degrees of acidity, including previously hidden stress-induced small proteins and novel key transcription factors for acid defense, and report mRNAs with pH-dependent differential translation efficiency. In addition, we distinguish between acid-specific adaptations and general stress response mechanisms using denoising autoencoders. This workflow represents a powerful approach that takes advantage of next-generation sequencing techniques and machine learning to systematically analyze bacterial stress responses.
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Affiliation(s)
- Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Rick Gelhausen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Willow Kion-Crosby
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Würzburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
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24
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Wu J, McAuliffe O, O'Byrne CP. A novel RofA-family transcriptional regulator, GadR, controls the development of acid resistance in Listeria monocytogenes. mBio 2023; 14:e0171623. [PMID: 37882515 PMCID: PMC10746197 DOI: 10.1128/mbio.01716-23] [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: 07/04/2023] [Accepted: 09/19/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE The ability to survive the acidic conditions found in the stomach is crucial for the food-borne pathogen Listeria monocytogenes to gain access to the mammalian gastrointestinal tract. Little is currently known about how acid resistance is regulated in this pathogen and why this trait is highly variable between strains. Here, we used comparative genomics to identify a novel RofA-family transcriptional regulator, GadR, that controls the development of acid resistance. The RofA family of regulators was previously found only in a small group of bacterial pathogens, including streptococci, where they regulate virulence properties. We show that gadR encodes the dominant regulator of acid resistance in L. monocytogenes and that its sequence variability accounts for previously observed differences between strains in this trait. Together, these findings significantly advance our understanding of how this important pathogen copes with acid stress and suggest a potential molecular target to aid its control in the food chain.
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Affiliation(s)
- Jialun Wu
- Bacterial Stress Response Group, Microbiology, Ryan Institute, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Olivia McAuliffe
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland
| | - Conor P. O'Byrne
- Bacterial Stress Response Group, Microbiology, Ryan Institute, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
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25
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Zhang M, Pi Y, Ma L, Li F, Luo J, Cai Y, Wu Y, Liu M, Dai Y, Zheng F, Yue H. Effects of ginseng on short-chain fatty acids and intestinal microbiota in rats with spleen-qi deficiency based on gas chromatography-mass spectrometry and 16s rRNA technology. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9640. [PMID: 37942687 DOI: 10.1002/rcm.9640] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/11/2023] [Accepted: 08/29/2023] [Indexed: 11/10/2023]
Abstract
RATIONALE Spleen-qi deficiency syndrome, a common weakness syndrome in traditional Chinese medicine, results from insufficient spleen-qi levels. For centuries, ginseng has been relied upon as a traditional Chinese medicine to treat spleen-qi deficiency syndrome. Until now, the mechanism feature of ginseng in treating temper deficiency through intestinal bacteria and short-chain fatty acid (SCFA) metabolites has not been fully elucidated. METHODS This study established a rat model of spleen-qi deficiency via multi-factor compound modeling that involved fatigue injury and a controlled diet. The content of SCFAs between different treatment groups was determined by gas chromatography-mass spectrometry. And the 16s rRNA sequencing technology was applied to reveal the effects of ginseng on the intestinal microecological environment of the rats. RESULTS It was found that the ginseng treatment group exhibited the most remarkable regulatory effect on propionic acid, surpassing all other administration groups. Ginseng increased the relative abundance of beneficial bacteria and decreased that of harmful bacteria at the genus level in rats with spleen-qi deficiency syndrome. And propionic acid is significantly positively correlated with Lactobacillus level and significantly negatively correlated with uncultured_bacterium_f_Muribaculaceae (p < 0.05). n-Butyric acid is negatively correlated with the Faecalibaculum level (p < 0.01). n-Valeric acid is significantly negatively correlated with the Romboutsia level (p < 0.01). CONCLUSION The mechanism of ginseng treatment for spleen-qi deficiency is elucidated from the perspective of gut microbiota and its metabolite SCFAs. It provides a new way for further development and utilization of ginseng and a theoretical basis.
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Affiliation(s)
- Meiyu Zhang
- Changchun University of Chinese Medicine, Changchun, China
| | - Yijun Pi
- Changchun University of Chinese Medicine, Changchun, China
| | - Liting Ma
- Changchun University of Chinese Medicine, Changchun, China
| | - Fangtong Li
- Changchun University of Chinese Medicine, Changchun, China
| | - Jing Luo
- Changchun University of Chinese Medicine, Changchun, China
| | - Yongyu Cai
- Changchun University of Chinese Medicine, Changchun, China
| | - Yongxi Wu
- Changchun University of Chinese Medicine, Changchun, China
| | - Ming Liu
- Changchun University of Chinese Medicine, Changchun, China
| | - Yulin Dai
- Changchun University of Chinese Medicine, Changchun, China
| | - Fei Zheng
- Changchun University of Chinese Medicine, Changchun, China
| | - Hao Yue
- Changchun University of Chinese Medicine, Changchun, China
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26
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Donkor L, Affrifah NS, Kunadu APH, Kwofie S, Yeboah S, Kuditchar B. Modelling the Survival of Acid-Adapted and Nonadapted Escherichia coli O157:H7 in Burkina: A Western African Traditional Fermented Milk Product. INTERNATIONAL JOURNAL OF FOOD SCIENCE 2023; 2023:1011319. [PMID: 38025392 PMCID: PMC10681757 DOI: 10.1155/2023/1011319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/21/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
Burkina, a traditional fermented dairy product, is consumed in most parts of West Africa, including Ghana. Studies on the microflora of Burkina have indicated the presence of Escherichia coli and other pathogenic organisms. Thus, predicting the survival of E. coli in the product will inform the best manufacturing and handling practices. This study investigated the combined effect of storage temperature and time on the survival of acid-adapted and acid-non-adapted E. coli O157:H7 in Burkina. Samples were pasteurised and inoculated with acid-adapted or acid-non-adapted E. coli O157:H7. They were stored at 5, 15, and 30°C for 0, 2, 4, 6, 8, 10, 12, 14, 18, and 48 h, and the bacteria colonies were enumerated. Growth rate (survival versus time) models were developed using MATLAB software. Observed data were fitted to the Baranyi model using the DMFit curve fitting software. The E. coli O157:H7 strain appeared inherently tolerant to acid, with storage time having the most significant effect on the response parameter, survival (log CFU/mL). A negative correlation was observed for the primary models (survival versus time), which accounted for 79-97% of the relationship (p < 0.05). Although E. coli survived, its growth was inhibited over time regardless of acid adaptation.
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Affiliation(s)
- Leticia Donkor
- Department of Food Process Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana
| | - Nicole Sharon Affrifah
- Department of Food Process Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana
| | - Angela Parry-Hanson Kunadu
- Department of Nutrition and Food Science, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 134, Legon, Accra, Ghana
| | - Samuel Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, PMB, Legon, Accra, Ghana
| | - Stephen Yeboah
- Department of Nutrition and Food Science, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 134, Legon, Accra, Ghana
| | - Bernard Kuditchar
- Department of Computer Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 1181, Legon, Accra, Ghana
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27
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Schumacher K, Brameyer S, Jung K. Bacterial acid stress response: from cellular changes to antibiotic tolerance and phenotypic heterogeneity. Curr Opin Microbiol 2023; 75:102367. [PMID: 37633223 DOI: 10.1016/j.mib.2023.102367] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/28/2023]
Abstract
Most bacteria are neutralophiles but can survive fluctuations in pH in their environment. Herein, we provide an overview of the adaptation of several human, soil, and food bacteria to acid stress, mainly based on next-generation sequencing studies, highlighting common and specific strategies. We also discuss the interplay between acid stress response and antibiotic tolerance, as well as the response of individual cells.
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Affiliation(s)
- Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany.
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28
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Wi SM, Kim SK, Lee JB, Yoon JW. Acid tolerance of enterohemorrhagic Escherichia coli O157:H7 strain ATCC 43894 and its relationship with a large virulence plasmid pO157. Vet Microbiol 2023; 284:109833. [PMID: 37515979 DOI: 10.1016/j.vetmic.2023.109833] [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: 02/08/2023] [Revised: 06/19/2023] [Accepted: 07/17/2023] [Indexed: 07/31/2023]
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a zoonotic pathogen that causes a severe intestinal infection including hemolytic uremic syndrome in humans. Various factors contribute to its pathogenesis, including a large virulence plasmid pO157. This F-like 92-kb plasmid is isolated in virtually all clinical EHEC isolates, and is considered a hallmark of EHEC virulence. A previous report stated that removal of pO157 from EHEC ATCC 43894 induced overexpression of GadAB that are essential in glutamate-dependent acid resistance (GDAR) system, yet the mechanism remains elusive. Based on this observation, we surmised that pO157 is involved in the regulation of GDAR system. We comparatively analyzed 43894 and its pO157-cured (ΔpO157) mutant 277 for i) their acid resistance, ii) changes in the transcriptional profiles and iii) expression of GDAR associated genes/proteins. Survivability of 43894 upon exposure to acidic conditions was significantly lower than the ΔpO157 mutant. In addition, RNA-sequencing revealed that genes involved in GDAR were significantly down-regulated in 43894 when compared to the ΔpO157 mutant. Exogenous expression of GadE in 43894 led to expression of GadAB, suggesting possible intervention of pO157 in GDAR regulation. Despite these findings, reintroduction of pO157 into 277 did not reverted Gad overexpression. Likewise, removing pO157 from 43894 using the plasmid incompatibility method did not induce Gad overexpression as shown in 277. Taken together, the results suggest that variation in acid resistance among EHEC isolates exists, and the large virulence plasmid pO157 has no effect on weak acid resistance phenotype displayed in 43894.
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Affiliation(s)
- Seon Mi Wi
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Se Kye Kim
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Jun Bong Lee
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Jang Won Yoon
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea.
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29
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Magesh K, Singh S, Wu SP, Velmathi S. One-step synthesis of a pH switched pyrene-based fluorescent probe for ratiometric detection of HS - in real water samples. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4159-4167. [PMID: 37577757 DOI: 10.1039/d3ay00987d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Only a few probes are suited for highly acidic environments and sensitive to pH values below 4. Thus, finding a solution for detecting strong acidic (pH value below 2) conditions is still challenging. Herein, we constructed and created a pH-switched fluorescent probe based on pyrene and a heteroatom containing pyridine unit. When exposed to acidic environments (pH 2.0), the probe's fluorescence redshifted with distinct colour and fluorescence changes owing to protonation on the nitrogen atom containing pyridine moiety, which could be deprotonated by HS- selectively compared to other competing analytes. Pyr can detect HS- with a rapid response within 5 s and showed very good quantum yield under acidic environments. The sensing mechanism was confirmed by Density Functional Theory (DFT) studies using the B3LYP and 6-31G+ (d) basis sets. Furthermore, the probe was utilized to monitor HS- in actual water samples and identify H2S gas by a simple paper strip test.
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Affiliation(s)
- Kuppan Magesh
- Organic and Polymer Synthesis Laboratory, Department of Chemistry, National Institute of Technology, Tiruchirappalli 620 015, India.
| | - Sukhvant Singh
- Organic and Polymer Synthesis Laboratory, Department of Chemistry, National Institute of Technology, Tiruchirappalli 620 015, India.
| | - Shu Pao Wu
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu 30010, Republic of China
| | - Sivan Velmathi
- Organic and Polymer Synthesis Laboratory, Department of Chemistry, National Institute of Technology, Tiruchirappalli 620 015, India.
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30
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Zeng S, Liu X, Kafuti YS, Kim H, Wang J, Peng X, Li H, Yoon J. Fluorescent dyes based on rhodamine derivatives for bioimaging and therapeutics: recent progress, challenges, and prospects. Chem Soc Rev 2023; 52:5607-5651. [PMID: 37485842 DOI: 10.1039/d2cs00799a] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Since their inception, rhodamine dyes have been extensively applied in biotechnology as fluorescent markers or for the detection of biomolecules owing to their good optical physical properties. Accordingly, they have emerged as a powerful tool for the visualization of living systems. In addition to fluorescence bioimaging, the molecular design of rhodamine derivatives with disease therapeutic functions (e.g., cancer and bacterial infection) has recently attracted increased research attention, which is significantly important for the construction of molecular libraries for diagnostic and therapeutic integration. However, reviews focusing on integrated design strategies for rhodamine dye-based diagnosis and treatment and their wide application in disease treatment are extremely rare. In this review, first, a brief history of the development of rhodamine fluorescent dyes, the transformation of rhodamine fluorescent dyes from bioimaging to disease therapy, and the concept of optics-based diagnosis and treatment integration and its significance to human development are presented. Next, a systematic review of several excellent rhodamine-based derivatives for bioimaging, as well as for disease diagnosis and treatment, is presented. Finally, the challenges in practical integration of rhodamine-based diagnostic and treatment dyes and the future outlook of clinical translation are also discussed.
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Affiliation(s)
- Shuang Zeng
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China.
- School of Bioengineering, Dalian University of Technology, 2 Linggong Road, Hi-tech Zone, Dalian 116024, China
| | - Xiaosheng Liu
- School of Bioengineering, Dalian University of Technology, 2 Linggong Road, Hi-tech Zone, Dalian 116024, China
| | - Yves S Kafuti
- School of Bioengineering, Dalian University of Technology, 2 Linggong Road, Hi-tech Zone, Dalian 116024, China
| | - Heejeong Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Korea.
| | - Jingyun Wang
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China.
- School of Bioengineering, Dalian University of Technology, 2 Linggong Road, Hi-tech Zone, Dalian 116024, China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China.
| | - Haidong Li
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China.
- School of Bioengineering, Dalian University of Technology, 2 Linggong Road, Hi-tech Zone, Dalian 116024, China
- Provincial Key Laboratory of Interdisciplinary Medical Engineering for Gastrointestinal Carcinoma, Cancer Hospital of Dalian University of Technology (Liaoning Cancer Hospital & Institute), Shenyang, Liaoning 110042, China
| | - Juyoung Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Korea.
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Herrera-Vázquez A, Arellano-Aranda R, Hernández-Cueto D, Rodríguez-Miranda E, López-Briones S, Hernández-Luna MA. Detection of Cyclomodulin CNF-1 Toxin-Producing Strains of Escherichia coli in Pig Kidneys at a Slaughterhouse. Microorganisms 2023; 11:2065. [PMID: 37630625 PMCID: PMC10458685 DOI: 10.3390/microorganisms11082065] [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: 06/29/2023] [Revised: 08/02/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Food is often contaminated with Escherichia coli (E. coli) bacteria strains, which have been associated with different diseases, including urinary tract infections. The consumption of meat by humans is a potential route of transmission of antimicrobial resistance, and food-producing animals have been associated as a major reservoir of resistant bacterial strains. The aim of this study was to determine the presence of the E. coli strains producing the CNF-1 toxin in pig kidneys. Pig kidneys were collected from a Mexican slaughterhouse and classified according to their coloration into reddish kidneys (RK) and yellowish kidneys (YK). A tissue sample from each kidney was processed for histological analysis, the presence of E. coli was determined by conventional PCR assay, and the CNF-1 toxin was detected by both conventional PCR and Western blotting. Herein, an inflammatory cell infiltrate was found in all collected kidneys, regardless of macroscopic differences. Surprisingly, E. coli and the CNF-1 toxin were detected in all kidney samples. We clearly demonstrate contamination by CNF-1 toxin-producing E. coli in pork kidneys from a slaughterhouse, even in those without apparent damage. This suggests that pork may serve as a reservoir for pathogens, representing an important risk to human health.
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Affiliation(s)
- Arturo Herrera-Vázquez
- Department of Medicine and Nutrition, Division of Health Sciences, University of Guanajuato, Campus León, Guanajuato 37670, Mexico (E.R.-M.); (S.L.-B.)
| | - Rebeca Arellano-Aranda
- Department of Veterinary, Division of Life Sciences, University of Guanajuato, Campus Irapuato Salamanca, Guanajuato 36500, Mexico
| | - Daniel Hernández-Cueto
- Unit of Investigative Research on Oncological Diseases, Children’s Hospital of Mexico Federico Gomez, Mexico City 06720, Mexico
| | - Esmeralda Rodríguez-Miranda
- Department of Medicine and Nutrition, Division of Health Sciences, University of Guanajuato, Campus León, Guanajuato 37670, Mexico (E.R.-M.); (S.L.-B.)
| | - Sergio López-Briones
- Department of Medicine and Nutrition, Division of Health Sciences, University of Guanajuato, Campus León, Guanajuato 37670, Mexico (E.R.-M.); (S.L.-B.)
| | - Marco Antonio Hernández-Luna
- Department of Medicine and Nutrition, Division of Health Sciences, University of Guanajuato, Campus León, Guanajuato 37670, Mexico (E.R.-M.); (S.L.-B.)
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Joniak J, Stankovičová H, Budzák Š, Sýkora M, Gaplovská-Kyselá K, Filo J, Cigáň M. Rigidized 3-aminocoumarins as fluorescent probes for strongly acidic environments and rapid yeast vacuolar lumen staining: mechanism and application. Phys Chem Chem Phys 2023. [PMID: 37470103 DOI: 10.1039/d3cp01090b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Coumarins remain one of the most important groups of fluorescent bio-probes, thanks to their high quantum yields, moderate photostability, efficient cell permeation and low (cyto)toxicity. Herein, we introduce new 3-aminocoumarins as turn-on pH probes under strongly acidic conditions and for indicators capable of significantly improving yeast vacuolar lumen staining compared to the commercial CMAC derivatives. We present the details of the on-off switching mechanism revealed by the TD-DFT and ab initio calculations complemented by a Franck-Condon analysis of the probes' emission profiles.
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Affiliation(s)
- Jakub Joniak
- Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University, 842 15, Bratislava, Slovakia.
| | - Henrieta Stankovičová
- Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University, 842 15, Bratislava, Slovakia.
| | - Šimon Budzák
- Department of Chemistry, Faculty of Natural Sciences, Matej Bel University, 974 01, Banská Bystrica, Slovakia
| | - Milan Sýkora
- Laboratory for Advanced Materials, Faculty of Natural Sciences, Comenius University, 842 15, Bratislava, Slovakia
| | - Katarína Gaplovská-Kyselá
- Department of Genetics, Faculty of Natural Sciences, Comenius University, 842 15, Bratislava, Slovakia
| | - Juraj Filo
- Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University, 842 15, Bratislava, Slovakia.
| | - Marek Cigáň
- Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University, 842 15, Bratislava, Slovakia.
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Dunn MF, Becerra-Rivera VA. The Biosynthesis and Functions of Polyamines in the Interaction of Plant Growth-Promoting Rhizobacteria with Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2671. [PMID: 37514285 PMCID: PMC10385936 DOI: 10.3390/plants12142671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR) are members of the plant rhizomicrobiome that enhance plant growth and stress resistance by increasing nutrient availability to the plant, producing phytohormones or other secondary metabolites, stimulating plant defense responses against abiotic stresses and pathogens, or fixing nitrogen. The use of PGPR to increase crop yield with minimal environmental impact is a sustainable and readily applicable replacement for a portion of chemical fertilizer and pesticides required for the growth of high-yielding varieties. Increased plant health and productivity have long been gained by applying PGPR as commercial inoculants to crops, although with uneven results. The establishment of plant-PGPR relationships requires the exchange of chemical signals and nutrients between the partners, and polyamines (PAs) are an important class of compounds that act as physiological effectors and signal molecules in plant-microbe interactions. In this review, we focus on the role of PAs in interactions between PGPR and plants. We describe the basic ecology of PGPR and the production and function of PAs in them and the plants with which they interact. We examine the metabolism and the roles of PAs in PGPR and plants individually and during their interaction with one another. Lastly, we describe some directions for future research.
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Affiliation(s)
- Michael F Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Víctor A Becerra-Rivera
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
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Castro VS, Ngo S, Stanford K. Influence of temperature and pH on induction of Shiga toxin Stx1a in Escherichia coli. Front Microbiol 2023; 14:1181027. [PMID: 37485504 PMCID: PMC10359099 DOI: 10.3389/fmicb.2023.1181027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Shiga toxin-producing strains represent pathogenic group that is of concern in food production. The present study evaluated forty-eight E. coli isolates (11 with intact stx gene, while remaining isolates presented only stx-fragments) for Shiga toxin production. The four most expressive stx-producers (O26, O103, O145, and O157) were selected to evaluate effects of pH (3.5, 4.5, and 7) and temperature (35, 40, and 50°C). After determining acid stress effects in media on Stx-induction, we mimicked "in natura" conditions using milk, apple, and orange juices. Only isolates that showed the presence of intact stx gene (11/48) produced Shiga toxin. In addition, acid pH had a role in down-regulating the production of Shiga toxin, in both lactic acid and juices. In contrast, non-lethal heating (40°C), when in neutral pH and milk was a favorable environment to induce Shiga toxin. Lastly, two isolates (O26 and O103) showed a higher capacity to produce Shiga toxin and were included in a genomic cluster with other E. coli involved in worldwide foodborne outbreaks. The induction of this toxin when subjected to 40°C may represent a potential risk to the consumer, since the pathogenic effect of oral ingestion of Shiga toxin has already been proved in an animal model.
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Fiorani M, Del Vecchio LE, Dargenio P, Kaitsas F, Rozera T, Porcari S, Gasbarrini A, Cammarota G, Ianiro G. Histamine-producing bacteria and their role in gastrointestinal disorders. Expert Rev Gastroenterol Hepatol 2023; 17:709-718. [PMID: 37394958 DOI: 10.1080/17474124.2023.2230865] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 06/22/2023] [Indexed: 07/04/2023]
Abstract
INTRODUCTION Gut microbiota produces thousands of metabolites, which have a huge impact on the host health. Specific microbial strains are able to synthesize histamine, a molecule with a crucial role in many physiologic and pathologic mechanisms of the host. This function is mediated by the histidine decarboxylase enzyme (HDC) that converts the amino acid histidine to histamine. AREAS COVERED This review summarizes the emerging data on histamine production by gut microbiota, and the effect of bacterial-derived histamine in different clinical contexts, including cancer, irritable bowel syndrome, and other gastrointestinal and extraintestinal pathologies. This review will also outline the impact of histamine on the immune system and the effect of probiotics that can secrete histamine. Search methodology: we searched the literature on PubMed up to February 2023. EXPERT OPINION The potential of modulating gut microbiota to influence histamine production is a promising area of research, and although our knowledge of histamine-secreting bacteria is still limited, recent advances are exploring their diagnostic and therapeutical potential. Diet, probiotics, and pharmacological treatments directed to the modulation of histamine-secreting bacteria may in the future potentially be employed in the prevention and management of several gastrointestinal and extraintestinal disorders.
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Affiliation(s)
- Marcello Fiorani
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell'Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Rome, Italy
| | - Livio Enrico Del Vecchio
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell'Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Rome, Italy
| | - Pasquale Dargenio
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Francesco Kaitsas
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Tommaso Rozera
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell'Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Rome, Italy
| | - Serena Porcari
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell'Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Rome, Italy
| | - Antonio Gasbarrini
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell'Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Rome, Italy
| | - Giovanni Cammarota
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell'Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Rome, Italy
| | - Gianluca Ianiro
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell'Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Rome, Italy
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Yang W, Sun H, Yan J, Kang C, Wu J, Yang B. Enterohemorrhagic Escherichia coli senses microbiota-derived nicotinamide to increase its virulence and colonization in the large intestine. Cell Rep 2023; 42:112638. [PMID: 37294635 DOI: 10.1016/j.celrep.2023.112638] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/05/2023] [Accepted: 05/25/2023] [Indexed: 06/11/2023] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a foodborne pathogen that specifically colonizes and infects the human large intestine. EHEC O157:H7 engages intricate regulatory pathways to detect host intestinal signals and regulate virulence-related gene expression during colonization and infection. However, the overall EHEC O157:H7 virulence regulatory network in the human large intestine remains incompletely understood. Here, we report a complete signal regulatory pathway where the EvgSA two-component system responds to high-nicotinamide levels produced by microbiota in the large intestine and directly activates loci of enterocyte effacement genes to promote EHEC O157:H7 adherence and colonization. This EvgSA-mediated nicotinamide signaling regulatory pathway is conserved and widespread among several other EHEC serotypes. Moreover, disruption of this virulence-regulating pathway by the deletion of evgS or evgA significantly decreased EHEC O157:H7 adherence and colonization in the mouse intestinal tract, indicating that these genes could be potential targets for the development of new therapeutics for EHEC O157:H7 infection.
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Affiliation(s)
- Wen Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, P.R. China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, P.R. China
| | - Hongmin Sun
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, P.R. China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, P.R. China
| | - Jun Yan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, P.R. China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, P.R. China
| | - Chenbo Kang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, P.R. China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, P.R. China
| | - Junli Wu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, P.R. China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, P.R. China
| | - Bin Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, P.R. China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, P.R. China.
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Fang X, Zhang Y, Guo Q, Yuan M, Liang X, Liu J, Fang S, Yang Y, Fang C. GadR4 mediates the acid resistance and pathogenicity of Listeria monocytogenes 10403S by negatively regulating the gadT2/gadD2 cluster. Food Microbiol 2023; 112:104248. [PMID: 36906312 DOI: 10.1016/j.fm.2023.104248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/29/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023]
Abstract
Listeria monocytogenes is an important foodborne pathogen that can survive under acidic conditions. The glutamate decarboxylase (GAD) system is one of the acid resistance systems of L. monocytogenes. It usually comprises two glutamate transporters (GadT1/T2) and three glutamate decarboxylases (GadD1/D2/D3). Among them, gadT2/gadD2 contributes most significantly to the acid resistance of L. monocytogenes. However, the regulation mechanisms of gadT2/gadD2 still remain unclear. The results of this study indicated that gadT2/gadD2 deletion significantly decreases the survival rate of L. monocytogenes under different acidic conditions, including brain and heart infusion (BHI) broth, with a pH of 2.5, 2% citric acid, 2% acetic acid and 2% lactic acid. Further, gadT2/gadD2 cluster was expressed in the representative strains in response to alkaline stress rather than acid stress. To explore the regulation of gadT2/gadD2, we knocked out the five transcriptional factors belonging to the Rgg family in L. monocytogenes 10403S. We found that the deletion of gadR4, which exhibits the highest homology with the gadR of Lactococcus lactis, resulted in a significant increase in the survival rate of L. monocytogenes upon acid stress. Western blot analysis showed that gadR4 deletion significantly increased the gadD2 expression of L. monocytogenes under alkaline and neutral conditions. Furthermore, the gfp reporter gene showed that gadR4 deletion significantly increased the expression of the gadT2/gadD2 cluster. Adhesion and invasion assays indicated that gadR4 deletion significantly increased the rates of adhesion and invasion of L. monocytogenes to epithelial Caco-2 cells. Virulence assays showed that gadR4 knockout significantly improved the colonization ability of L. monocytogenes in the livers and spleens of the infected mice. Taken together, our results showed that GadR4, a transcription factor belonging to the Rgg family, negatively regulates the gadT2/gadD2 cluster, thus, reducing the acid stress tolerance and pathogenicity of L. monocytogens 10403S. Our results provide a better understanding of the regulation of the GAD system of L. monocytogenes and a novel approach to potentially prevent and control listeriosis.
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Affiliation(s)
- Xiaowei Fang
- College of Animal Science, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China; College of Agriculture, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China
| | - Yu Zhang
- College of Animal Science, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China
| | - Qian Guo
- College of Animal Science, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China
| | - Mei Yuan
- College of Animal Science, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China
| | - Xiongyan Liang
- College of Animal Science, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China
| | - Jing Liu
- College of Animal Science, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China
| | - Shouguo Fang
- College of Agriculture, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China
| | - Yuying Yang
- College of Animal Science, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, China
| | - Chun Fang
- College of Animal Science, Yangtze University, No.88, Jingmi Road, Jingzhou, 434025, 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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Niu H, Li T, Du Y, Lv Z, Cao Q, Zhang Y. Glutamate Transporters GltS, GltP and GltI Are Involved in Escherichia coli Tolerance In Vitro and Pathogenicity in Mouse Urinary Tract Infections. Microorganisms 2023; 11:1173. [PMID: 37317147 DOI: 10.3390/microorganisms11051173] [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: 02/08/2023] [Revised: 04/02/2023] [Accepted: 04/09/2023] [Indexed: 06/16/2023] Open
Abstract
To verify the roles of GltS, GltP, and GltI in E. coli tolerance and pathogenicity, we quantified and compared the relative abundance of gltS, gltP, and gltI in log-phase and stationary-phase E. coli and constructed their knockout mutant strains in E. coli BW25113 and uropathogenic E. coli (UPEC) separately, followed by analysis of their abilities to tolerate antibiotics and stressors, their capacity for adhesion to and invasion of human bladder epithelial cells, and their survival ability in mouse urinary tracts. Our results showed that gltS, gltP, and gltI transcripts were higher in stationary phase E. coli than in log-phase incubation. Furthermore, deletion of gltS, gltP, and gltI genes in E. coli BW25113 results in decreased tolerance to antibiotics (levofloxacin and ofloxacin) and stressors (acid pH, hyperosmosis, and heat), and loss of gltS, gltP, and gltI in uropathogenic E. coli UTI89 caused attenuated adhesion and invasion in human bladder epithelial cells and markedly reduced survival in mice. The results showed the important roles of the glutamate transporter genes gltI, gltP, and gltS in E. coli tolerance to antibiotics (levofloxacin and ofloxacin) and stressors (acid pH, hyperosmosis, and heat) in vitro and in pathogenicity in mouse urinary tracts and human bladder epithelial cells, as shown by reduced survival and colonization, which improves our understanding of the molecular mechanisms of bacterial tolerance and pathogenicity.
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Affiliation(s)
- Hongxia Niu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Tuodi Li
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yunjie Du
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Zhuoxuan Lv
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Qianqian Cao
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Ying Zhang
- The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310053, China
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Oguadinma I, Mishra A, Dev Kumar G. Antibiotic resistance associated lactic acid cross tolerance in Shiga-toxin producing E. coli. Front Microbiol 2023; 14:1059144. [PMID: 37180239 PMCID: PMC10169816 DOI: 10.3389/fmicb.2023.1059144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/21/2023] [Indexed: 05/16/2023] Open
Abstract
Introduction The occurrence of antibiotic resistant (ABR) bacteria in foods is a growing public health challenge. We evaluated sanitizer cross-tolerance among ABR Escherichia coli (E. coli) O157:H7 and non-O157:H7 Shiga-toxin producing E. coli (STEC) serogroups. Sanitizer tolerance in STEC could be a public health concern as mitigation strategies against the pathogen might be compromised. Methods Resistance to ampicillin and streptomycin were evolved in E. coli serogroups: O157:H7 (H1730, and ATCC 43895), O121:H19 and O26:H11. Resistance to antibiotics was evolved chromosomally through incremental exposure to ampicillin (amp C) and streptomycin (strep C). Transformation using a plasmid was performed to confer resistance to ampicillin to generate amp P strep C. Results The minimum inhibitory concentration (MIC) of lactic acid for all strains evaluated was 0.375% v/v. Analysis of bacterial growth parameters in tryptic soy broth amended with 0.0625% v/v, 0.125% v/v, and 0.25% v/v (subMIC) lactic acid indicated that growth correlated positively with the lag phase duration, and negatively with both the maximum growth rate and change in population density for all strains evaluated except for the highly tolerant variant- O157:H7 amp P strep C. Strains O121 NR (non-ABR), O121 amp C, O121 amp P strep C, O157:H7 H1730 amp C and O157:H7 H1730 amp P strep C were not inactivated after exposure to 1% and 2.5% v/v lactic acid for 300 s. No recovery of cells was observed after the strains were exposed to 5% v/v lactic acid for 300 s. ABR strains O157:H7 H1730 amp C and O157: H7 H1730 amp P strep C demonstrated a high tolerance to lactic acid (P ≤ 0.05). Conclusion ABR in isolate E. coli O157: H7 H1730 may improve tolerance to lactic acid. Increased tolerance may be discerned by evaluating growth parameters of bacteria in presence of sub-MIC levels of lactic acid.
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Affiliation(s)
- Ikechukwu Oguadinma
- Center for Food Safety, The University of Georgia, Griffin, GA, United States
| | - Abhinav Mishra
- Department of Food Science & Technology, The University of Georgia, Athens, GA, United States
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Mallick S, Das S. Acid-tolerant bacteria and prospects in industrial and environmental applications. Appl Microbiol Biotechnol 2023; 107:3355-3374. [PMID: 37093306 DOI: 10.1007/s00253-023-12529-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/06/2023] [Accepted: 04/11/2023] [Indexed: 04/25/2023]
Abstract
Acid-tolerant bacteria such as Streptococcus mutans, Acidobacterium capsulatum, Escherichia coli, and Propionibacterium acidipropionici have developed several survival mechanisms to sustain themselves in various acid stress conditions. Some bacteria survive by minor changes in the environmental pH. In contrast, few others adapt different acid tolerance mechanisms, including amino acid decarboxylase acid resistance systems, mainly glutamate-dependent acid resistance (GDAR) and arginine-dependent acid resistance (ADAR) systems. The cellular mechanisms of acid tolerance include cell membrane alteration in Acidithiobacillus thioxidans, proton elimination by F1-F0-ATPase in Streptococcus pyogenes, biofilm formation in Pseudomonas aeruginosa, cytoplasmic urease activity in Streptococcus mutans, synthesis of the protective cloud of ammonia, and protection or repair of macromolecules in Bacillus caldontenax. Apart from cellular mechanisms, there are several acid-tolerant genes such as gadA, gadB, adiA, adiC, cadA, cadB, cadC, speF, and potE that help the bacteria to tolerate the acidic environment. This acid tolerance behavior provides new and broad prospects for different industrial applications and the bioremediation of environmental pollutants. The development of engineered strains with acid-tolerant genes may improve the efficiency of the transgenic bacteria in the treatment of acidic industrial effluents. KEY POINTS: • Bacteria tolerate the acidic stress by methylating unsaturated phospholipid tail • The activity of decarboxylase systems for acid tolerance depends on pH • Genetic manipulation of acid-tolerant genes improves acid tolerance by the bacteria.
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Affiliation(s)
- Souradip Mallick
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India.
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Wang Y, Lang Y, Yang Q, Wu P. Breaking the Photostability and pH Limitation of Halo-Fluoresceins through Chitosan Conjugation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2210956. [PMID: 36738115 DOI: 10.1002/adma.202210956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Halo-fluoresceins are widely used in cell and tissue staining, intracellular sensing, and photodynamic therapy, but their notorious photo-instability and pH dependence restrict their applications, especially in long-term visible light exposure and acidic environments. To overcome these limitations, here a strategy is proposed of conjugating chitosan with the carboxyl group of halo-fluorescein (CS-halofluorescein). The cross-linked polymer chains and the hydrogen-bonding networks of chitosan help shielding out 1 O2 from direct attacking the encapsulated halo-fluoresceins, leading to a two orders of magnitude lower photobleaching rate. Meanwhile, the condensation of primary amines of chitosan with the carboxyl group on halo-fluorescein blocks the pH-dependent intramolecular spirocyclization, leading to pH-inert fluorescein derivatives. The greatly improved photostability and pH inertness of CS-halofluoresceins can be harvested for aerobic photoredox synthesis and photodynamic bacteria inactivation in extremely acidic media. Moreover, food additive nature of chitosan and erythrosine (TIF) and excellent film-forming property of chitosan allow coating-based light-assisted preservation of perishable fruits, leading to appreciably extended shelf life of fruits (e.g., perishable strawberry, rt: > 3 days; 4 °C: > 5 days).
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Affiliation(s)
- Ying Wang
- Analytical and Testing Centre, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
| | - Yunhe Lang
- Analytical and Testing Centre, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
| | - Qin Yang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610064, China
| | - Peng Wu
- Analytical and Testing Centre, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
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Derdouri N, Ginet N, Denis Y, Ansaldi M, Battesti A. The prophage-encoded transcriptional regulator AppY has pleiotropic effects on E. coli physiology. PLoS Genet 2023; 19:e1010672. [PMID: 36930675 PMCID: PMC10057817 DOI: 10.1371/journal.pgen.1010672] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/29/2023] [Accepted: 02/18/2023] [Indexed: 03/18/2023] Open
Abstract
Bacterial genome diversity is influenced by prophages, which are viral genomes integrated into the bacterial chromosome. Most prophage genes are silent but those that are expressed can provide unexpected properties to their host. Using as a model E. coli K-12 that carries 9 defective prophages in its genome, we aimed at highlighting the impact of genes encoded by prophages on host physiology. We focused our work on AppY, a transcriptional regulator encoded on the DLP12 prophage. By performing RNA-Seq experiments, we showed that AppY production modulates the expression of more than 200 genes. Among them, 11 were identified by ChIP-Seq as direct AppY targets. AppY directly and positively regulates several genes involved in the acid stress response including the master regulator gene gadE but also nhaR and gadY, two genes important for biofilm formation. Moreover, AppY indirectly and negatively impacts bacterial motility by favoring the degradation of FlhDC, the master regulator of the flagella biosynthesis. As a consequence of these regulatory effects, AppY increases acid stress resistance and biofilm formation while also causing a strong defect in motility. Our research shed light on the importance to consider the genetic interactions occurring between prophages and bacteria to fully understand bacterial physiology. It also highlights how a prophage-encoded transcriptional regulator integrates in a complex manner into the host regulatory network and how it benefits its host, allowing it to cope with changing environmental conditions.
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Affiliation(s)
- Naoual Derdouri
- Aix Marseille Université, Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Nicolas Ginet
- Aix Marseille Université, Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Yann Denis
- Aix Marseille Université, Centre National de la Recherche Scientifique, Plateforme Transcriptome, Institut de Microbiologie de la Méditerranée-, Marseille, France
| | - Mireille Ansaldi
- Aix Marseille Université, Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Aurélia Battesti
- Aix Marseille Université, Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
- * E-mail:
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The Colorectal Cancer Microbiota Alter Their Transcriptome To Adapt to the Acidity, Reactive Oxygen Species, and Metabolite Availability of Gut Microenvironments. mSphere 2023; 8:e0062722. [PMID: 36847536 PMCID: PMC10117117 DOI: 10.1128/msphere.00627-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
The gut microbiome is implicated in the pathology of colorectal cancer (CRC). However, the mechanisms by which the microbiota actively contribute to disease onset and progression remain elusive. In this pilot study, we sequenced fecal metatranscriptomes of 10 non-CRC and 10 CRC patient gut microbiomes and conducted differential gene expression analyses to assess any changed functionality in disease. We report that oxidative stress responses were the dominant activity across cohorts, an overlooked protective housekeeping role of the human gut microbiome. However, expression of hydrogen peroxide and nitric oxide-scavenging genes was diminished and augmented, respectively, positing that these regulated microbial responses have implications for CRC pathology. CRC microbes enhanced expression of genes for host colonization, biofilm formation, genetic exchange, virulence determinants, antibiotic, and acid resistances. Moreover, microbes promoted transcription of genes involved in metabolism of several beneficial metabolites, suggesting their contribution to patient metabolite deficiencies previously solely attributed to tumor cells. We showed in vitro that expression of genes involved in amino acid-dependent acid resistance mechanisms of meta-gut Escherichia coli responded differently to acid, salt, and oxidative pressures under aerobic conditions. These responses were mostly dictated by the host health status of origin of the microbiota, suggesting their exposure to fundamentally different gut conditions. These findings for the first time highlight mechanisms by which the gut microbiota can either protect against or drive colorectal cancer and provide insights into the cancerous gut environment that drives functional characteristics of the microbiome. IMPORTANCE The human gut microbiota has the genetic potential to drive colorectal cancer onset and progression; however, the expression of this genetic potential during the disease has not been investigated. We found that microbial expression of genes that detoxify DNA-damaging reactive oxygen species, which drive colorectal cancer, is compromised in cancer. We observed a greater activation of expression of genes involved in virulence, host colonization, exchange of genetic material, metabolite utilization, defense against antibiotics, and environmental pressures. Culturing gut Escherichia coli of cancerous and noncancerous metamicrobiota revealed different regulatory responses of amino acid-dependent acid resistance mechanisms in a health-dependent manner under environmental acid, oxidative, and osmotic pressures. Here, for the first time, we demonstrate that the activity of microbial genomes is regulated by the health status of the gut in vivo and in vitro and provides new insights for shifts in microbial gene expression in colorectal cancer.
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Xiang X, Wang H, Man B, Xu Y, Gong L, Tian W, Yang H. Diverse Bathyarchaeotal Lineages Dominate Archaeal Communities in the Acidic Dajiuhu Peatland, Central China. MICROBIAL ECOLOGY 2023; 85:557-571. [PMID: 35332366 DOI: 10.1007/s00248-022-01990-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
Bathyarchaeota are believed to have roles in the carbon cycle in marine systems. However, the ecological knowledge of Bathyarchaeota is limited in peatland ecosystems. Here, we investigated the vertical distribution of Bathyarchaeota community structure using quantitative PCR and high-throughput sequencing technology of ribosomal 16S rRNA gene integrated with detailed chemical profiling in the Dajiuhu Peatland, central China. Eight archaeal phyla were observed in peat samples, which mainly composed of Bathyarchaeota with a mean relative abundance about 88%, followed by Thaumarchaeota (9%). Bathyarchaeota were further split into 17 subgroups, and some subgroups showed habitat specificity to peat horizons with distinct lithological and physicochemical properties, for example, Bathy-6 and Bathy-15 had preference for the acrotelm, Bathy-5b, Bathy-16, and Bathy-19 were enriched in the catotelm, Bathy-5a, Bathy-8, and Bathy-11 were specific for the clay horizon. This spatial distribution pattern of archaeal communities along peat profile was mainly influenced by water content as indicated by RDA ordination and permutational MANOVA, whereas organic matter content exclusively affected Bathyarchaeota distribution along the peat profile significantly. The abundance of archaeal 16S rRNA genes ranged from 105 to 107 copies per gram dry sediment, and the highest archaeal biomass was observed in the periodically oxic mesotelm horizon with more dynamic archaeal interaction relationship as indicated by the network analysis. Bathyarchaeota dominated the archaeal interaction network with 82% nodes, 96% edges, and 71% keystone species. Our results provide an overview of the archaeal population, community structure, and relationship with environmental factors that affect the vertical distribution of archaeal communities and emphasize the ecology of bathyarchaeotal lineages in terrestrial peatland ecosystems.
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Affiliation(s)
- Xing Xiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
- College of Life Science, Shangrao Normal University, Shangrao, 334001, China
- Hubei Key Laboratory of Critical Zone Evolution, China University of Geosciences, Wuhan, 430074, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China.
| | - Baiying Man
- College of Life Science, Shangrao Normal University, Shangrao, 334001, China
| | - Ying Xu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Linfeng Gong
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, SOA, Xiamen, 361005, China
| | - Wen Tian
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Huan Yang
- Hubei Key Laboratory of Critical Zone Evolution, China University of Geosciences, Wuhan, 430074, China
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Bondegaard PW, Torp AM, Guerra P, Kristensen KA, Christfort JF, Krogfelt KA, Nielsen LH, Zor K, Boisen A, Mortensen MS, Bahl MI, Licht TR. Delivery of E. coli Nissle to the mouse gut by mucoadhesive microcontainers does not improve its competitive ability against strains linked to ulcerative colitis. FEMS Microbiol Lett 2023; 370:fnad110. [PMID: 37863838 PMCID: PMC10612143 DOI: 10.1093/femsle/fnad110] [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: 07/18/2023] [Revised: 10/02/2023] [Accepted: 10/19/2023] [Indexed: 10/22/2023] Open
Abstract
For patients with ulcerative colitis (UC), administration of the probiotic E. coli Nissle (EcN) holds promise for alleviation of disease symptoms. The mechanisms are unclear, but it has been hypothesised that a capacity of the probiotic to outcompete potentially detrimental UC-associated E. coli strains plays an important role. However, this could previously not be confirmed in a mouse model of competition between EcN and two UC-associated strains, as reported by Petersen et al. 2011. In the present study, we re-evaluated the idea, hypothesising that delivery of EcN by a micro device dosing system (microcontainers), designed for delivery into the intestinal mucus, could support colonisation and confer a competition advantage compared to classical oral dosing. Six groups of mice were pre-colonised with one of two UC-associated E. coli strains followed by oral delivery of EcN, either in capsules containing microcontainers with freeze-dried EcN powder, capsules containing freeze-dried EcN powder, or as a fresh sucrose suspension. Co-colonisation between the probiotic and the disease-associated strains was observed regardless of dosing method, and no competition advantages linked to microcontainer delivery were identified within this setup. Other approaches are thus needed if the competitive capacity of EcN in the gut should be improved.
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Affiliation(s)
- Pi Westi Bondegaard
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Anders Meyer Torp
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Priscila Guerra
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Katja Ann Kristensen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Karen Angeliki Krogfelt
- Department of Science and Environment, Molecular and Medical Biology, Roskilde University, Roskilde, 4000, Denmark
| | - Line Hagner Nielsen
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Kinga Zor
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Anja Boisen
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
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Porbahaie M, van den Belt M, Ulfman L, Ruijschop RMAJ, Lucas–van de Bos E, Hartog A, Lenz S, van Alen-Boerrigter IJ, Teodorowicz M, Savelkoul HFJ, Calame W, van Hoffen E, van Neerven RJJ, Kardinaal A. Low doses of diarrhoeagenic E. coli induce enhanced monocyte and mDC responses and prevent development of symptoms after homologous rechallenge. PLoS One 2023; 18:e0279626. [PMID: 36607972 PMCID: PMC9821474 DOI: 10.1371/journal.pone.0279626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 12/08/2022] [Indexed: 01/07/2023] Open
Abstract
The experimental challenge with attenuated enterotoxigenic E. coli strain E1392/75-2A prevents diarrhea upon a secondary challenge with the same bacteria. A dose-response pilot study was performed to investigate which immunological factors are associated with this protection. Healthy subjects were inoculated with increasing E. coli doses of 1E6-1E10 CFU, and three weeks later, all participants were rechallenged with the highest dose (1E10 CFU). Gastrointestinal discomfort symptoms were recorded, and stool and blood samples were analyzed. After the primary challenge, stool frequency, diarrhea symptom scores, and E. coli-specific serum IgG (IgG-CFA/II) titer increased in a dose-dependent manner. Fecal calprotectin and serum IgG-CFA/II response after primary challenge were delayed in the lower dose groups. Even though stool frequency after the secondary challenge was inversely related to the primary inoculation dose, all E. coli doses protected against clinical symptoms upon rechallenge. Ex vivo stimulation of PBMCs with E. coli just before the second challenge resulted in increased numbers of IL-6+/TNF-α+ monocytes and mDCs than before the primary challenge, without dose-dependency. These data demonstrate that primary E. coli infection with as few as 1E6 CFU protects against a high-dose secondary challenge with a homologous attenuated strain. Increased serum IgG-CFA/II levels and E. coli-induced mDC and monocyte responses after primary challenge suggest that protection against secondary E. coli challenges is associated with adaptive as well as innate immune responses.
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Affiliation(s)
- Mojtaba Porbahaie
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, The Netherlands
- * E-mail: (MP); (RJJN)
| | | | | | | | | | | | | | | | - Malgorzata Teodorowicz
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Huub F. J. Savelkoul
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, The Netherlands
| | | | | | - R. J. Joost van Neerven
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, The Netherlands
- FrieslandCampina, Amersfoort, The Netherlands
- * E-mail: (MP); (RJJN)
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Cao X, van Putten JPM, Wösten MMSM. Biological functions of bacterial lysophospholipids. Adv Microb Physiol 2023; 82:129-154. [PMID: 36948653 DOI: 10.1016/bs.ampbs.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Lysophospholipids (LPLs) are lipid-derived metabolic intermediates in the cell membrane. The biological functions of LPLs are distinct from their corresponding phospholipids. In eukaryotic cells LPLs are important bioactive signaling molecules that regulate many important biological processes, but in bacteria the function of LPLs is still not fully defined. Bacterial LPLs are usually present in cells in very small amounts, but can strongly increase under certain environmental conditions. In addition to their basic function as precursors in membrane lipid metabolism, the formation of distinct LPLs contributes to the proliferation of bacteria under harsh circumstances or may act as signaling molecules in bacterial pathogenesis. This review provides an overview of the current knowledge of the biological functions of bacterial LPLs including lysoPE, lysoPA, lysoPC, lysoPG, lysoPS and lysoPI in bacterial adaptation, survival, and host-microbe interactions.
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Affiliation(s)
- Xuefeng Cao
- Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Jos P M van Putten
- Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Marc M S M Wösten
- Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands.
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Zhou Y, Lewis JH, Lu Z. Tracking multiple conformations occurring on angstrom-and-millisecond scales in single amino-acid-transporter molecules. eLife 2023; 12:82175. [PMID: 36800214 PMCID: PMC9937647 DOI: 10.7554/elife.82175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/15/2023] [Indexed: 02/18/2023] Open
Abstract
Most membrane protein molecules undergo conformational changes as they transition from one functional state to another one. An understanding of the mechanism underlying these changes requires the ability to resolve individual conformational states, whose changes often occur on millisecond and angstrom scales. Tracking such changes and acquiring a sufficiently large amount of data remain challenging. Here, we use the amino-acid transporter AdiC as an example to demonstrate the application of a high-resolution fluorescence-polarization-microscopy method in tracking multistate conformational changes of a membrane protein. We have successfully resolved four conformations of AdiC by monitoring the emission-polarization changes of a fluorophore label and quantified their probabilities in the presence of a series of concentrations of its substrate arginine. The acquired data are sufficient for determining all equilibrium constants that fully establish the energetic relations among the four states. The KD values determined for arginine in four individual conformations are statistically comparable to the previously reported overall KD determined using isothermal titration calorimetry. This demonstrated strong resolving power of the present polarization-microscopy method will enable an acquisition of the quantitative information required for understanding the expected complex conformational mechanism underlying the transporter's function, as well as those of other membrane proteins.
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Affiliation(s)
- Yufeng Zhou
- Department of Physiology, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - John H Lewis
- Department of Physiology, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Zhe Lu
- Department of Physiology, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
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50
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Van Riet S, Tadesse W, Mortier J, Schlegel S, Simoens K, Bernaerts K, Dal Co A, Aertsen A. Heterogeneity and Evolutionary Tunability of Escherichia coli Resistance against Extreme Acid Stress. Microbiol Spectr 2022; 10:e0375722. [PMID: 36453903 PMCID: PMC9769608 DOI: 10.1128/spectrum.03757-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/27/2022] [Indexed: 12/05/2022] Open
Abstract
Since acidic environments often serve as an important line of defense against bacterial pathogens, it is important to fully understand how the latter manage to mount and evolve acid resistance mechanisms. Escherichia coli, a species harboring many pathovars, is typically equipped with the acid fitness island (AFI), a genomic region encoding the GadE master regulator together with several GadE-controlled functions to counter acid stress. This study reveals that gadE and consequently AFI functions are heterogeneously expressed even in the absence of any prior acid stress, thereby preemptively creating acid-resistant subpopulations within a clonal E. coli population. Directed evolution efforts selecting for modulated gadE expression confirm that a gain-of-function mutation in the EvgS sensor kinase can constitutively upregulate gadE expression and concomitant acid resistance. However, we reveal that such upregulation of EvgS also causes cross-resistance to heat stress because of SafA-mediated cross-activation of the PhoPQ regulon. Surprisingly, loss of function of the serC gene (encoding phosphoserine/phosphohydroxythreonine aminotransferase) can also significantly upregulate gadE expression, acid resistance, and heat cross-resistance, although via a currently cryptic mechanism. As such, our data reveal a noisy expression of gadE in E. coli that is functional for the survival of sudden acid stress and that can readily be genetically tuned. IMPORTANCE Acidic environments constitute one of the most important stresses for enteric bacteria and can be encountered in both natural (e.g., host gastrointestinal tract) and manmade (e.g., food processing) environments. The enteric species Escherichia coli harbors many pathovars and is well known for its ability to cope with acid stress. In this study, we uncover that E. coli's acid fitness island (AFI), a genomic region that encodes important functions to deal with acid stress, is by default expressed in a heterogeneous manner. In fact, using microfluidics-based single-cell approaches, we further demonstrate that this heterogeneity preemptively creates a clonal subpopulation that is much better equipped to survive a sudden acid shock. In addition, we reveal that environments with recurring acid stress can readily select for mutants displaying a higher fraction of AFI-expressing cells. These new insights are important to properly understand and anticipate the survival characteristics of E. coli.
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Affiliation(s)
- Stefanie Van Riet
- Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
| | - Wubishet Tadesse
- Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
| | - Julien Mortier
- Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
| | - Susan Schlegel
- Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Kenneth Simoens
- Department of Chemical Engineering, KU Leuven, Leuven, Belgium
| | | | - Alma Dal Co
- Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Abram Aertsen
- Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
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