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Pepelnjak M, Velten B, Näpflin N, von Rosen T, Palmiero UC, Ko JH, Maynard HD, Arosio P, Weber-Ban E, de Souza N, Huber W, Picotti P. In situ analysis of osmolyte mechanisms of proteome thermal stabilization. Nat Chem Biol 2024; 20:1053-1065. [PMID: 38424171 PMCID: PMC11288892 DOI: 10.1038/s41589-024-01568-7] [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: 08/19/2022] [Accepted: 02/03/2024] [Indexed: 03/02/2024]
Abstract
Organisms use organic molecules called osmolytes to adapt to environmental conditions. In vitro studies indicate that osmolytes thermally stabilize proteins, but mechanisms are controversial, and systematic studies within the cellular milieu are lacking. We analyzed Escherichia coli and human protein thermal stabilization by osmolytes in situ and across the proteome. Using structural proteomics, we probed osmolyte effects on protein thermal stability, structure and aggregation, revealing common mechanisms but also osmolyte- and protein-specific effects. All tested osmolytes (trimethylamine N-oxide, betaine, glycerol, proline, trehalose and glucose) stabilized many proteins, predominantly via a preferential exclusion mechanism, and caused an upward shift in temperatures at which most proteins aggregated. Thermal profiling of the human proteome provided evidence for intrinsic disorder in situ but also identified potential structure in predicted disordered regions. Our analysis provides mechanistic insight into osmolyte function within a complex biological matrix and sheds light on the in situ prevalence of intrinsically disordered regions.
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Affiliation(s)
- Monika Pepelnjak
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Britta Velten
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Centre for Organismal Studies (COS) & Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Nicolas Näpflin
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Tatjana von Rosen
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute of Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Jeong Hoon Ko
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Heather D Maynard
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute of Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Eilika Weber-Ban
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Natalie de Souza
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Paola Picotti
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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Kairamkonda M, Saxena H, Gulati K, Poluri KM. Analyzing the impact of T7L variants overexpression on the metabolic profile of Escherichia coli. Metabolomics 2024; 20:68. [PMID: 38941046 DOI: 10.1007/s11306-024-02133-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/16/2024] [Indexed: 06/29/2024]
Abstract
INTRODUCTION Exploring metabolic changes within host E. coli through an untargeted metabolomic study of T7L variants overexpression to optimize engineered endolysins for clinical/therapeutic use. AIM AND OBJECTIVE This study aims to assess the impact of overexpressing T7L variants on the metabolic profiles of E. coli. The two variants considered include T7L-H37A, which has enhanced lytic activity compared to its wild-type protein, and T7L-H48K, a dead mutant with no significant activity. METHODS 1H NMR-based metabolomics was employed to compare the metabolic profiles of E. coli cells overexpressing T7L wild-type protein and its variants. RESULTS Overexpression of the T7L wild-type (T7L-WT) protein and its variants (T7L-H48K and T7L-H37A) was compared to RNAP overexpression in E. coli cells using 1H NMR-based metabolomics, analyzing a total of 75 annotated metabolites, including organic acids, amino acids, sugars, and nucleic acids. The results showed distinct clustering patterns for the two T7L variant groups compared with the WT, in which the dead mutant (H48K) group showed clustering close to that of RNAP. Pathway impact analysis revealed different effects of T7L variants on E. coli metabolic profiles, with T7L-H48K showing minimal alterations in energy and amino acid pathways linked to osmotic stress compared to noticeable alterations in these pathways for both T7L-H37A and T7L-WT. CONCLUSIONS This study uncovered distinct metabolic fingerprints when comparing the overexpression of active and inactive mutants of T7L lytic enzymes in E. coli cells. These findings could contribute to the optimization and enhancement of suitable endolysins as potential alternatives to antibiotics.
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Affiliation(s)
- Manikyaprabhu Kairamkonda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Harshi Saxena
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Khushboo Gulati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
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Bai Y, Zhou Y, Chang R, Hu X, Zhou Y, Chen J, Zhang Z, Yao J. Transcription profiles and phenotype reveal global response of Staphylococcus aureus exposed to ultrasound and ultraviolet stressors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169146. [PMID: 38061661 DOI: 10.1016/j.scitotenv.2023.169146] [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: 08/24/2023] [Revised: 11/05/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
Ultrasound and ultraviolet light have good inactivation performance against pathogens in sewage. In this study, the inactivation mechanisms of 60 kHz ultrasound and ultraviolet radiation against Staphylococcus aureus (S. aureus) were studied from the perspectives of cell phenotype and transcriptome for the first time. The results showed that both ultrasound and ultraviolet treatments had adverse impacts on the cellular morphology of S. aureus to varying degrees at cellular level. The transcriptomic analysis revealed that there were 225 and 1077 differentially expressed genes (DEGs) in the ultrasound and ultraviolet treatments, respectively. The result revealed that both ultrasound and ultraviolet could interfere with the expression of the genes involved in ABC transporters, amino acid and fatty acid metabolism to influence the membrane permeability. Besides the membrane permeability, ultraviolet also could disturb the ATP synthesis, DNA replication and cell division through restraining the expression of several genes related to carbohydrate metabolism, peptidoglycan synthesis, DNA-binding/repair protein synthesis. Compared with the single inactivation pathway of ultrasound, ultraviolet inactivation of S. aureus is multi-target and multi-pathway. We believe that the bactericidal mechanisms of ultrasound and ultraviolet radiation presented by this study could provide theoretical guidance for the synergistic inactivation of pathogens in sewage by ultrasound and ultraviolet radiation in the future.
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Affiliation(s)
- Yun Bai
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Yuanhang Zhou
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Ruiting Chang
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Xueli Hu
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Yingying Zhou
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Jiabo Chen
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Zhi Zhang
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China.
| | - Juanjuan Yao
- Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China.
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Qiu X, Hu XM, Tang XX, Huang CH, Jian HH, Lin DH. Metabolic adaptations of Microbacterium sediminis YLB-01 in deep-sea high-pressure environments. Appl Microbiol Biotechnol 2024; 108:170. [PMID: 38265689 DOI: 10.1007/s00253-023-12906-5] [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: 07/10/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 01/25/2024]
Abstract
The deep-sea environment is an extremely difficult habitat for microorganisms to survive in due to its intense hydrostatic pressure. However, the mechanisms by which these organisms adapt to such extreme conditions remain poorly understood. In this study, we investigated the metabolic adaptations of Microbacterium sediminis YLB-01, a cold and stress-tolerant microorganism isolated from deep-sea sediments, in response to high-pressure conditions. YLB-01 cells were cultured at normal atmospheric pressure and 28 ℃ until they reached the stationary growth phase. Subsequently, the cells were exposed to either normal pressure or high pressure (30 MPa) at 4 ℃ for 7 days. Using NMR-based metabolomic and proteomic analyses of YLB-01 cells exposed to high-pressure conditions, we observed significant metabolic changes in several metabolic pathways, including amino acid, carbohydrate, and lipid metabolism. In particular, the high-pressure treatment stimulates cell division and triggers the accumulation of UDP-glucose, a critical factor in cell wall formation. This finding highlights the adaptive strategies used by YLB-01 cells to survive in the challenging high-pressure environments of the deep sea. Specifically, we discovered that YLB-01 cells regulate amino acid metabolism, promote carbohydrate metabolism, enhance cell wall synthesis, and improve cell membrane fluidity in response to high pressure. These adaptive mechanisms play essential roles in supporting the survival and growth of YLB-01 in high-pressure conditions. Our study offers valuable insights into the molecular mechanisms underlying the metabolic adaptation of deep-sea microorganisms to high-pressure environments. KEY POINTS: • NMR-based metabolomic and proteomic analyses were conducted on Microbacterium sediminis YLB-01 to investigate the significant alterations in several metabolic pathways in response to high-pressure treatment. • YLB-01 cells used adaptive strategies (such as regulated amino acid metabolism, promoted carbohydrate metabolism, enhanced cell wall synthesis, and improved cell membrane fluidity) to survive in the challenging high-pressure environment of the deep sea. • High-pressure treatment stimulated cell division and triggered the accumulation of UDP-glucose, a critical factor in cell wall formation, in Microbacterium sediminis YLB-01 cells.
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Affiliation(s)
- Xu Qiu
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Xiao-Min Hu
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Xi-Xiang Tang
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
| | - Cai-Hua Huang
- Research and Communication Center of Exercise and Health, Xiamen University of Technology, Xiamen, China
| | - Hua-Hua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Hai Lin
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
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Wang Y, Chen Z, Zhao F, Yang H. Metabolome shifts triggered by chlorine sanitisation induce Escherichia coli on fresh produce into the viable but nonculturable state. Food Res Int 2023; 171:113084. [PMID: 37330837 DOI: 10.1016/j.foodres.2023.113084] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/19/2023]
Abstract
Facing the increasing occurrence of "big six" Escherichia coli outbreaks linked to fresh produce, chlorine-based sanitisers are widely used for fresh produce decontamination in recent years. However, latest finding that chlorine may induce E. coli cells into a viable not nonculturable (VBNC) state is bringing a new challenge to the fresh produce industry. VBNC cells are undetectable by the plate count test, and yet they retain pathogenicity and are more antibiotic-resistant than culturable cells. As a result, their eradication is critical to ensure the safety of fresh produce. Understanding VBNC cells at the metabolic level may provide a breakthrough for their eradication. Therefore, this study was carried out to collect the VBNC pathogenic E. coli (O26:H11, O121:H19, and O157:H7) cells from chlorine-treated pea sprouts and characterise them using NMR-based metabolomics. From the globally increased metabolite contents detected in the VBNC E. coli cells as compared to the culturable cells, mechanisms underlying E. coli's VBNC induction were elucidated. These include rendering the energy generation scheme to become more compatible with the lowered energy needs, disaggregating protein aggregates to release amino acids for osmoprotection and later resuscitation, as well as increasing cAMP content to downregulate RpoS. These identified metabolic characteristics can inspire future development of targeted measures for VBNC E. coli cell inhibition. Our methods can also be applied to other pathogens to help lower the risk of overall foodborne diseases.
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Affiliation(s)
- Yue Wang
- Department of Food Science and Technology, National University of Singapore, Singapore 117542, Singapore.
| | - Zihui Chen
- Department of Food Science and Technology, National University of Singapore, Singapore 117542, Singapore
| | - Fengnian Zhao
- Department of Food Science and Technology, National University of Singapore, Singapore 117542, Singapore
| | - Hongshun Yang
- Shaoxing Key Laboratory of Traditional Fermentation Food and Human Health, Jiangnan University (Shaoxing) Industrial Technology Research Institute, Zhejiang, 312000, China.
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Lin W, He Y, Li R, Mu C, Wang C, Shi C, Ye Y. Adaptive changes of swimming crab (Portunus trituberculatus) associated bacteria helping host against dibutyl phthalate toxification. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 324:121328. [PMID: 36828355 DOI: 10.1016/j.envpol.2023.121328] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/17/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
The pollution of dibutyl phthalate (DBP) in aquatic environments is becoming an extensive environmental problem and detrimental to aquatic animals. Here, we quantified the response pattern of the bacterial community and metabolites of swimming crab (Portunus trituberculatus) juveniles exposed to 0.2, 2, and 10 mg/L DBP using 16 S rRNA gene amplicon sequencing coupled with metabolomic technique. The results showed that DBP changed the bacterial community compositions in a concentration-dependent pattern and decreased the Shannon index at the second developmental stage of the swimming crabs. The Rhodobacteraceae taxa were specifically enriched by crabs when challenged by 2 and 10 mg/L DBP, with an increased in Shannon index and enhanced drift in its assembly. Moreover, DBP changed the metabolic profiling of the swimming crab, highlighted by increased levels of lactate, valine, methionine, lysine, and phenylalanine in the 10 mg/L DBP-exposed crabs. Rhodobacteraceae presented the most considerable contribution to the metabolic potentials in phthalate and benzoate degradation, lactate production, and amino acid biosynthesis. Overall, our results indicated an adaptive change of crab-associated bacteria helped the host resist DBP stress. The findings extend our insights into the relationship between the microbiota and its host metabolism under DBP stress and reveal the potential microbiota modalities for DBP detoxification.
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Affiliation(s)
- Weichuan Lin
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315832, China
| | - Yimin He
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315832, China
| | - Ronghua Li
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, 315832, China
| | - Changkao Mu
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, 315832, China
| | - Chunlin Wang
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, 315832, China
| | - Ce Shi
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, 315832, China; Key Laboratory of Green Mariculture (Co-construction By Ministry and Province), Ministry of Agriculture and Rural, China
| | - Yangfang Ye
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315832, China.
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Chen L, Li X, Lou X, Shu W, Hai Y, Wen X, Yang H. NMR-based metabolomics reveals the antibacterial effect of electrolysed water combined with citric acid on Aeromonas spp. in barramundi (Lates calcarifer) fillets. Food Res Int 2022; 162:112046. [DOI: 10.1016/j.foodres.2022.112046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 10/03/2022] [Accepted: 10/10/2022] [Indexed: 11/15/2022]
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8
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Wang Y, Yang H. Metabolomics elucidating the effect of water activity on the thermal resistance of Salmonella in wheat flour. Food Res Int 2022; 162:112203. [DOI: 10.1016/j.foodres.2022.112203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022]
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Dual-Species Biofilms Formed by Escherichia coli and Salmonella Enhance Chlorine Tolerance. Appl Environ Microbiol 2022; 88:e0148222. [PMID: 36300924 PMCID: PMC9680634 DOI: 10.1128/aem.01482-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Outbreaks of
Escherichia coli
and
Salmonella
in food might be associated with the cross-contamination of biofilms on food-contact surfaces. The knowledge of the sanitization of mono-species biofilm on the food-contact surface is well established, while mixed-species biofilm occurs more naturally, which could profoundly affect the efficacy of sanitizer.
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Kairamkonda M, Sharma M, Gupta P, Poluri KM. Overexpression of bacteriophage T4 and T7 endolysins differentially regulate the metabolic fingerprint of host Escherichia coli. Int J Biol Macromol 2022; 221:212-223. [PMID: 36075302 DOI: 10.1016/j.ijbiomac.2022.09.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/26/2022] [Accepted: 09/02/2022] [Indexed: 12/21/2022]
Abstract
Bioactive proteins are often overexpressed in different host systems for biotechnological/biomedical applications. Endolysins are natural bactericidal proteins that cleave the bacterial peptidoglycan membrane, and have the potential to be the next-generation enzybiotics. Therefore, the present study aims to elucidate the impact of two endolysins (T4L, T7L) overexpression on metabolic fingerprint of E. coli using NMR spectroscopy. The 1H NMR-based metabolomics analysis revealed global metabolite profiles of E. coli in response to endolysins. The study has identified nearly 75 metabolites, including organic acids, amino acids, sugars and nucleic acids. RNA Polymerase (RNAP) has been considered as reference protein for marking the specific alterations in metabolic pathways. The data suggested downregulation of central carbon metabolic pathway in both endolysins overexpression, but to a different extent. Also, the endolysin overexpression have highlighted the enhanced metabolic load and stress generation in the host cells, thus leading to the activation of osmoregulatory pathways. The overall changes in metabolic fingerprint of E. coli highlights the enhanced perturbations during the overexpression of T4L as compared to T7L. These untargeted metabolic studies shed light on the regulation of molecular pathways during the heterologous overexpression of these lytic enzymes that are lethal to the host.
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Affiliation(s)
- Manikyaprabhu Kairamkonda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Meenakshi Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Payal Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India; Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India.
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Nanoemulsified clove essential oils-based edible coating controls Pseudomonas spp.-causing spoilage of tilapia (Oreochromis niloticus) fillets: Working mechanism and bacteria metabolic responses. Food Res Int 2022; 159:111594. [DOI: 10.1016/j.foodres.2022.111594] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/16/2022] [Accepted: 06/27/2022] [Indexed: 11/21/2022]
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Metabolic Responses of "Big Six" Escherichia coli in Wheat Flour to Thermal Treatment Revealed by Nuclear Magnetic Resonance Spectroscopy. Appl Environ Microbiol 2022; 88:e0009822. [PMID: 35285244 DOI: 10.1128/aem.00098-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Escherichia coli outbreaks linked to wheat flour consumption have kept emerging in recent years, which necessitated an antimicrobial step being incorporated into the flour production process. The objectives of this in vivo study were to holistically evaluate the sanitizing efficacy of thermal treatment at 60 and 70°C against the "big six" E. coli strains (O26:H11, O45:H2, O103:H11, O111, O121:H19, and O145) in wheat flour and to assess the strain-specific metabolic responses using nuclear magnetic resonance (NMR) spectroscopy. The 70°C treatment temperature indiscriminatingly inactivated all strains by over 4.3-log CFU/g within 20 min, suggesting the high sanitization effectiveness of this treatment temperature, whereas the treatment at 60°C inactivated the strains to various degrees during the 1-h process. The most resistant strains at 60°C, O26 and O45, were characterized by amino acid and sugar depletion, and their high resistance was attributed to the dual effects of activated heat shock protein (HSP) synthesis and promoted glycolysis. O121 also demonstrated these metabolic changes, yet its thermal resistance was largely impaired by the weakened membrane structure and diminished osmotic protection due to phosphorylcholine exhaustion. In contrast, O111, O145, and O103 presented a substantial elevation of metabolites after stress at 60°C; their moderate thermal resistance was mainly explained by the accumulation of amino acids as osmolytes. Overall, the study enhanced our understanding of the metabolic responses of big six E. coli to heat stress and provided a model for conducting NMR-based metabolomic studies in powdered food matrices. IMPORTANCE "Big six" Escherichia coli strains have caused several outbreaks linked to wheat flour consumption in the last decade, revealing the vital importance of adopting an antimicrobial treatment during the flour production process. Therefore, the present study was carried out to evaluate the efficacy of a typical sanitizing approach, thermal treatment, against the big six strains in wheat flour along with the underlying antimicrobial mechanisms. Findings showed that thermal treatment at 60 and 70°C could markedly mitigate the loads of all strains in wheat flour. Moreover, activated heat shock protein synthesis combined with expedited glycolysis and enhanced osmotic protection were identified as two major metabolic alteration patterns in the E. coli strains to cope with the heat stress. With the responses of big six in wheat flour to thermal treatment elucidated, scientific basis for incorporating a thermal inactivation step in wheat flour production was provided.
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Shi YG, Li DH, Kong YM, Zhang RR, Gu Q, Hu MX, Tian SY, Jin WG. Enhanced antibacterial efficacy and mechanism of octyl gallate/beta-cyclodextrins against Pseudomonas fluorescens and Vibrio parahaemolyticus and incorporated electrospun nanofibers for Chinese giant salamander fillets preservation. Int J Food Microbiol 2022; 361:109460. [PMID: 34785387 DOI: 10.1016/j.ijfoodmicro.2021.109460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/24/2021] [Accepted: 10/25/2021] [Indexed: 10/20/2022]
Abstract
A series of alkyl gallates were evaluated for the antibacterial activity against two common Gram-negative foodborne bacteria (Pseudomonas fluorescens and Vibrio parahaemolyticus) associated with seafood. The length of the alkyl chain plays a pivotal role in eliciting their antibacterial activities and octyl gallate (OG) exerted an excellent inhibitory efficacy. To extend the aqueous solubility, stability, and bactericidal properties of octyl gallate (OG), an inclusion complex between OG and β-cyclodextrin (βCD), OG/βCD, was prepared and identified with various methods including X-ray diffraction (XRD), differential scanning calorimeter (DSC) and Fourier transform infrared spectroscopy (FTIR). Furthermore, the enhanced inhibitory effect and potential antibacterial mechanism of OG/βCD against two Gram-negative and Gram-positive foodborne bacteria were comprehensively investigated. The results show that OG/βCD could function against bacteria through effectively damaging the membrane, permeating into cells, and then disturbing the activity of the respiratory electron transport chain to cause the production of high-level intracellular hydroxyl radicals. Moreover, the reinforced OG/βCD-incorporated polylactic acid (PLA) nanofibers were fabricated using the electrospinning technique as food packaging to extend the Chinese giant salamander fillet's shelf life at 4 °C. This research highlights the antibacterial effectiveness of OG/βCD in aqueous media, which can be used as a safe multi-functionalized food additive combined with the benefits of electrospun nanofibers to extend the Chinese giant salamander fillets shelf life by 15 d at 4 °C.
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Affiliation(s)
- Yu-Gang Shi
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310035, China; Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang Gongshang University, Hangzhou, Zhejiang 310035, China.
| | - Dong-Hui Li
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310035, China
| | - Yi-Ming Kong
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310035, China
| | - Run-Run Zhang
- Department of Food Science and Nutrition, National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, China
| | - Qing Gu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310035, China; Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang Gongshang University, Hangzhou, Zhejiang 310035, China.
| | - Meng-Xin Hu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310035, China
| | - Shi-Yi Tian
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310035, China
| | - Wen-Gang Jin
- Bio-resources Key Laboratory of Shaanxi Province, School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China
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Comparison of the metabolic responses of eight Escherichia coli strains including the “big six” in pea sprouts to low concentration electrolysed water by NMR spectroscopy. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108458] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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15
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Shao L, Liu Y, Zhao Y, Zou B, Li X, Dai R. Integrated transcriptomic and metabolomic analysis of the global response of Staphylococcus aureus to ohmic heating. INNOV FOOD SCI EMERG 2021. [DOI: 10.1016/j.ifset.2021.102870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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16
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Pan Y, Cheng JH, Sun DW. Metabolomic analyses on microbial primary and secondary oxidative stress responses. Compr Rev Food Sci Food Saf 2021; 20:5675-5697. [PMID: 34601780 DOI: 10.1111/1541-4337.12835] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/20/2021] [Accepted: 08/23/2021] [Indexed: 12/16/2022]
Abstract
Food safety is veryimportant in our daily life. In food processing or disinfection, microorganisms are commonly exposed to oxidative stress perturbations. However, microorganisms can adapt and respond to physicochemical interventions, leading to difficulty and complexity for food safety assurance. Therefore, understanding the response mechanisms of microbes and providing an overview of the responses under oxidative stress conditions are beneficial for ensuring food safety for the industry. The current review takes the metabolomics approach to reveal small metabolite signatures and key pathway alterations during oxidative stress at the molecular and technical levels. These alterations are involved in primary oxidative stress responses due to inactivation treatments such as using hypochlorite (HOCl), hydrogen peroxide (H2 O2 ), electrolyzed water (EW), irradiation, pulsed light (PL), electron beam (EB), and secondary oxidative stress responses due to exposures to excessive conditions such as heat, pressure, acid, and alkaline. Details on the putative origin of exogenous or endogenous reactive oxygen species (ROS) are discussed, with particular attention paid to their effects on lipid, amino acid, nucleotide, and carbohydrate metabolism. In addition, mechanisms on counteracting oxidative stresses, stabilization of cell osmolality as well as energy provision for microbes to survive are also discussed.
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Affiliation(s)
- Yuanyuan Pan
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China
| | - Jun-Hu Cheng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China
| | - Da-Wen Sun
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China.,Food Refrigeration and Computerized Food Technology (FRCFT), Agriculture and Food Science Centre, University College Dublin, National University of Ireland, Belfield, Dublin, Ireland
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17
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Shao L, Liu Y, Tian X, Zou B, Zhao Y, Li X, Dai R. Global proteomic responses of sublethally injured Staphylococcus aureus induced by ohmic heating. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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18
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Wu J, Zhao L, Lai S, Yang H. NMR-based metabolomic investigation of antimicrobial mechanism of electrolysed water combined with moderate heat treatment against Listeria monocytogenes on salmon. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107974] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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19
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Jiang M, Chen H, Luo Y, Han Q, Peng R, Jiang X. Combined metabolomics and histological analysis of the tissues from cuttlefish Sepia pharaonis exposed to inking stress. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 38:100829. [PMID: 33812154 DOI: 10.1016/j.cbd.2021.100829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 11/18/2022]
Abstract
Inking is part of a defensive stress response in cephalopods (cuttlefish, squid, and octopus). Some individual cuttlefish (Sepia pharaonis) die after continued stress and inking; however, the physiological effects of cephalopods in response to stress and inking remain unknown. The present study investigated the metabolic profile and discussed the physiological roles of S. pharaonis tissues in response to continuous inking using the 1H NMR spectroscopy coupled with multivariate data analysis. A total of 50 metabolites, including amino acids, organic osmolytes, nucleotides, energy storage compounds, and obvious tissue-specific metabolites induced by inking stress, were identified in S. pharaonis tissues. Exposure to inking stress had different effects on the levels of the studied metabolites, for example, the levels of isoleucine, trimethylamine-N-oxide, and betaine increased, but those of arginine and ATP decreased in the liver; inosine and lactate were accumulated whereas glutamate and choline were depleted in the gill; the levels of lactate and isoleucine were elevated but those of arginine and glycogen were depleted in the muscle tissue. Furthermore, the corresponding metabolic pathways of the characteristic metabolites indicated major changes in the functions of these metabolites. Histological changes in the studied tissues revealed liver lobule damage immediately after inking, with the presence of disordered epithelial cells and partial cell necrosis in the gill. Our results demonstrated that a combination of metabolomics and histological analyses could provide molecular-level insights for elucidating the defense response of cuttlefish against predators.
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Affiliation(s)
- Maowang Jiang
- Key Laboratory of Applied Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang Province 315211, PR China
| | - Huan Chen
- Key Laboratory of Applied Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang Province 315211, PR China
| | - Yuanyuan Luo
- Key Laboratory of Applied Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang Province 315211, PR China
| | - Qingxi Han
- Key Laboratory of Applied Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang Province 315211, PR China
| | - Ruibing Peng
- Key Laboratory of Applied Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang Province 315211, PR China
| | - Xiamin Jiang
- Key Laboratory of Applied Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang Province 315211, PR China.
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20
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Zhang RR, Shi YG, Gu Q, Fang M, Chen YW, Fang S, Dang YL, Chen JS. Antimicrobial effect and mechanism of non-antibiotic alkyl gallates against Pseudomonas fluorescens on the surface of Russian sturgeon (Acipenser gueldenstaedti). Int J Food Microbiol 2021; 342:109093. [PMID: 33607540 DOI: 10.1016/j.ijfoodmicro.2021.109093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/05/2021] [Indexed: 12/13/2022]
Abstract
Since Pseudomonas fluorescens is the main microorganism causing severe spoilage in refrigerated aquatic products, the searching for non-antibiotic antibacterial agents effective against it continues to receive increasing interest. This study aimed to investigate the antibacterial effects and mechanisms of alkyl gallic esters against P. fluorescens isolated from the Russian sturgeon (Acipenser gueldenstaedti), as well as the effectiveness in combination with chitosan films on the preservation of sturgeon meats at 4 °C. Our data shows that the alkyl chain length plays a significant role in eliciting their antibacterial activities and octyl gallate (GAC8) exhibited an outstanding inhibitory efficacy. GAC8 can rapidly enter into the membrane lipid bilayer portion to disorder the membrane, and further inhibit the growth of the P. fluorescens through interfering both tricarboxylic acid cycle related to energy supply and amino acid metabolism associated with cell membranes, suppressing oxygen consumption and disturbing the respiration chain. Moreover, the alteration in membrane fatty acids indicated that GAC8 could disrupt the composition of cell membrane fatty acids, rendering the bacteria more sensitive to the antibacterial. The SEM results also substantiate the damage of the structure of the bacterial membrane caused by GAC8. Additionally, the edible chitosan-based films incorporated with GAC8 showed the enhanced antibacterial efficacy to remarkably extend the shelf life of Russian sturgeon. Overall, our findings not only provide new insight into the mode of action of GAC8 against P. fluorescens but also demonstrate composite films containing GAC8, as a kind of safe and antibacterial material, have a great promise for application in food preservations.
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Affiliation(s)
- Run-Run Zhang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310035, China
| | - Yu-Gang Shi
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310035, China; Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang Gongshang University, Hangzhou, Zhejiang 310035, China.
| | - Qing Gu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310035, China; Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang Gongshang University, Hangzhou, Zhejiang 310035, China
| | - Mei Fang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310035, China
| | - Yue-Wen Chen
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310035, China
| | - Sheng Fang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310035, China
| | - Ya-Li Dang
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, Ningbo University, Ningbo 315211, China.
| | - Jian-She Chen
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang 310035, China; School of Food Science and Nutrition, University of Leeds, Leeds, LS2 9JT, UK
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21
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Intracellular Metabolomics Switching Alters Extracellular Acid Production and Insoluble Phosphate Solubilization Behavior in Penicillium oxalicum. Metabolites 2020; 10:metabo10110441. [PMID: 33142690 PMCID: PMC7692655 DOI: 10.3390/metabo10110441] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
This research aims to understand the precise intracellular metabolic processes of how microbes solubilize insoluble phosphorus (Insol-P) to increase bio-available P. Newly isolated Penicillium oxalicum PSF-4 exhibited outstanding tricalcium phosphate (TP) and iron phosphate (IP) solubilization performance—as manifested by microbial growth and the secretion of low-molecular-weight organic acids (LMWOAs). Untargeted metabolomics approach was employed to assess the metabolic alterations of 73 intracellular metabolites induced by TP and IP compared with soluble KH2PO4 in P. oxalicum. Based on the changes of intracellular metabolites, it was concluded that (i) the enhanced intracellular glyoxylate and carbohydrate metabolisms increased the extracellular LMWOAs production; (ii) the exposure of Insol-P poses potential effects to P. oxalicum in destructing essential cellular functions, affecting microbial growth, and disrupting amino acid, lipid, and nucleotide metabolisms; and (iii) the intracellular amino acid utilization played a significant role to stimulate microbial growth and the extracellular LMWOAs biosynthesis.
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22
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Kim S, Kim Y, Suh DH, Lee CH, Yoo SM, Lee SY, Yoon SH. Heat-responsive and time-resolved transcriptome and metabolome analyses of Escherichia coli uncover thermo-tolerant mechanisms. Sci Rep 2020; 10:17715. [PMID: 33077799 PMCID: PMC7572479 DOI: 10.1038/s41598-020-74606-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/05/2020] [Indexed: 11/27/2022] Open
Abstract
Current understanding of heat shock response has been complicated by the fact that heat stress is inevitably accompanied by changes in specific growth rates and growth stages. In this study, a chemostat culture was successfully performed to avoid the physico-chemical and biological changes that accompany heatshock, which provided a unique opportunity to investigate the full range of cellular responses to thermal stress, ranging from temporary adjustment to phenotypic adaptation at multi-omics levels. Heat-responsive and time-resolved changes in the transcriptome and metabolome of a widely used E. coli strain BL21(DE3) were explored in which the temperature was upshifted from 37 to 42 °C. Omics profiles were categorized into early (2 and 10 min), middle (0.5, 1, and 2 h), and late (4, 8, and 40 h) stages of heat stress, each of which reflected the initiation, adaptation, and phenotypic plasticity steps of the stress response. The continued heat stress modulated global gene expression by controlling the expression levels of sigma factors in different time frames, including unexpected downregulation of the second heatshock sigma factor gene (rpoE) upon the heat stress. Trehalose, cadaverine, and enterobactin showed increased production to deal with the heat-induced oxidative stress. Genes highly expressed at the late stage were experimentally validated to provide thermotolerance. Intriguingly, a cryptic capsular gene cluster showed considerably high expression level only at the late stage, and its expression was essential for cell growth at high temperature. Granule-forming and elongated cells were observed at the late stage, which was morphological plasticity occurred as a result of acclimation to the continued heat stress. Whole process of thermal adaptation along with the genetic and metabolic changes at fine temporal resolution will contribute to far-reaching comprehension of the heat shock response. Further, the identified thermotolerant genes will be useful to rationally engineer thermotolerant microorganisms.
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Affiliation(s)
- Sinyeon Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Youngshin Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Dong Ho Suh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Choong Hwan Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, Daejeon, 34141, Republic of Korea
| | - Sung Ho Yoon
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea.
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23
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3-Hydroxybutyrate Derived from Poly-3-Hydroxybutyrate Mobilization Alleviates Protein Aggregation in Heat-Stressed Herbaspirillum seropedicae SmR1. Appl Environ Microbiol 2020; 86:AEM.01265-20. [PMID: 32631857 DOI: 10.1128/aem.01265-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/26/2020] [Indexed: 12/14/2022] Open
Abstract
Under conditions of carbon starvation or thermal, osmotic, or oxidative shock, mutants affected in the synthesis or mobilization of poly-3-hydroxybutyrate (PHB) are known to survive less well. It is still unclear if the synthesis and accumulation of PHB are sufficient to protect bacteria against stress conditions or if the stored PHB has to be mobilized. Here, we demonstrated that mobilization of PHB in Herbaspirillum seropedicae SmR1 was heat-shock activated at 45°C. In situ proton (1H) nuclear magnetic resonance spectroscopy (i.e., 1H-nuclear magnetic resonance) showed that heat shock increased amounts of 3-hydroxybutyrate (3HB) only in H. seropedicae strains able to synthesize and mobilize PHB. H. seropedicae SmR1 mutants unable to synthesize or mobilize PHB were more susceptible to heat shock and survived less well than the parental strain. When 100 mM 3-hydroxybutyrate was added to the medium, the ΔphaC1 strain (an H. seropedicae mutant unable to synthesize PHB) and the double mutant with deletion of both phaZ1 and phaZ2 (i.e., ΔphaZ1.2) (unable to mobilize PHB) showed partial rescue of heat adaptability (from 0% survival without 3HB to 40% of the initial viable population). Addition of 200 mM 3HB before the imposition of heat shock reduced protein aggregation to 15% in the ΔphaC1 mutant and 12% in the ΔphaZ1.2 mutant. We conclude that H. seropedicae SmR1 is naturally protected by 3HB released by PHB mobilization, while mutants unable to generate large amounts of 3HB under heat shock conditions are less able to cope with heat damage.IMPORTANCE Bacteria are subject to abrupt changes in environmental conditions affecting their growth, requiring rapid adaptation. Increasing the concentration of some metabolites can protect bacteria from hostile conditions that lead to protein denaturation and precipitation, as well as damage to plasma membranes. In this work, we demonstrated that under thermal shock, the bacterium Herbaspirillum seropedicae depolymerized its intracellular stock polymer known as poly-3-hydroxybutyrate (PHB), rapidly increasing the concentration of 3-hydroxybutyrate (3HB) and decreasing protein precipitation by thermal denaturation. Mutant H. seropedicae strains unable to produce or depolymerize PHB suffered irreparable damage during thermal shock, resulting in fast death when incubated at 45°C. Our results will contribute to the development of bacteria better adapted to high temperatures found either in natural conditions or in industrial processes. In the case of H. seropedicae and other bacteria that interact beneficially with plants, the understanding of PHB metabolism can be decisive for the development of more-competitive strains and their application as biofertilizers in agriculture.
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24
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Steward KF, Eilers B, Tripet B, Fuchs A, Dorle M, Rawle R, Soriano B, Balasubramanian N, Copié V, Bothner B, Hatzenpichler R. Metabolic Implications of Using BioOrthogonal Non-Canonical Amino Acid Tagging (BONCAT) for Tracking Protein Synthesis. Front Microbiol 2020; 11:197. [PMID: 32117186 PMCID: PMC7031258 DOI: 10.3389/fmicb.2020.00197] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 01/28/2020] [Indexed: 12/11/2022] Open
Abstract
BioOrthogonal Non-Canonical Amino acid Tagging (BONCAT) is a powerful tool for tracking protein synthesis on the level of single cells within communities and whole organisms. A basic premise of BONCAT is that the non-canonical amino acids (NCAA) used to track translational activity do not significantly alter cellular physiology. If the NCAA would induce changes in the metabolic state of cells, interpretation of BONCAT studies could be challenging. To address this knowledge-gap, we have used a global metabolomics analyses to assess the intracellular effects of NCAA incorporation. Two NCAA were tested: L-azidohomoalanine (AHA) and L-homopropargylglycine (HPG); L-methionine (MET) was used as a minimal stress baseline control. Liquid Chromatography Mass Spectrometry (LC-MS) and Nuclear Magnetic Resonance (NMR) were used to characterize intracellular metabolite profiles of Escherichia coli cultures, with multivariate statistical analysis using XCMS and MetaboAnalyst. Results show that doping with NCAA induces metabolic changes, however, the metabolic impact was not dramatic. A second set of experiments in which cultures were placed under mild stress to simulate real-world environmental conditions showed a more consistent and more robust perturbation. Pathways that changed include amino acid and protein synthesis, choline and betaine, and the TCA cycle. Globally, these changes were statistically minor, indicating that NCAA are unlikely to exert a significant impact on cells during incorporation. Our results are consistent with previous reports of NCAA doping under replete conditions and extend these results to bacterial growth under environmentally relevant conditions. Our work highlights the power of metabolomics studies in detecting cellular response to growth conditions and the complementarity of NMR and LCMS as omics tools.
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Affiliation(s)
- Katherine F Steward
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Brian Eilers
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Brian Tripet
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Amanda Fuchs
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Michael Dorle
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Rachel Rawle
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Berliza Soriano
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | | | - Valérie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States.,Thermal Biology Institute, Montana State University, Bozeman, MT, United States
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States.,Thermal Biology Institute, Montana State University, Bozeman, MT, United States
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States.,Thermal Biology Institute, Montana State University, Bozeman, MT, United States.,Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
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25
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Hossain SMZ, Razzak SA, Hossain MM. Application of Essential Oils as Green Corrosion Inhibitors. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2020. [DOI: 10.1007/s13369-019-04305-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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26
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Xia JM, Hu XM, Huang CH, Yu LB, Xu RF, Tang XX, Lin DH. Metabolic profiling of cold adaptation of a deep-sea psychrotolerant Microbacterium sediminis to prolonged low temperature under high hydrostatic pressure. Appl Microbiol Biotechnol 2019; 104:277-289. [PMID: 31728583 DOI: 10.1007/s00253-019-10134-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/30/2019] [Accepted: 09/08/2019] [Indexed: 12/01/2022]
Abstract
The most wide-spread "hostile" environmental factor for marine microorganisms is low temperature, which is usually accompanied by high hydrostatic pressure (HHP). Metabolic mechanisms of marine microorganisms adapting to prolonged low temperature under HHP remain to be clarified. To reveal the underlying metabolic mechanisms, we performed NMR-based metabolomic analysis of aqueous extracts derived from a psychrotolerant Microbacterium sediminis YLB-01, which was isolated from deep-sea sediment and possess great biotechnology potentials. The YLB-01 cells were firstly cultivated at the optimal condition (28 °C, 0.1 MPa) for either 18 h (logarithmic phase) or 24 h (stationary phase), then continually cultivated at either 28 °C or 4 °C under HHP (30 MPa) for 7 days. The cells cultivated at low temperature, which experienced cold stress, were distinctly distinguished from those at normal temperature. Cold stress primarily induced metabolic changes in amino acid metabolism and carbohydrate metabolism. Furthermore, the logarithmic and stationary phase cells cultivated at low temperature exhibited distinct metabolic discrimination, which was mostly reflected in the significantly disturbed carbohydrate metabolism. The logarithmic phase cells displayed suppressed TCA cycle, while the stationary phase cells showed decreased pyruvate and increased lactate. In addition, we performed transcriptome analysis for the stationary phase cells to support the metabolomic analysis. Our results suggest that the cold adaptation of the psychrotroph YLB-01 is closely associated with profoundly altered amino acid metabolism and carbohydrate metabolism. Our work provides a mechanistic understanding of the metabolic adaptation of marine psychrotrophs to prolonged low temperature under HHP.
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Affiliation(s)
- Jin-Mei Xia
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen, 361005, China
| | - Xiao-Min Hu
- College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, Xiamen, 361005, China
| | - Cai-Hua Huang
- Research and Communication Center of Exercise and Health, Xiamen University of Technology, Xiamen, 361024, China
| | - Li-Bo Yu
- China Ocean Sample Respository (Biology), 184 Daxue Road, Xiamen, 361005, China
| | - Ru-Fang Xu
- China Ocean Sample Respository (Biology), 184 Daxue Road, Xiamen, 361005, China
| | - Xi-Xiang Tang
- China Ocean Sample Respository (Biology), 184 Daxue Road, Xiamen, 361005, China.
| | - Dong-Hai Lin
- College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, Xiamen, 361005, China.
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27
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Xue D, Liu W, Chen Y, Liu Y, Han J, Geng X, Li J, Jiang S, Zhou Z, Zhang W, Chen M, Lin M, Ongena M, Wang J. RNA-Seq-Based Comparative Transcriptome Analysis Highlights New Features of the Heat-Stress Response in the Extremophilic Bacterium Deinococcus radiodurans. Int J Mol Sci 2019; 20:ijms20225603. [PMID: 31717497 PMCID: PMC6888292 DOI: 10.3390/ijms20225603] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/31/2019] [Accepted: 11/07/2019] [Indexed: 12/25/2022] Open
Abstract
Deinococcus radiodurans is best known for its extraordinary resistance to diverse environmental stress factors, such as ionizing radiation, ultraviolet (UV) irradiation, desiccation, oxidation, and high temperatures. The heat response of this bacterium is considered to be due to a classical, stress-induced regulatory system that is characterized by extensive transcriptional reprogramming. In this study, we investigated the key functional genes involved in heat stress that were expressed and accumulated in cells (R48) following heat treatment at 48 °C for 2 h. Considering that protein degradation is a time-consuming bioprocess, we predicted that to maintain cellular homeostasis, the expression of the key functional proteins would be significantly decreased in cells (RH) that had partly recovered from heat stress relative to their expression in cells (R30) grown under control conditions. Comparative transcriptomics identified 15 genes that were significantly downregulated in RH relative to R30, seven of which had previously been characterized to be heat shock proteins. Among these genes, three hypothetical genes (dr_0127, dr_1083, and dr_1325) are highly likely to be involved in response to heat stress. Survival analysis of mutant strains lacking DR_0127 (a DNA-binding protein), DR_1325 (an endopeptidase-like protein), and DR_1083 (a hypothetical protein) showed a reduction in heat tolerance compared to the wild-type strain. These results suggest that DR_0127, DR_1083, and DR_1325 might play roles in the heat stress response. Overall, the results of this study provide deeper insights into the transcriptional regulation of the heat response in D. radiodurans.
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Affiliation(s)
- Dong Xue
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
- Microbial Processes and Interactions (MiPI), TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - Wenzheng Liu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China;
| | - Yun Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yingying Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
| | - Jiahui Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
| | - Xiuxiu Geng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China;
| | - Jiang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China;
| | - Shijie Jiang
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China;
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
| | - Marc Ongena
- Microbial Processes and Interactions (MiPI), TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
- Correspondence: (M.O.); (J.W.)
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
- Correspondence: (M.O.); (J.W.)
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Zhao L, Zhao X, Wu J, Lou X, Yang H. Comparison of metabolic response between the planktonic and air-dried Escherichia coli to electrolysed water combined with ultrasound by 1H NMR spectroscopy. Food Res Int 2019; 125:108607. [PMID: 31554111 DOI: 10.1016/j.foodres.2019.108607] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/28/2019] [Accepted: 08/04/2019] [Indexed: 01/08/2023]
Abstract
The antimicrobial effects of electrolysed water and ultrasound have been well reported; however, little attention was paid to their effects on the metabolite changes of bacteria in different states. In this study, the metabolomic variations of Escherichia coli ATCC 25922 in planktonic and adherent state (air-dried on stainless steel coupons) after the combination treatment of low-concentration acidic electrolysed water (AEW, free available chlorine (FAC): 4 mg/L) and ultrasound were characterised, by conducting multivariate data analysis based on nuclear magnetic resonance (NMR) spectroscopy. Overall, 43 metabolites were identified in two states of E. coli, including a wide range of amino acids, organic acids, nucleotides and their derivatives. The quantification of whole-cell metabolism in planktonic and air-dried cultures was quite different: air-dried E. coli exhibited more resistance to ultrasound and AEW treatments due to initiating a protective response against oxidative and acid stresses, which was not observed in planktonic E. coli, whose levels of all identified metabolites were decreased significantly after the combined treatment. Further pathway analysis revealed that alanine, aspartate and glutamate metabolism, glycolysis, pyruvate metabolism and tricarboxylic acid (TCA) cycle were changed significantly in planktonic culture, but to a less extent in air-dried culture, in which some shifts in glutamate decarboxylase (GAD) system and some shunts like mixed acid fermentation and pentose phosphate pathway were observed for maintaining metabolic balance. These findings suggest that NMR-based metabolomics strategy is promising in identifying different metabolic shifts in different states of bacteria. They also provide some guidance for food equipment sanitisation, especially for organic food processing.
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Affiliation(s)
- Lin Zhao
- Food Science and Technology Programme, c/o Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore; National University of Singapore (Suzhou) Research Institute, 377 Lin Quan Street, Suzhou Industrial Park, Suzhou, Jiangsu 215123, PR China
| | - Xue Zhao
- Food Science and Technology Programme, c/o Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore; National University of Singapore (Suzhou) Research Institute, 377 Lin Quan Street, Suzhou Industrial Park, Suzhou, Jiangsu 215123, PR China
| | - Ji'en Wu
- Setsco Services Pte Ltd, 18 Teban Gardens Crescent, Singapore 608925, Singapore
| | - Xiaowei Lou
- Food Science and Technology Programme, c/o Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore; National University of Singapore (Suzhou) Research Institute, 377 Lin Quan Street, Suzhou Industrial Park, Suzhou, Jiangsu 215123, PR China
| | - Hongshun Yang
- Food Science and Technology Programme, c/o Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore; National University of Singapore (Suzhou) Research Institute, 377 Lin Quan Street, Suzhou Industrial Park, Suzhou, Jiangsu 215123, PR China.
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29
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Zhai Q, Xiao Y, Narbad A, Chen W. Comparative metabolomic analysis reveals global cadmium stress response of Lactobacillus plantarum strains. Metallomics 2019; 10:1065-1077. [PMID: 29998247 DOI: 10.1039/c8mt00095f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Our previous work demonstrated the protective effects of Lactobacillus plantarum (L. plantarum) strains against cadmium (Cd) toxicity in vivo, and also indicated that the Cd tolerance of the strains played an important role in this protection. The goal of this study was to investigate the Cd resistance mechanism of L. plantarum by liquid chromatography-mass spectrometry (LC-MS) based metabolomic analysis, with a focus on the global Cd stress response. L. plantarum CCFM8610 (strongly resistant to Cd) and L. plantarum CCFM191 (sensitive to Cd) were selected as target strains, and their metabolomic profiles with and without Cd exposure were compared. The underlying mechanisms of the intra-species distinction between CCFM8610 and CCFM191 in terms of Cd tolerance can be attributed to the following aspects: (a) CCFM8610 possesses a higher intracellular content of osmolytes; (b) CCFM8610 can induce more effective biosynthesis of extracellular polymeric substance (EPS) to sequestrate Cd;
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Affiliation(s)
- Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China.
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30
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Feng X, He C, Jiao L, Liang X, Zhao R, Guo Y. Analysis of differential expression proteins reveals the key pathway in response to heat stress in Alicyclobacillus acidoterrestris DSM 3922T. Food Microbiol 2019; 80:77-84. [DOI: 10.1016/j.fm.2019.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 11/12/2018] [Accepted: 01/06/2019] [Indexed: 11/27/2022]
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31
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Rai N, Huynh L, Kim M, Tagkopoulos I. Population collapse and adaptive rescue during long‐term chemostat fermentation. Biotechnol Bioeng 2019; 116:693-703. [DOI: 10.1002/bit.26898] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/02/2018] [Accepted: 12/06/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Navneet Rai
- UC Davis Genome Center, University of California Davis California
- Department of Computer Science University of California Davis California
| | - Linh Huynh
- UC Davis Genome Center, University of California Davis California
- Department of Computer Science University of California Davis California
| | - Minseung Kim
- UC Davis Genome Center, University of California Davis California
- Department of Computer Science University of California Davis California
| | - Ilias Tagkopoulos
- UC Davis Genome Center, University of California Davis California
- Department of Computer Science University of California Davis California
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32
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Esteves AM, Graça G, Peyriga L, Torcato IM, Borges N, Portais JC, Santos H. Combined transcriptomics-metabolomics profiling of the heat shock response in the hyperthermophilic archaeon Pyrococcus furiosus. Extremophiles 2018; 23:101-118. [PMID: 30430272 DOI: 10.1007/s00792-018-1065-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/28/2018] [Indexed: 12/25/2022]
Abstract
Pyrococcus furiosus is a remarkable archaeon able to grow at temperatures around 100 °C. To gain insight into how this model hyperthermophile copes with heat stress, we compared transcriptomic and metabolomic data of cells subjected to a temperature shift from 90 °C to 97 °C. In this study, we used RNA-sequencing to characterize the global variation in gene expression levels, while nuclear magnetic resonance (NMR) and targeted ion exchange liquid chromatography-mass spectrometry (LC-MS) were used to determine changes in metabolite levels. Of the 552 differentially expressed genes in response to heat shock conditions, 257 were upregulated and 295 were downregulated. In particular, there was a significant downregulation of genes for synthesis and transport of amino acids. At the metabolite level, 37 compounds were quantified. The level of di-myo-inositol phosphate, a canonical heat stress solute among marine hyperthermophiles, increased considerably (5.4-fold) at elevated temperature. Also, the levels of mannosylglycerate, UDP-N-acetylglucosamine (UDPGlcNac) and UDP-N-acetylgalactosamine were enhanced. The increase in the pool of UDPGlcNac was concurrent with an increase in the transcript levels of the respective biosynthetic genes. This work provides the first metabolomic analysis of the heat shock response of a hyperthermophile.
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Affiliation(s)
- Ana M Esteves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal
| | - Gonçalo Graça
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal
| | - Lindsay Peyriga
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France
| | - Inês M Torcato
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal
| | - Nuno Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal
| | - Jean-Charles Portais
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France.,Université Paul Sabatier, Université de Toulouse, 31062, Toulouse, France
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal.
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de Melo Pereira GV, de Oliveira Coelho B, Magalhães Júnior AI, Thomaz-Soccol V, Soccol CR. How to select a probiotic? A review and update of methods and criteria. Biotechnol Adv 2018; 36:2060-2076. [PMID: 30266342 DOI: 10.1016/j.biotechadv.2018.09.003] [Citation(s) in RCA: 221] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 09/18/2018] [Accepted: 09/24/2018] [Indexed: 02/07/2023]
Abstract
International competition within the dairy market and increasing public awareness about the importance of functional food consumption are providing new challenges for innovation in the probiotic sector. In this context, countless references are currently dedicated to the selection and characterization of new species and more specific strains of probiotic bacteria. In general, these studies adopt basic selection criteria established by the World Health Organization (WHO), including host-associated stress resistance, epithelium adhesion ability, and antimicrobial activity. These aspects are applied to ensure that the candidate probiotic could withstand the stressful conditions of the human digestive system and exert functional proprieties. However, it cannot be assumed that these novel microbial strains are capable of offering several biological benefits attributed to probiotics. Additionally, safety-associated selection criteria, such as plasmid-associated antibiotic resistance spreading and enterotoxin production, are often neglected. This article reviews the recent developments in the processes, strategies, and methods, such as anticarcinogenic, antidepression, antianxiety, antiobesity, antidiabetic, immunostimulatory, and cholesterol-lowering assessments, to select probiotic strains with the ultimate objective of assisting future probiotic microbe evaluation studies.
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Affiliation(s)
| | - Bruna de Oliveira Coelho
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | | | - Vanete Thomaz-Soccol
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Carlos Ricardo Soccol
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná (UFPR), Curitiba, PR, Brazil.
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Metabolome analysis of Escherichia coli ATCC25922 cells treated with high hydrostatic pressure at 400 and 600 MPa. J Biosci Bioeng 2018; 126:611-616. [PMID: 29853298 DOI: 10.1016/j.jbiosc.2018.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 04/24/2018] [Accepted: 05/08/2018] [Indexed: 11/21/2022]
Abstract
Escherichia coli cells were treated with high hydrostatic pressure (HHP) at 400 and 600 MPa. Metabolites (70-1027 m/z) extracted from HHP-treated cells were analyzed using capillary electrophoresis-time-of-flight mass spectrometry and were compared with those extracted from control cells (not treated with HHP). A total of 133 metabolites were identified and mapped to metabolic pathways, and many of these (42.1%) decreased due to the HHP treatment, including NAD+, NADP+, ATP, and substrates for DNA synthesis. Principal component analysis suggested that the central sugar and nucleic acid metabolic pathways were strongly influenced by HHP. A bottleneck in the central sugar metabolic pathway was observed in HHP-treated cells, which created a metabolic imbalance; metabolites mapped upstream (glucose 6-phosphate, fructose 6-phosphate, and fructose 1,6-diphosphate) were accumulated and those downstream (3-phosphoglycerate, 2-phosphoglycerate, and phosphoenolpyruvate) were depleted. Ribonucleotides were decreased, but the reduction was moderate compared with that of substrates for DNA synthesis; the exception was ATP, which also substantially decreased. The bottleneck in the glycolytic pathway partly explained the exhaustion of ATP. NAD+/NADH ratio of HHP treated cells was comparable with that of untreated control cells.
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35
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Miguez AM, McNerney MP, Styczynski MP. Metabolomics Analysis of the Toxic Effects of the Production of Lycopene and Its Precursors. Front Microbiol 2018; 9:760. [PMID: 29774011 PMCID: PMC5944366 DOI: 10.3389/fmicb.2018.00760] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 04/04/2018] [Indexed: 01/01/2023] Open
Abstract
Using cells as microbial factories enables highly specific production of chemicals with many advantages over chemical syntheses. A number of exciting new applications of this approach are in the area of precision metabolic engineering, which focuses on improving the specificity of target production. In recent work, we have used precision metabolic engineering to design lycopene-producing Escherichia coli for use as a low-cost diagnostic biosensor. To increase precursor availability and thus the rate of lycopene production, we heterologously expressed the mevalonate pathway. We found that simultaneous induction of these pathways increases lycopene production, but induction of the mevalonate pathway before induction of the lycopene pathway decreases both lycopene production and growth rate. Here, we aim to characterize the metabolic changes the cells may be undergoing during expression of either or both of these heterologous pathways. After establishing an improved method for quenching E. coli for metabolomics analysis, we used two-dimensional gas chromatography coupled to mass spectrometry (GCxGC-MS) to characterize the metabolomic profile of our lycopene-producing strains in growth conditions characteristic of our biosensor application. We found that the metabolic impacts of producing low, non-toxic levels of lycopene are of much smaller magnitude than the typical metabolic changes inherent to batch growth. We then used metabolomics to study differences in metabolism caused by the time of mevalonate pathway induction and the presence of the lycopene biosynthesis genes. We found that overnight induction of the mevalonate pathway was toxic to cells, but that the cells could recover if the lycopene pathway was not also heterologously expressed. The two pathways appeared to have an antagonistic metabolic effect that was clearly reflected in the cells’ metabolic profiles. The metabolites homocysteine and homoserine exhibited particularly interesting behaviors and may be linked to the growth inhibition seen when the mevalonate pathway is induced overnight, suggesting potential future work that may be useful in engineering increased lycopene biosynthesis.
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Affiliation(s)
- April M Miguez
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Monica P McNerney
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States
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36
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Liu Q, Wu J, Lim ZY, Lai S, Lee N, Yang H. Metabolite profiling of Listeria innocua for unravelling the inactivation mechanism of electrolysed water by nuclear magnetic resonance spectroscopy. Int J Food Microbiol 2018; 271:24-32. [PMID: 29477806 DOI: 10.1016/j.ijfoodmicro.2018.02.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 01/06/2018] [Accepted: 02/11/2018] [Indexed: 01/23/2023]
Abstract
Bactericidal effects of low concentration electrolysed water (LcEW) on microorganisms are previously well reported; however, the inactivation mechanism of EW is not understood. The lethal and sublethal injuries of L. monocytogenes and L. innocua by EW treatments were determined and the metabolic profile changes for L. innocua were characterised using nuclear magnetic resonance (NMR). Microbial metabolomics approach combined with multivariate data analyses was used to interpret the cellular chemical fingerprints of L. innocua. The relative amount of intracellular reactive oxygen species (ROS) was assayed using 2',7-dichlorodihydrofluorescein diacetate (H2DCFDA). The results showed that the proportion of the sublethally injured microbial cells L. monocytogenes and L. innocua increased from 40% to 70% and from 35% to 65%, respectively, when the free available chlorine (FAC) of LcEW increased from 2 to 8 mg/L. Overall, 36 low-molecular-weight metabolic compounds in L. innocua extracts were characterised by NMR spectroscopy. EW perturbation resulted in a drastic and multitude disruption across a wide range of biochemical process including peptidoglycan synthesis, nucleotides biosynthesis and amino acid metabolism. Elevated levels of α-ketoglutarate and succinate implicated the enhanced glutamate decarboxylase (GAD) system and γ-aminobutyric acid (GABA) shunt for the protection against oxidative stress. These findings provided the comprehensive insights into the metabolic response of Listeria to EW oxidative stress and can serve as a basis for better utilisation for sanitisation.
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Affiliation(s)
- Qin Liu
- Food Science and Technology Programme, c/o Department of Chemistry, National University of Singapore, Singapore 117543, Singapore; National University of Singapore (Suzhou) Research Institute, 377 Lin Quan Street, Suzhou Industrial Park, Suzhou, Jiangsu 215123, PR China
| | - Ji'en Wu
- The Nuclear Magnetic Resonance Laboratory, Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Zhi Yang Lim
- Food Science and Technology Programme, c/o Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Shaojuan Lai
- Guangzhou Pulu Medical Technology Co., Ltd, Guangzhou, Guangdong 510800, PR China
| | - Norman Lee
- Science Research Programme, Temasek Junior College, Singapore 469278, Singapore
| | - Hongshun Yang
- Food Science and Technology Programme, c/o Department of Chemistry, National University of Singapore, Singapore 117543, Singapore; National University of Singapore (Suzhou) Research Institute, 377 Lin Quan Street, Suzhou Industrial Park, Suzhou, Jiangsu 215123, PR China.
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37
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Gandhi A, Shah NP. Integrating omics to unravel the stress-response mechanisms in probiotic bacteria: Approaches, challenges, and prospects. Crit Rev Food Sci Nutr 2018; 57:3464-3471. [PMID: 26853094 DOI: 10.1080/10408398.2015.1136805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Identifying the stress-response mechanism of probiotic bacteria has always captivated the interest of food producers. It is crucial to identify probiotic bacteria that have increased stress tolerance to survive during production, processing, and storage of food products. However, in order to achieve high resistance to environmental factors, there is a need to better understand stress-induced responses and adaptive mechanisms. With advances in bacterial genomics, there has been an upsurge in the application of other omic platforms such as transcriptomics, proteomics, metabolomics, and some more recent ones such as interactomics, fluxomics, and phenomics. These omic technologies have revolutionized the functional genomics and their application. There have been several studies implementing various omic technologies to investigate the stress responses of probiotic bacteria. Integrated omics has the potential to provide in-depth information about the mechanisms of stress-induced responses in bacteria. However, there remain challenges in integrating information from different omic platforms. This review discusses current omic techniques and challenges faced in integrating various omic platforms with focus on their use in stress-response studies.
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Affiliation(s)
- Akanksha Gandhi
- a Food and Nutritional Science, School of Biological Sciences , The University of Hong Kong , Hong Kong
| | - Nagendra P Shah
- a Food and Nutritional Science, School of Biological Sciences , The University of Hong Kong , Hong Kong
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38
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Jousse C, Dalle C, Canet I, Lagrée M, Traïkia M, Lyan B, Mendes C, Sancelme M, Amato P, Delort AM. Metabolomic study of the response to cold shock in a strain of Pseudomonas syringae isolated from cloud water. Metabolomics 2017; 14:11. [PMID: 30830325 DOI: 10.1007/s11306-017-1295-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 11/07/2017] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Active microorganisms have been recently discovered in clouds, thus demonstrating the capacity of microorganisms to exist in harsh environments, including exposure to UV and oxidants, osmotic and cold shocks, etc. It is important to understand how microorganisms respond to and survive such stresses at the metabolic level. OBJECTIVES The objective of this work is to assess metabolome modulation in a strain of Pseudomonas syringae isolated from cloud water and facing temperature downshift from 17 to 5 °C by identifying key molecules and pathways of the response/adaptation to cold shock. METHODS Bacterial extracts from suspensions of cells grown at 17 °C and further incubated in microcosms at 5 and 17 °C to mimic cloud conditions were analysed by combining LC-MS and NMR; the results were evaluated in comparison to similar suspensions kept at constant temperature. The differences in the metabolome profiles were deciphered using multivariate statistics (PLS-DA). RESULTS Key cold shock biomarkers were observed, including cryoprotectants (trehalose, glucose, glycerol, carnitine, glutamate), antioxidants (glutathione and carnitine) and their precursors, alkaloids (bellendine and slaframine) and metabolites involved in energy metabolism (ATP, carbohydrates). Furthermore, new short peptides (nine dipeptides and a tetrapeptide) were found that have no known function. CONCLUSIONS This study shows that in response to cold temperatures, Pseudomonas syringae PDD-32b-74 demonstrates numerous metabolism modifications to counteract the impacts of low temperatures.
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Affiliation(s)
- Cyril Jousse
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Céline Dalle
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Isabelle Canet
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
| | - Marie Lagrée
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Mounir Traïkia
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Bernard Lyan
- Université Clermont Auvergne - INRA, UNH, 63000, Clermont-Ferrand, France
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Cédric Mendes
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Martine Sancelme
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
| | - Pierre Amato
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
| | - Anne-Marie Delort
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France.
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France.
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Hu WT, Guo WL, Meng AY, Sun Y, Wang SF, Xie ZY, Zhou YC, He C. A metabolomic investigation into the effects of temperature on Streptococcus agalactiae from Nile tilapia (Oreochromis niloticus) based on UPLC-MS/MS. Vet Microbiol 2017; 210:174-182. [PMID: 29103689 DOI: 10.1016/j.vetmic.2017.09.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 09/16/2017] [Accepted: 09/19/2017] [Indexed: 12/22/2022]
Abstract
Streptococcosis caused by Streptococcus agalactiae is one of the most serious diseases in farmed tilapia, and temperature is one of the most important environmental factors related to its outbreak. To elucidate the influence of temperature variation on the pathogen from a metabolic perspective, the global metabolomics of 2 pathogenic strains of S. agalactiae from sick tilapia were analyzed at 35°C and 25°C using ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) combined with pattern recognition approaches and pathway analysis. The result showed that the metabolic status of S. agalactiae was extensively affected by its culture temperature. Based on the results of metabolites contributing to these differences, a large number of nucleotides and their ramifications were markedly elevated at 35°C. Various energy substances, components of the cell wall and substances associated with stress regulation such as glyceraldehyde 3-phosphate, pyroglutamic acid, glutamate, d-Alanyl-d-alanine, glycerophosphocholine, dephospho-CoA, and oxidized glutathione increased when the strains were cultured at 35°C. Additionally, a general decrease in various precursors of capsule, antigen, and virulence protein formation were detected including mannose, maltotriose, N-acetyl-d-glucosamine 6-phosphate, uracil, proline, and citrulline. These metabolic changes indicated that metabolic activity decreased, while adaptive ability to environment and pathogenicity to host increased at high temperature. This study is the first to determine the metabolomic responses of S. agalactiae to temperature, and the results are useful to reveal its pathogenic mechanism and find effective disease control.
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Affiliation(s)
- Wen-Ting Hu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Rd, Haikou, 570228 PR China; Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, 58 Renmin Rd, Haikou, 570228 PR China; Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, 58 Renmin Rd, Haikou, 570228 PR China
| | - Wei-Liang Guo
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Rd, Haikou, 570228 PR China; Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, 58 Renmin Rd, Haikou, 570228 PR China
| | - Ai-Yun Meng
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, 58 Renmin Rd, Haikou, 570228 PR China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, 58 Renmin Rd, Haikou, 570228 PR China
| | - Yun Sun
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Rd, Haikou, 570228 PR China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, 58 Renmin Rd, Haikou, 570228 PR China
| | - Shi-Feng Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Rd, Haikou, 570228 PR China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, 58 Renmin Rd, Haikou, 570228 PR China
| | - Zhen-Yu Xie
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Rd, Haikou, 570228 PR China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, 58 Renmin Rd, Haikou, 570228 PR China
| | - Yong-Can Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Rd, Haikou, 570228 PR China; Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, 58 Renmin Rd, Haikou, 570228 PR China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, 58 Renmin Rd, Haikou, 570228 PR China.
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, 58 Renmin Rd, Haikou, 570228 PR China.
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40
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Tandem mass tag-based quantitative proteomics analyses reveal the response of Bacillus licheniformis to high growth temperatures. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1279-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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41
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Liu Q, Wu J, Lim ZY, Aggarwal A, Yang H, Wang S. Evaluation of the metabolic response of Escherichia coli to electrolysed water by 1 H NMR spectroscopy. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.01.066] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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42
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Planchon M, Léger T, Spalla O, Huber G, Ferrari R. Metabolomic and proteomic investigations of impacts of titanium dioxide nanoparticles on Escherichia coli. PLoS One 2017; 12:e0178437. [PMID: 28570583 PMCID: PMC5453534 DOI: 10.1371/journal.pone.0178437] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/13/2017] [Indexed: 11/18/2022] Open
Abstract
In a previous study, it was demonstrated that the toxic impact of titanium dioxide nanoparticles on Escherichia coli starts at 10 ppm and is closely related to the presence of little aggregates. It was also assumed that only a part of the bacterial population is able to adapt to this stress and attempts to survive. Proteomic analyses, supported by results from metabolomics, reveal that exposure of E. coli to nano-TiO2 induces two main effects on bacterial metabolism: firstly, the up-regulation of proteins and the increase of metabolites related to energy and growth metabolism; secondly, the down-regulation of other proteins resulting in an increase of metabolites, particularly amino acids. Some proteins, e.g. chaperonin 1 or isocitrate dehydrogenase, and some metabolites, e.g. phenylalanine or valine, might be used as biomarkers of nanoparticles stress. Astonishingly, the ATP content gradually rises in relation with the nano-TiO2 concentration in the medium, indicating a dramatic release of ATP by the damaged cells. These apparently contradictory results accredit the thesis of a heterogeneity of the bacterial population. This heterogeneity is also confirmed by SEM images which show that while some bacteria are fully covered by nano-TiO2, the major part of the bacterial population remains free from nanoparticles, resulting in a difference of proteome and metabolome. The use of combined-omics has allowed to better understand the heterogeneous bacterial response to nano-TiO2 stress due to heterogeneous contacts between the protagonists under environmental conditions.
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Affiliation(s)
- Mariane Planchon
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay 91191 Gif-sur-Yvette, France
- Université Paris Diderot, Sorbonne Paris Cité, IPGP, UMR 7154, Paris Cedex 13 France
- iCEINT, International Consortium for the Environmental Implications of Nanotechnology
| | - Thibaut Léger
- Mass Spectrometry Laboratory, Institut Jacques Monod, UMR 7592, Univ Paris Diderot, CNRS, Sorbonne Paris Cité, Paris, France
| | - Olivier Spalla
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay 91191 Gif-sur-Yvette, France
- iCEINT, International Consortium for the Environmental Implications of Nanotechnology
| | - Gaspard Huber
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay 91191 Gif-sur-Yvette, France
- * E-mail: (GH); (RF)
| | - Roselyne Ferrari
- Université Paris Diderot, Sorbonne Paris Cité, IPGP, UMR 7154, Paris Cedex 13 France
- Université Paris Diderot, Sorbonne Paris Cité, LIED, UMR 8236, Paris, France
- * E-mail: (GH); (RF)
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43
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Chen T, Sheng J, Fu Y, Li M, Wang J, Jia AQ. 1H NMR-Based Global Metabolic Studies of Pseudomonas aeruginosa upon Exposure of the Quorum Sensing Inhibitor Resveratrol. J Proteome Res 2017; 16:824-830. [PMID: 28094526 DOI: 10.1021/acs.jproteome.6b00800] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Quorum sensing (QS) is a process of bacterial communication that has been a novel target for drug discovery. Pyocyanin quantification assay confirmed that resveratrol was an effective quorum sensing inhibitor (QSI) against Pseudomonas aeruginosa PAO1. In this study, the global metabolite changes of P. aeruginosa PAO1 exposed to QSI resveratrol were investigated by 1H NMR spectroscopy. A total of 40 metabolites containing amino acids, organic acid, organic amine, and energy storage compounds were identified. The changed metabolic profile indicated that resveratrol influenced pathways including oxidative stress, protein synthesis, and energy metabolism. Oxidative stress could upregulate the expression of genes related to QS in P. aeruginosa. It suggested that resveratrol could inhibit the QS systems in P. aeruginosa PAO1 by relieving oxidative stress due to its antioxidant activity. On the other hand, resveratrol could attenuate the pathogenicity of P. aeruginosa PAO1 by disturbing the TCA cycle so that anaerobic respiration could suppress the virulence because anaerobiosis could induce the loss of cytotoxicity regulated by QS in P. aeruginosa. These findings deepened our comprehending of the metabolic responses of P. aeruginosa PAO1 to resveratrol and pinpointed the possible underlying mechanism of resveratrol's inhibition effect on QS in P. aeruginosa PAO1.
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Affiliation(s)
- Tongtong Chen
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Xiao Ling Wei No. 200, Nanjing 210094, China
| | - Jiyang Sheng
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Xiao Ling Wei No. 200, Nanjing 210094, China
| | - Yonghong Fu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Xiao Ling Wei No. 200, Nanjing 210094, China
| | - Minghui Li
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Xiao Ling Wei No. 200, Nanjing 210094, China
| | - Junsong Wang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Xiao Ling Wei No. 200, Nanjing 210094, China
| | - Ai-Qun Jia
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Xiao Ling Wei No. 200, Nanjing 210094, China.,State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University , Haikou 570228, China
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44
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Cao X, Qi Y, Xu C, Yang Y, Wang J. Transcriptome and metabolome responses of Shewanella oneidensis MR-1 to methyl orange under microaerophilic and aerobic conditions. Appl Microbiol Biotechnol 2017; 101:3463-3472. [PMID: 28070664 DOI: 10.1007/s00253-016-8087-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 02/08/2023]
Abstract
Shewanella oneidensis MR-1 degrades various azo dyes under microaerophilic and anaerobic conditions, but this process is inhibited under aerobic conditions. The mechanisms underlying azo dye biodegradation and inhibition remain unknown. Therefore, we investigated metabolic and transcriptional changes in strain MR-1, which was cultured under different conditions, to elucidate these mechanisms. At the transcriptional level, genes involved in certain metabolic processes, particularly the tricarboxylic acid (TCA) cycle, amino acid biodegradation, and the electron transfer system, were significantly altered (M ≧ 2, p > 0.8 ) in the presence of methyl orange (MO). Moreover, a high concentration of dissolved oxygen heavily impacted the expression levels of genes involved in fatty acid biodegradation. Metabolome analysis revealed significant alteration (p < 0.05) in the concentrations of nine metabolites when strain MR-1 was cultured under aerobic conditions; the majority of these metabolites were closely associated with amino acid metabolism and DNA replication. Accordingly, we propose a possible pathway for MO biodegradation and discuss the most likely causes of biodegradation inhibition due to dissolved oxygen.
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Affiliation(s)
- Xinhua Cao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yueling Qi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Xu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Jun Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
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45
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Sengupta A, Sarkar D, Das P, Panja S, Parikh C, Ramanathan D, Bagley S, Datta R. Tetracycline uptake and metabolism by vetiver grass (Chrysopogon zizanioides L. Nash). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:24880-24889. [PMID: 27662856 DOI: 10.1007/s11356-016-7688-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 09/12/2016] [Indexed: 06/06/2023]
Abstract
Environmental contamination by antibiotics not only perturbs the ecological balance but also poses a risk to human health by promoting the development of multiantibiotic-resistant bacteria. This study focuses on identifying the biochemical pathways associated with tetracycline (TC) transformation/degradation in vetiver grass that has the potential to be used as a biological remediation system in TC-contaminated water sources. A hydroponic experimental setup was used with four initial TC concentrations (0, 5, 35, 75 ppm), and TC uptake was monitored over a 30-day period. Results show that TC transformation in the media occurred during the first 5 days, where a decrease in the parent compound and an increase in the concentration of the isomers such as epitetracycline (ETC) and anhyrotetracycline (ATC) occurred, and TC disappeared in 20 days in tanks with vetiver grass. However, the isomers ETC and ATC remained in the control tanks for the duration of the trial. Transformation products of TC in plant tissue were analyzed by using ultra HPLC high-resolution Orbitrap mass spectrometery (HRMS/MS), which indicates amide hydrolysis of TC in vetiver roots. Metabolic profiling revealed that glyoxylate metabolism, TCA cycle, biosynthesis of secondary metabolites, tryptophan metabolism, and inositol phosphate metabolism were impacted in vetiver root by TC treatment.
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Affiliation(s)
- Aparupa Sengupta
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Dibyendu Sarkar
- Department of Civil, Environmental and Ocean Engineering, Stevens Institute of Technology, Hoboken, NJ, USA
| | - Padmini Das
- Department of Biology, Nazareth College, Rochester, NY, USA
| | - Saumik Panja
- Department of Civil, Environmental and Ocean Engineering, Stevens Institute of Technology, Hoboken, NJ, USA
| | - Chinmayi Parikh
- New Jersey Center for Science, Technology and Mathematics, Kean University, Union, NJ, USA
| | - Dilrukshi Ramanathan
- New Jersey Center for Science, Technology and Mathematics, Kean University, Union, NJ, USA
| | - Susan Bagley
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Rupali Datta
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA.
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46
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Sarup P, Petersen SMM, Nielsen NC, Loeschcke V, Malmendal A. Mild heat treatments induce long-term changes in metabolites associated with energy metabolism in Drosophila melanogaster. Biogerontology 2016; 17:873-882. [DOI: 10.1007/s10522-016-9657-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 06/27/2016] [Indexed: 01/07/2023]
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47
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Govers SK, Gayan E, Aertsen A. Intracellular movement of protein aggregates reveals heterogeneous inactivation and resuscitation dynamics in stressed populations ofEscherichia coli. Environ Microbiol 2016; 19:511-523. [DOI: 10.1111/1462-2920.13460] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/15/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Sander K. Govers
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M S), Faculty of Bioscience Engineering; KU Leuven; Leuven Belgium
| | - Elisa Gayan
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M S), Faculty of Bioscience Engineering; KU Leuven; Leuven Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems (M S), Faculty of Bioscience Engineering; KU Leuven; Leuven Belgium
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48
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Xu Q, Liu Y, Li S, Jiang L, Huang H, Wen J. Transcriptome analysis of Rhizopus oryzae in response to xylose during fumaric acid production. Bioprocess Biosyst Eng 2016; 39:1267-80. [DOI: 10.1007/s00449-016-1605-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/04/2016] [Indexed: 12/20/2022]
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49
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Xu J, He W, Li Y, Zhang D, Zhou J, Zhang C, Li Y, Wang R, Su X. Selective colonization mechanism of Shewanella putrefaciens in dyeing wastewater outlets. RSC Adv 2016. [DOI: 10.1039/c6ra18576b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The responses ofS. putrefaciensto dyeing wastewater have been investigated using differential proteomics, metabolomics, and real-time fluorescent quantitative PCR techniques.
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Affiliation(s)
- Jiajie Xu
- School of Marine Science
- Ningbo University
- People's Republic China
- College of Engineering
- China Agricultural University
| | - Weina He
- School of Marine Science
- Ningbo University
- People's Republic China
| | - Yanyan Li
- School of Marine Science
- Ningbo University
- People's Republic China
- Department of Food Science
- Cornell University
| | - DiJun Zhang
- School of Marine Science
- Ningbo University
- People's Republic China
| | - Jun Zhou
- School of Marine Science
- Ningbo University
- People's Republic China
| | - Chundan Zhang
- School of Marine Science
- Ningbo University
- People's Republic China
| | - Ye Li
- School of Marine Science
- Ningbo University
- People's Republic China
| | - Rixin Wang
- School of Marine Science
- Ningbo University
- People's Republic China
| | - Xiurong Su
- School of Marine Science
- Ningbo University
- People's Republic China
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50
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Song Y, Zhao R, Hu Y, Hao F, Li N, Nie G, Tang H, Wang Y. Assessment of the Biological Effects of a Multifunctional Nano-Drug-Carrier and Its Encapsulated Drugs. J Proteome Res 2015; 14:5193-201. [PMID: 26531143 DOI: 10.1021/acs.jproteome.5b00513] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Polymer-nanoparticle-encapsulated doxorubicin (DOX) and paclitaxel (TAX) have the potential for novel therapeutic use against cancer in the clinic. However, the systemic biological effect of the nanoparticle material, namely, methoxypoly(ethylene glycol)-poly(lactide-co-glycolide) (mPEG-PLGA), and its encapsulated drugs have not been fully studied. We have applied NMR-based metabonomics methodology to characterize and analyze the systemic metabolic changes in mice after being exposed to mPEG-PLGA, mPEG-PLGA-encapsulated DOX and TAX (NP-D/T), and their free forms. The study revealed that mPEG-PLGA exposure only induces temporary and slight metabolic alternations and that there are detoxification effects of nanoparticle packed with D/T drugs on the heart when comparing with free-form D/T drugs. Both NP-D/T and their free forms induce a shift in energy metabolism, stimulate antioxidation pathways, and disturb the gut microbial activity of the host. However, mPEG-PLGA packaging can relieve the energy metabolism inhibition and decrease the activation of antioxidation pathways caused by D/T exposure. These findings provide a holistic insight into the biological effect of polymer nanoparticle and nanoparticle-encapsulated drugs. This study also furthers our understanding of the molecular mechanisms involved in the amelioration effects of mPEG-PLGA packaging on the toxicity of the incorporated drugs.
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Affiliation(s)
- Yipeng Song
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences , Wuhan, 430071, P. R. China
| | - Ruifang Zhao
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences , Beijing, 100190, P. R. China
| | - Yili Hu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences , Wuhan, 430071, P. R. China
| | - Fuhua Hao
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences , Wuhan, 430071, P. R. China
| | - Ning Li
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences , Wuhan, 430071, P. R. China
| | - Guangjun Nie
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, University of Chinese Academy of Sciences , Beijing, 100190, P. R. China
| | - Huiru Tang
- State Key Laboratory of Genetic Engineering, Biospectroscopy and Metabolomics, School of Life Sciences, Fudan University , Shanghai, 200433, P. R. China
| | - Yulan Wang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, University of Chinese Academy of Sciences , Wuhan, 430071, P. R. China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310058, P. R. China
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