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Huang PJ, Lin YL, Chen CH, Lin HY, Fang SC. A chloroplast sulphate transporter modulates glutathione-mediated redox cycling to regulate cell division. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39189939 DOI: 10.1111/pce.15113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/07/2024] [Accepted: 08/12/2024] [Indexed: 08/28/2024]
Abstract
Glutathione redox cycling is important for cell cycle regulation, but its mechanisms are not well understood. We previously identified a small-sized mutant, suppressor of mat3 15-1 (smt15-1) that has elevated cellular glutathione. Here, we demonstrated that SMT15 is a chloroplast sulphate transporter. Reducing expression of γ-GLUTAMYLCYSTEINE SYNTHETASE, encoding the rate-limiting enzyme required for glutathione biosynthesis, corrected the size defect of smt15-1 cells. Overexpressing GLUTATHIONE SYNTHETASE (GSH2) recapitulated the small-size phenotype of smt15-1 mutant, confirming the role of glutathione in cell division. Hence, SMT15 may regulate chloroplast sulphate concentration to modulate cellular glutathione levels. In wild-type cells, glutathione and/or thiol-containing molecules (GSH/thiol) accumulated in the cytosol at the G1 phase and decreased as cells entered the S/M phase. While the cytosolic GSH/thiol levels in the small-sized mutants, smt15-1 and GSH2 overexpressors, mirrored those of wild-type cells (accumulating during G1 and declining at early S/M phase), GSH/thiol was specifically accumulated in the basal bodies at early S/M phase in the small-sized mutants. Therefore, we propose that GSH/thiol-mediated redox signalling in the basal bodies may regulate mitotic division number in Chlamydomonas reinhardtii. Our findings suggest a new mechanism by which glutathione regulates the multiple fission cell cycle in C. reinhardtii.
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Affiliation(s)
- Pin-Jui Huang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan
| | - Yen-Ling Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chun-Han Chen
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsiang-Yin Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Su-Chiung Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan
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2
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Quintero-Yanes A, Léger L, Collignon M, Mignon J, Mayard A, Michaux C, Hallez R. Regulation of potassium uptake in Caulobacter crescentus. J Bacteriol 2024:e0010724. [PMID: 39133005 DOI: 10.1128/jb.00107-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 07/13/2024] [Indexed: 08/13/2024] Open
Abstract
Potassium (K+) is an essential physiological element determining membrane potential, intracellular pH, osmotic/turgor pressure, and protein synthesis in cells. Here, we describe the regulation of potassium uptake systems in the oligotrophic α-proteobacterium Caulobacter crescentus known as a model for asymmetric cell division. We show that C. crescentus can grow in concentrations from the micromolar to the millimolar range by mainly using two K+ transporters to maintain potassium homeostasis, the low-affinity Kup and the high-affinity Kdp uptake systems. When K+ is not limiting, we found that the kup gene is essential while kdp inactivation does not impact the growth. In contrast, kdp becomes critical but not essential and kup dispensable for growth in K+-limited environments. However, in the absence of kdp, mutations in kup were selected to improve growth in K+-depleted conditions, likely by increasing the affinity of Kup for K+. In addition, mutations in the KdpDE two-component system, which regulates kdpABCDE expression, suggest that the inner membrane sensor regulatory component KdpD mainly works as a phosphatase to limit the growth when cells reach late exponential phase. Our data therefore suggest that KdpE is phosphorylated by another non-cognate histidine kinase. On top of this, we determined the KdpE-dependent and independent K+ transcriptome. Together, our work illustrates how an oligotrophic bacterium responds to fluctuation in K+ availability.IMPORTANCEPotassium (K+) is a key metal ion involved in many essential cellular processes. Here, we show that the oligotroph Caulobacter crescentus can support growth at micromolar concentrations of K+ by mainly using two K+ uptake systems, the low-affinity Kup and the high-affinity Kdp. Using genome-wide approaches, we also determined the entire set of genes required for C. crescentus to survive at low K+ concentration as well as the full K+-dependent regulon. Finally, we found that the transcriptional regulation mediated by the KdpDE two-component system is unconventional since unlike Escherichia coli, the inner membrane sensor regulatory component KdpD seems to work rather as a phosphatase on the phosphorylated response regulator KdpE~P.
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Affiliation(s)
- Alex Quintero-Yanes
- Bacterial Cell cycle & Development (BCcD), Biology of Microorganisms Research Unit (URBM), Namur Research Institute for Life Science (NARILIS), Universite de Namur, Namur, Belgium
| | - Loïc Léger
- Bacterial Cell cycle & Development (BCcD), Biology of Microorganisms Research Unit (URBM), Namur Research Institute for Life Science (NARILIS), Universite de Namur, Namur, Belgium
| | - Madeline Collignon
- Bacterial Cell cycle & Development (BCcD), Biology of Microorganisms Research Unit (URBM), Namur Research Institute for Life Science (NARILIS), Universite de Namur, Namur, Belgium
| | - Julien Mignon
- Laboratoire de Chimie Physique des Biomolécules, UCPTS, Namur Institute of Structured Matter (NISM), Namur Research Institute for Life Sciences (NARILIS), Universite de Namur, Namur, Belgium
| | - Aurélie Mayard
- Bacterial Cell cycle & Development (BCcD), Biology of Microorganisms Research Unit (URBM), Namur Research Institute for Life Science (NARILIS), Universite de Namur, Namur, Belgium
| | - Catherine Michaux
- Laboratoire de Chimie Physique des Biomolécules, UCPTS, Namur Institute of Structured Matter (NISM), Namur Research Institute for Life Sciences (NARILIS), Universite de Namur, Namur, Belgium
| | - Régis Hallez
- Bacterial Cell cycle & Development (BCcD), Biology of Microorganisms Research Unit (URBM), Namur Research Institute for Life Science (NARILIS), Universite de Namur, Namur, Belgium
- WEL Research Institute, University of Namur, Namur, Belgium
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3
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Dinu S, Dumitrel SI, Buzatu R, Dinu DC, Popovici R, Szuhanek C, Matichescu A. New Perspectives about Relevant Natural Compounds for Current Dentistry Research. Life (Basel) 2024; 14:951. [PMID: 39202693 PMCID: PMC11355384 DOI: 10.3390/life14080951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/24/2024] [Accepted: 07/24/2024] [Indexed: 09/03/2024] Open
Abstract
Natural compounds have been used since the earliest civilizations and remain, to this day, a safer alternative for treating various dental problems. These present antimicrobial, anti-inflammatory, antioxidant, analgesic, and antimutagenic effects, making them useful in the prophylactic and curative treatment of various oral diseases such as infections, gingivitis, periodontitis, and even cancer. Due to the high incidence of unpleasant adverse reactions to synthetic compounds, natural products tend to gradually replace conventional treatment, as they can be just as potent and cause fewer, milder adverse effects. Researchers use several methods to measure the effectiveness and safety profile of these compounds, and employing standard techniques also contributes to progress across all medical disciplines.
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Affiliation(s)
- Stefania Dinu
- Department of Pedodontics, Faculty of Dental Medicine, Victor Babes University of Medicine and Pharmacy, 9 No., Revolutiei 1989 Bv., 300041 Timisoara, Romania;
- Pediatric Dentistry Research Center, Faculty of Dental Medicine, Victor Babes University of Medicine and Pharmacy, 9 No., Revolutiei 1989 Bv., 300041 Timisoara, Romania
| | - Stefania-Irina Dumitrel
- Department of Toxicology, Drug Industry, Management and Legislation, Faculty of Pharmacy, Victor Babes University of Medicine and Pharmacy, 2nd Eftimie Murgu Sq., 30004 Timisoara, Romania;
| | - Roxana Buzatu
- Department of Dental Aesthetics, Faculty of Dental Medicine, Victor Babes University of Medicine and Pharmacy, 9 No., Revolutiei 1989 Bv., 300041 Timisoara, Romania
| | - Dorin Cristian Dinu
- Family Dental Clinic, Private Practice, 24 Budapesta Street, 307160 Dumbravita, Romania;
| | - Ramona Popovici
- Department of Management, Legislation and Communication in Dentistry, Faculty of Dental Medicine, Victor Babes University of Medicine and Pharmacy, 9 No., Revolutiei 1989 Bv., 300041 Timisoara, Romania;
| | - Camelia Szuhanek
- Department of Orthodontics, Faculty of Dental Medicine, Victor Babes University of Medicine and Pharmacy, 9 No., Revolutiei 1989 Bv., 300041 Timisoara, Romania;
| | - Anamaria Matichescu
- Department of Preventive, Community Dentistry and Oral Health, Faculty of Dental Medicine, Victor Babes University of Medicine and Pharmacy, 14A Tudor Vladimirescu Ave., 300173 Timisoara, Romania;
- Translational and Experimental Clinical Research Centre in Oral Health, Victor Babes University of Medicine and Pharmacy, 14A Tudor Vladimirescu Ave., 300173 Timisoara, Romania
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4
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Kaczmarczyk A, van Vliet S, Jakob RP, Teixeira RD, Scheidat I, Reinders A, Klotz A, Maier T, Jenal U. A genetically encoded biosensor to monitor dynamic changes of c-di-GMP with high temporal resolution. Nat Commun 2024; 15:3920. [PMID: 38724508 PMCID: PMC11082216 DOI: 10.1038/s41467-024-48295-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
Monitoring changes of signaling molecules and metabolites with high temporal resolution is key to understanding dynamic biological systems. Here, we use directed evolution to develop a genetically encoded ratiometric biosensor for c-di-GMP, a ubiquitous bacterial second messenger regulating important biological processes like motility, surface attachment, virulence and persistence. The resulting biosensor, cdGreen2, faithfully tracks c-di-GMP in single cells and with high temporal resolution over extended imaging times, making it possible to resolve regulatory networks driving bimodal developmental programs in different bacterial model organisms. We further adopt cdGreen2 as a simple tool for in vitro studies, facilitating high-throughput screens for compounds interfering with c-di-GMP signaling and biofilm formation. The sensitivity and versatility of cdGreen2 could help reveal c-di-GMP dynamics in a broad range of microorganisms with high temporal resolution. Its design principles could also serve as a blueprint for the development of similar, orthogonal biosensors for other signaling molecules, metabolites and antibiotics.
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Affiliation(s)
- Andreas Kaczmarczyk
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
| | - Simon van Vliet
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Roman Peter Jakob
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | | | - Inga Scheidat
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Alberto Reinders
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Alexander Klotz
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Timm Maier
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Urs Jenal
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
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5
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Fang M, Lei Z, Ruilin M, Jing W, Leqiang D. High temperature stress induced oxidative stress, gut inflammation and disordered metabolome and microbiome in tsinling lenok trout. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 266:115607. [PMID: 37862746 DOI: 10.1016/j.ecoenv.2023.115607] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/09/2023] [Accepted: 10/14/2023] [Indexed: 10/22/2023]
Abstract
Tsinling lenok trout (Brachymystax lenok tsinlingensis Li) is a species of cold-water salmon that faces serious challenges due to global warming. High temperature stress has been found to damage the gut integrity of cold-water fish, impacting their growth and immunity. However, limited research exists on the causal relationship between gut microbial disturbance and metabolic dysfunction in cold-water fish induced by high temperature stress. To address this gap, we conducted a study to investigate the effects of high temperature stress (24 °C) on the gut tissue structure, antioxidant capacity, gut microorganisms, and metabolome reactions of tsinling lenok trout. Our analysis using 16 S rDNA gene sequencing revealed significant changes in the gut microbial composition and metabolic profile. Specifically, the abundance of Firmicutes and Gemmatimonadetes decreased significantly with increasing temperature, while the abundance of Bacteroidetes increased significantly. Metabolic analysis revealed a significant decrease in the abundance of glutathione, which is synthesized from glutamate and glycine, under high temperature stress. Additionally, there was a notable reduction in the levels of adenosine, inosine, xanthine, guanosine, and deoxyguanosine, which are essential for DNA/RNA synthesis. Conversely, there was a significant increase in the abundance of D-glucose 6 P. Furthermore, high temperature stress adversely affects intestinal structure and barrier function. Our findings provide valuable insights into the mechanism of high temperature stress in cold-water fish and serve as a foundation for future research aimed at mitigating the decline in production performance caused by such stress.
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Affiliation(s)
- M Fang
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, South Xihe Road, Qinzhou, Tianshui 741000, Gansu, PR China.
| | - Z Lei
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, South Xihe Road, Qinzhou, Tianshui 741000, Gansu, PR China
| | - M Ruilin
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, South Xihe Road, Qinzhou, Tianshui 741000, Gansu, PR China
| | - W Jing
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, South Xihe Road, Qinzhou, Tianshui 741000, Gansu, PR China
| | - D Leqiang
- Key Laboratory of Resource Utilization of Agricultural Solid Waste in Gansu Province, Tianshui Normal University, South Xihe Road, Qinzhou, Tianshui 741000, Gansu, PR China
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6
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Jia H, Zhao Y, Deng H, Yu H, Ge C, Li J. Integrated microbiome and multi-omics analysis reveal the molecular mechanisms of Eisenia fetida in response to biochar-derived dissolved and particulate matters. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132422. [PMID: 37657322 DOI: 10.1016/j.jhazmat.2023.132422] [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: 06/17/2023] [Revised: 08/17/2023] [Accepted: 08/26/2023] [Indexed: 09/03/2023]
Abstract
At present, most ecotoxicological studies are still confined to focusing on the harmful effects of biochar itself on soil fauna. However, the potential ecotoxicity of different components separated from biochar to terrestrial invertebrates remains poorly understood. In this study, the dissolved matter (DM) and particulate matter (PM) were separated from biochar (BC) and then introduced into the soil-earthworm system to investigate the response mechanism of earthworms at the molecular level. The results showed that BC and DM exposure caused an increase in the abundance of Proteobacteria in the cast bacterial community, suggesting the dysbiosis of intestinal microbiota. It was also observed that the cast bacterial communities were more sensitive to DM exposure than PM exposure. Transcriptomic analysis showed that BC and DM exposure induced significant enrichment of functional pathways related to infectious and neuropathic diseases. Metabolomic profiling manifested that DM exposure caused metabolic dysfunction, antioxidant and detoxification abilities recession. Furthermore, significant differences in the responses of earthworms at transcriptomic and metabolic levels confirmed that DM exhibited greater ecotoxicity than PM. This study highlighted the significant contributions of dissolved matter to the ecotoxicity of biochar from the perspective of transcriptomic and metabolomic profiles.
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Affiliation(s)
- Huiting Jia
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou 570228, China; Key Laboratory of Environmental Toxicology, Hainan University, Haikou 570228, China; College of Ecology and Environment, Hainan University, Renmin Road, Haikou 570228, China
| | - Yuanyuan Zhao
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou 570228, China; Key Laboratory of Environmental Toxicology, Hainan University, Haikou 570228, China; College of Ecology and Environment, Hainan University, Renmin Road, Haikou 570228, China
| | - Hui Deng
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou 570228, China; Key Laboratory of Environmental Toxicology, Hainan University, Haikou 570228, China; College of Ecology and Environment, Hainan University, Renmin Road, Haikou 570228, China.
| | - Huamei Yu
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou 570228, China; Key Laboratory of Environmental Toxicology, Hainan University, Haikou 570228, China; College of Ecology and Environment, Hainan University, Renmin Road, Haikou 570228, China
| | - Chengjun Ge
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou 570228, China; Key Laboratory of Environmental Toxicology, Hainan University, Haikou 570228, China; College of Ecology and Environment, Hainan University, Renmin Road, Haikou 570228, China.
| | - Jiatong Li
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou 570228, China; Key Laboratory of Environmental Toxicology, Hainan University, Haikou 570228, China; College of Ecology and Environment, Hainan University, Renmin Road, Haikou 570228, China.
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7
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Soultanas P, Janniere L. The metabolic control of DNA replication: mechanism and function. Open Biol 2023; 13:230220. [PMID: 37582405 PMCID: PMC10427196 DOI: 10.1098/rsob.230220] [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: 07/11/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023] Open
Abstract
Metabolism and DNA replication are the two most fundamental biological functions in life. The catabolic branch of metabolism breaks down nutrients to produce energy and precursors used by the anabolic branch of metabolism to synthesize macromolecules. DNA replication consumes energy and precursors for faithfully copying genomes, propagating the genetic material from generation to generation. We have exquisite understanding of the mechanisms that underpin and regulate these two biological functions. However, the molecular mechanism coordinating replication to metabolism and its biological function remains mostly unknown. Understanding how and why living organisms respond to fluctuating nutritional stimuli through cell-cycle dynamic changes and reproducibly and distinctly temporalize DNA synthesis in a wide-range of growth conditions is important, with wider implications across all domains of life. After summarizing the seminal studies that founded the concept of the metabolic control of replication, we review data linking metabolism to replication from bacteria to humans. Molecular insights underpinning these links are then presented to propose that the metabolic control of replication uses signalling systems gearing metabolome homeostasis to orchestrate replication temporalization. The remarkable replication phenotypes found in mutants of this control highlight its importance in replication regulation and potentially genetic stability and tumorigenesis.
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Affiliation(s)
- Panos Soultanas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Laurent Janniere
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057 Evry, France
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8
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Singh U, Alsuhaymi S, Al-Nemi R, Emwas AH, Jaremko M. Compound-Specific 1D 1H NMR Pulse Sequence Selection for Metabolomics Analyses. ACS OMEGA 2023; 8:23651-23663. [PMID: 37426221 PMCID: PMC10324067 DOI: 10.1021/acsomega.3c01688] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/13/2023] [Indexed: 07/11/2023]
Abstract
NMR-based metabolomics approaches have been used in a wide range of applications, for example, with medical, plant, and marine samples. One-dimensional (1D) 1H NMR is routinely used to find out biomarkers in biofluids such as urine, blood plasma, and serum. To mimic biological conditions, most NMR studies have been carried out in an aqueous solution where the high intensity of the water peak is a major problem in obtaining a meaningful spectrum. Different methods have been used to suppress the water signal, including 1D Carr-Purcell-Meiboom-Gill (CPMG) presat, consisting of a T2 filter to suppress macromolecule signals and reduce the humped curve in the spectrum. 1D nuclear Overhauser enhancement spectroscopy (NOESY) is another method for water suppression that is used routinely in plant samples with fewer macromolecules than in biofluid samples. Other common 1D 1H NMR methods such as 1D 1H presat and 1D 1H ES have simple pulse sequences; their acquisition parameters can be set easily. The proton with presat has just one pulse and the presat block causes water suppression, while other 1D 1H NMR methods including those mentioned above have more pulses. However, it is not well known in metabolomics studies because it is used only occasionally and in a few types of samples by metabolomics experts. Another effective method is excitation sculpting to suppress water. Herein, we evaluate the effect of method selection on signal intensities of commonly detected metabolites. Different classes of samples including biofluid, plant, and marine samples were investigated, and recommendations on the advantages and limitations of each method are presented.
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Affiliation(s)
- Upendra Singh
- Smart-Health
Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological
and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah 23955-6900, Saudi
Arabia
| | - Shuruq Alsuhaymi
- Smart-Health
Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological
and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah 23955-6900, Saudi
Arabia
| | - Ruba Al-Nemi
- Smart-Health
Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological
and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah 23955-6900, Saudi
Arabia
| | - Abdul-Hamid Emwas
- Core
Lab of NMR, King Abdullah University of
Science and Technology (KAUST), Thuwal, Makkah 23955-6900, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health
Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological
and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah 23955-6900, Saudi
Arabia
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9
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Farke N, Schramm T, Verhülsdonk A, Rapp J, Link H. Systematic analysis of in-source modifications of primary metabolites during flow-injection time-of-flight mass spectrometry. Anal Biochem 2023; 664:115036. [PMID: 36627043 PMCID: PMC9902335 DOI: 10.1016/j.ab.2023.115036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/09/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
Flow-injection mass spectrometry (FI-MS) enables metabolomics studies with a very high sample-throughput. However, FI-MS is prone to in-source modifications of analytes because samples are directly injected into the electrospray ionization source of a mass spectrometer without prior chromatographic separation. Here, we spiked authentic standards of 160 primary metabolites individually into an Escherichia coli metabolite extract and measured the thus derived 160 spike-in samples by FI-MS. Our results demonstrate that FI-MS can capture a wide range of chemically diverse analytes within 30 s measurement time. However, the data also revealed extensive in-source modifications. Across all 160 spike-in samples, we identified significant increases of 11,013 ion peaks in positive and negative mode combined. To explain these unknown m/z features, we connected them to the m/z feature of the (de-)protonated metabolite using information about mass differences and MS2 spectra. This resulted in networks that explained on average 49 % of all significant features. The networks showed that a single metabolite undergoes compound specific and often sequential in-source modifications like adductions, chemical reactions, and fragmentations. Our results show that FI-MS generates complex MS1 spectra, which leads to an overestimation of significant features, but neutral losses and MS2 spectra explain many of these features.
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Affiliation(s)
| | | | | | | | - Hannes Link
- Bacterial Metabolomics, CMFI, University Tübingen, Auf der Morgenstelle 24, 7206, Tübingen, Germany.
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10
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Xue P, Liu X, Shi X, Yuan H, Wang J, Zhang J, He Z. Stereoselective accumulation and biotransformation of chiral fungicide epoxiconazole and oxidative stress, detoxification, and endogenous metabolic disturbance in earthworm (Eisenia foetida). THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159932. [PMID: 36343825 DOI: 10.1016/j.scitotenv.2022.159932] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/29/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
>80 % of applied pesticides in agriculture will enter the soil and be exposed to soil animals. Little is known about the stereoselective metabolic effects of epoxiconazole (EPO) on soil animals. In this study, EPO-mediated stereoselective enrichment, biotransformation, oxidative stress, detoxification, and global metabolic profiles in earthworms were investigated by exposure to EPO and its enantiomers at 1 mg/kg and 10 mg/kg doses. Preferential enrichment of (-)-EPO was observed, and the five transformation products (TPs) exhibited the chemically specific stereoselective accumulation with inconsistent configurations. Biochemical markers related to reactive oxygen species (ROS) and detoxification (·OH- content, SOD, CAT, GST, and CYP450 enzymes) showed a significant stereoselective activation overall at the low-level exposure (p-value <0.05). Based on untargeted metabolomic analysis, the steroid biosynthesis and ROS-related biotransformation, glutathione metabolism, TCA cycle, amino acid metabolism, purine and pyrimidine metabolism of earthworms were significantly interfered with by EPO and its enantiomer exposure. More pronounced stereoselectivity was observed at the level of the global metabolic profile, while comparable levels of metabolic perturbations were identified at the individual metabolite level. This study provides novel insights into the stereoselective effects of the chiral fungicide EPO, and valuable evidence for soil environmental risk assessments.
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Affiliation(s)
- Pengfei Xue
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Xiaowei Liu
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Xiaomeng Shi
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Haiyue Yuan
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Jiafu Wang
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Jingran Zhang
- SCIEX, Analytical Instrument Trading Co., Ltd., Beijing 100015, China
| | - Zeying He
- Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
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11
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Ye C, Zhang S, Zhang D, Shen Y, Wang Z, Wang H, Ren J, Jiang XD, Du J, Shang R, Wang G. Engineering J-aggregates for NIR-induced meso-CF3-BODIPY nanoparticles by activated apoptosis mechanism in photothermal therapy. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2023.108223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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12
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Peptidoglycan recycling mediated by an ABC transporter in the plant pathogen Agrobacterium tumefaciens. Nat Commun 2022; 13:7927. [PMID: 36566216 PMCID: PMC9790009 DOI: 10.1038/s41467-022-35607-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 12/13/2022] [Indexed: 12/25/2022] Open
Abstract
During growth and division, the bacterial cell wall peptidoglycan (PG) is remodelled, resulting in the liberation of PG muropeptides which are typically reinternalized and recycled. Bacteria belonging to the Rhizobiales and Rhodobacterales orders of the Alphaproteobacteria lack the muropeptide transporter AmpG, despite having other key PG recycling enzymes. Here, we show that an alternative transporter, YejBEF-YepA, takes over this role in the Rhizobiales phytopathogen Agrobacterium tumefaciens. Muropeptide import by YejBEF-YepA governs expression of the β-lactamase AmpC in A. tumefaciens, contributing to β-lactam resistance. However, we show that the absence of YejBEF-YepA causes severe cell wall defects that go far beyond lowered AmpC activity. Thus, contrary to previously established Gram-negative models, PG recycling is vital for cell wall integrity in A. tumefaciens. YepA is widespread in the Rhizobiales and Rhodobacterales, suggesting that YejBEF-YepA-mediated PG recycling could represent an important but overlooked aspect of cell wall biology in these bacteria.
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Potential and Metabolic Pathways of Eugenol in the Management of Xanthomonas perforans, a Pathogen of Bacterial Spot of Tomato. Int J Mol Sci 2022; 23:ijms232314648. [PMID: 36498976 PMCID: PMC9739100 DOI: 10.3390/ijms232314648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022] Open
Abstract
Bacterial spot of tomato continues to pose a significant problem to tomato production worldwide. In Florida, bacterial spot of tomato caused by Xanthomonas perforans is one of the most important diseases responsible for tomato yield loss. This disease is difficult to control, and new strategies are continually being investigated to combat the devastating effect of this disease. Recent efforts focusing on essential oils based on small molecules have spurred interests in the utilization of this class of chemicals for disease management. In this study, we evaluated the efficacy of eugenol for the management of bacterial spot of tomato caused by X. perforans. In the greenhouse experiments, eugenol applied as a foliar spray significantly (p < 0.5) reduced bacterial spot disease compared to the untreated control. In the field experiments, the area under the disease progress curve (AUDPC) was significantly (p < 0.5) lower in the plots treated with eugenol or eugenol combined with the surfactant Cohere than in the untreated control plots, and it was comparable to the copper-based treatments. To provide additional insights into the possible pathways of eugenol activities, we applied a liquid chromatography mass spectrometry (LC-MS)-based metabolomic study using a thermo Q-Exactive orbitrap mass spectrometer with Dionex ultra high-performance liquid chromatography (UHPLC) on X. perforans strain 91−118 treated with eugenol. Our results showed that eugenol affected metabolite production in multiple pathways critical to bacterial survival. For example, treatment of cells with eugenol resulted in the downregulation of the glutathione metabolism pathway and associated metabolites, except for 5-oxoproline, which accumulation is known to be toxic to living cells. While the peaks corresponding to the putatively identified sarmentosin showed the most significant impact and reduced in response to eugenol treatment, branched-chain amino acids, such as L-isoleucine, increased in production, suggesting that eugenol may not negatively affect the protein biosynthesis pathways. The results from our study demonstrated the efficacy of eugenol in the management of bacterial spot of tomato under greenhouse and field conditions and identified multiple pathways that are targeted.
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14
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Horemans S, Pitoulias M, Holland A, Pateau E, Lechaplais C, Ekaterina D, Perret A, Soultanas P, Janniere L. Pyruvate kinase, a metabolic sensor powering glycolysis, drives the metabolic control of DNA replication. BMC Biol 2022; 20:87. [PMID: 35418203 PMCID: PMC9009071 DOI: 10.1186/s12915-022-01278-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/11/2022] [Indexed: 12/04/2022] Open
Abstract
Background In all living organisms, DNA replication is exquisitely regulated in a wide range of growth conditions to achieve timely and accurate genome duplication prior to cell division. Failures in this regulation cause DNA damage with potentially disastrous consequences for cell viability and human health, including cancer. To cope with these threats, cells tightly control replication initiation using well-known mechanisms. They also couple DNA synthesis to nutrient richness and growth rate through a poorly understood process thought to involve central carbon metabolism. One such process may involve the cross-species conserved pyruvate kinase (PykA) which catalyzes the last reaction of glycolysis. Here we have investigated the role of PykA in regulating DNA replication in the model system Bacillus subtilis. Results On analysing mutants of the catalytic (Cat) and C-terminal (PEPut) domains of B. subtilis PykA we found replication phenotypes in conditions where PykA is dispensable for growth. These phenotypes are independent from the effect of mutations on PykA catalytic activity and are not associated with significant changes in the metabolome. PEPut operates as a nutrient-dependent inhibitor of initiation while Cat acts as a stimulator of replication fork speed. Disruption of either PEPut or Cat replication function dramatically impacted the cell cycle and replication timing even in cells fully proficient in known replication control functions. In vitro, PykA modulates activities of enzymes essential for replication initiation and elongation via functional interactions. Additional experiments showed that PEPut regulates PykA activity and that Cat and PEPut determinants important for PykA catalytic activity regulation are also important for PykA-driven replication functions. Conclusions We infer from our findings that PykA typifies a new family of cross-species replication control regulators that drive the metabolic control of replication through a mechanism involving regulatory determinants of PykA catalytic activity. As disruption of PykA replication functions causes dramatic replication defects, we suggest that dysfunctions in this new family of universal replication regulators may pave the path to genetic instability and carcinogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01278-3.
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Affiliation(s)
- Steff Horemans
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Matthaios Pitoulias
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Alexandria Holland
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Emilie Pateau
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Christophe Lechaplais
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Dariy Ekaterina
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Alain Perret
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Panos Soultanas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Laurent Janniere
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France.
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15
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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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16
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Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research. Nat Methods 2021; 18:733-746. [PMID: 33972782 DOI: 10.1038/s41592-021-01116-4] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/12/2021] [Indexed: 02/03/2023]
Abstract
Ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS) variants currently represent the best tools to tackle the challenges of complexity and lack of comprehensive coverage of the metabolome. UHPLC offers flexible and efficient separation coupled with high-sensitivity detection via HRMS, allowing for the detection and identification of a broad range of metabolites. Here we discuss current common strategies for UHPLC-HRMS-based metabolomics, with a focus on expanding metabolome coverage.
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17
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Maertens L, Cherry P, Tilquin F, Van Houdt R, Matroule JY. Environmental Conditions Modulate the Transcriptomic Response of Both Caulobacter crescentus Morphotypes to Cu Stress. Microorganisms 2021; 9:1116. [PMID: 34064119 PMCID: PMC8224329 DOI: 10.3390/microorganisms9061116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/13/2022] Open
Abstract
Bacteria encounter elevated copper (Cu) concentrations in multiple environments, varying from mining wastes to antimicrobial applications of copper. As the role of the environment in the bacterial response to Cu ion exposure remains elusive, we used a tagRNA-seq approach to elucidate the disparate responses of two morphotypes of Caulobacter crescentus NA1000 to moderate Cu stress in a complex rich (PYE) medium and a defined poor (M2G) medium. The transcriptome was more responsive in M2G, where we observed an extensive oxidative stress response and reconfiguration of the proteome, as well as the induction of metal resistance clusters. In PYE, little evidence was found for an oxidative stress response, but several transport systems were differentially expressed, and an increased need for histidine was apparent. These results show that the Cu stress response is strongly dependent on the cellular environment. In addition, induction of the extracytoplasmic function sigma factor SigF and its regulon was shared by the Cu stress responses in both media, and its central role was confirmed by the phenotypic screening of a sigF::Tn5 mutant. In both media, stalked cells were more responsive to Cu stress than swarmer cells, and a stronger basal expression of several cell protection systems was noted, indicating that the swarmer cell is inherently more Cu resistant. Our approach also allowed for detecting several new transcription start sites, putatively indicating small regulatory RNAs, and additional levels of Cu-responsive regulation.
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Affiliation(s)
- Laurens Maertens
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; (L.M.); (R.V.H.)
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium; (P.C.); (F.T.)
| | - Pauline Cherry
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium; (P.C.); (F.T.)
| | - Françoise Tilquin
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium; (P.C.); (F.T.)
| | - Rob Van Houdt
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; (L.M.); (R.V.H.)
| | - Jean-Yves Matroule
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium; (P.C.); (F.T.)
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18
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Schroeder K, Jonas K. The Protein Quality Control Network in Caulobacter crescentus. Front Mol Biosci 2021; 8:682967. [PMID: 33996917 PMCID: PMC8119881 DOI: 10.3389/fmolb.2021.682967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/08/2021] [Indexed: 11/13/2022] Open
Abstract
The asymmetric life cycle of Caulobacter crescentus has provided a model in which to study how protein quality control (PQC) networks interface with cell cycle and developmental processes, and how the functions of these systems change during exposure to stress. As in most bacteria, the PQC network of Caulobacter contains highly conserved ATP-dependent chaperones and proteases as well as more specialized holdases. During growth in optimal conditions, these systems support a regulated circuit of protein synthesis and degradation that drives cell differentiation and cell cycle progression. When stress conditions threaten the proteome, most components of the Caulobacter proteostasis network are upregulated and switch to survival functions that prevent, revert, and remove protein damage, while simultaneously pausing the cell cycle in order to regain protein homeostasis. The specialized physiology of Caulobacter influences how it copes with proteotoxic stress, such as in the global management of damaged proteins during recovery as well as in cell type-specific stress responses. Our mini-review highlights the discoveries that have been made in how Caulobacter utilizes its PQC network for regulating its life cycle under optimal and proteotoxic stress conditions, and discusses open research questions in this model.
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Affiliation(s)
- Kristen Schroeder
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Kristina Jonas
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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19
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Zinatullina KM, Kasaikina OT, Khrameeva NP, Indeykina MI, Kononikhin AS. Interaction between Glutathione and Resveratrol in the Presence of Hydrogen Peroxide: A Kinetic Model. KINETICS AND CATALYSIS 2021. [DOI: 10.1134/s0023158421020130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Ledermann R, Emmenegger B, Couzigou JM, Zamboni N, Kiefer P, Vorholt JA, Fischer HM. Bradyrhizobium diazoefficiens Requires Chemical Chaperones To Cope with Osmotic Stress during Soybean Infection. mBio 2021; 12:e00390-21. [PMID: 33785618 PMCID: PMC8092242 DOI: 10.1128/mbio.00390-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 01/24/2023] Open
Abstract
When engaging in symbiosis with legume hosts, rhizobia are confronted with environmental changes, including nutrient availability and stress exposure. Genetic circuits allow responding to these environmental stimuli to optimize physiological adaptations during the switch from the free-living to the symbiotic life style. A pivotal regulatory system of the nitrogen-fixing soybean endosymbiont Bradyrhizobium diazoefficiens for efficient symbiosis is the general stress response (GSR), which relies on the alternative sigma factor σEcfG However, the GSR-controlled process required for symbiosis has not been identified. Here, we demonstrate that biosynthesis of trehalose is under GSR control, and mutants lacking the respective biosynthetic genes otsA and/or otsB phenocopy GSR-deficient mutants under symbiotic and selected free-living stress conditions. The role of trehalose as a cytoplasmic chemical chaperone and stress protectant can be functionally replaced in an otsA or otsB mutant by introducing heterologous genetic pathways for biosynthesis of the chemically unrelated compatible solutes glycine betaine and (hydroxy)ectoine. Alternatively, uptake of exogenously provided trehalose also restores efficient symbiosis and tolerance to hyperosmotic and hyperionic stress of otsA mutants. Hence, elevated cytoplasmic trehalose levels resulting from GSR-controlled biosynthesis are crucial for B. diazoefficiens cells to overcome adverse conditions during early stages of host infection and ensure synchronization with root nodule development.IMPORTANCE The Bradyrhizobium-soybean symbiosis is of great agricultural significance and serves as a model system for fundamental research in bacterium-plant interactions. While detailed molecular insight is available about mutual recognition and early nodule organogenesis, our understanding of the host-imposed conditions and the physiology of infecting rhizobia during the transition from a free-living state in the rhizosphere to endosymbiotic bacteroids is currently limited. In this study, we show that the requirement of the rhizobial general stress response (GSR) during host infection is attributable to GSR-controlled biosynthesis of trehalose. Specifically, trehalose is crucial for an efficient symbiosis by acting as a chemical chaperone to protect rhizobia from osmostress during host infection.
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Affiliation(s)
| | | | | | - Nicola Zamboni
- ETH Zurich, Institute of Molecular Systems Biology, Zurich, Switzerland
| | - Patrick Kiefer
- ETH Zurich, Institute of Microbiology, Zurich, Switzerland
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21
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When the metabolism meets the cell cycle in bacteria. Curr Opin Microbiol 2021; 60:104-113. [PMID: 33677348 DOI: 10.1016/j.mib.2021.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/20/2022]
Abstract
Nutrients availability is the sinews of the war for single microbial cells, driving growth and cell cycle progression. Therefore, coordinating cellular processes with nutrients availability is crucial, not only to survive upon famine or fluctuating conditions but also to rapidly thrive and colonize plentiful environments. While metabolism is traditionally seen as a set of chemical reactions taking place in cells to extract energy and produce building blocks from available nutrients, numerous connections between metabolic pathways and cell cycle phases have been documented. The few regulatory systems described at the molecular levels show that regulation is mediated either by a second messenger molecule or by a metabolite and/or a metabolic enzyme. In the latter case, a secondary moonlighting regulatory function evolved independently of the primary catalytic function of the enzyme. In this review, we summarize our current understanding of the complex cross-talks between metabolism and cell cycle in bacteria.
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22
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Zhang Y, Gao B, Valdiviez L, Zhu C, Gallagher T, Whiteson K, Fiehn O. Comparing Stable Isotope Enrichment by Gas Chromatography with Time-of-Flight, Quadrupole Time-of-Flight, and Quadrupole Mass Spectrometry. Anal Chem 2021; 93:2174-2182. [PMID: 33434014 PMCID: PMC10782559 DOI: 10.1021/acs.analchem.0c04013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Stable isotope tracers are applied for in vivo and in vitro studies to reveal the activity of enzymes and intracellular metabolic pathways. Most often, such tracers are used with gas chromatography coupled to mass spectrometry (GC-MS) owing to its ease of operation and reproducible mass spectral databases. Differences in isotope tracer performance of the classic GC-quadrupole MS instrument and newer time-of-flight instruments are not well studied. Here, we used three commercially available instruments for the analysis of identical samples from a stable isotope labeling study that used [U-13C6] d-glucose to investigate the metabolism of the bacterium Rothia mucilaginosa with respect to 29 amino acids and hydroxyl acids involved in primary metabolism. The prokaryote R. mucilaginosa belongs to the family of Micrococcaceae and is present and metabolically active in the airways and sputum of cystic fibrosis patients. Overall, all three GC-MS instruments (low-resolution GC-SQ MS, low-resolution GC-TOF MS, and high-resolution GC-QTOF MS) can be used to perform stable isotope tracing studies for glycolytic intermediates, tricarboxylic acid (TCA) metabolites, and amino acids, yielding similar biological results, with high-resolution GC-QTOF MS offering additional capabilities to identify the chemical structures of unknown compounds that might show significant isotope enrichments in biological studies.
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Affiliation(s)
- Ying Zhang
- West Coast Metabolomics Center, University of California, Davis, 95616, CA, USA
- Department of Chemistry, University of California, Davis, 95616, CA, USA
| | - Bei Gao
- Department of Medicine, University of California, San Diego, San Diego, 92093, CA, USA
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Luis Valdiviez
- West Coast Metabolomics Center, University of California, Davis, 95616, CA, USA
| | - Chao Zhu
- College of Medicine & Nursing, Dezhou University, De Zhou, Shandong, 253023, China
| | - Tara Gallagher
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Katrine Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, 95616, CA, USA
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23
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Zhang LJ, Qian L, Ding LY, Wang L, Wong MH, Tao HC. Ecological and toxicological assessments of anthropogenic contaminants based on environmental metabolomics. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2021; 5:100081. [PMID: 36158612 PMCID: PMC9488080 DOI: 10.1016/j.ese.2021.100081] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/06/2021] [Accepted: 01/23/2021] [Indexed: 05/02/2023]
Abstract
There has long been a great concern with growing anthropogenic contaminants and their ecological and toxicological effects on living organisms and the surrounding environment for decades. Metabolomics, a functional readout of cellular activity, can capture organismal responses to various contaminant-related stressors, acquiring direct signatures to illustrate the environmental behaviours of anthropogenic contaminants better. This review entails the application of metabolomics to profile metabolic responses of environmental organisms, e.g. animals (rodents, fish, crustacean and earthworms) and microorganisms (bacteria, yeast and microalgae) to different anthropogenic contaminants, including heavy metals, nanomaterials, pesticides, pharmaceutical and personal products, persistent organic pollutants, and assesses their ecotoxicological impacts with regard to literature published in the recent five years. Contaminant-induced metabolism alteration and up/down-regulation of metabolic pathways are revealed in typical organisms. The obtained insights of variations in global metabolism provide a distinct understanding of how anthropogenic contaminants exert influences on specific metabolic pathways on living organisms. Thus with a novel ecotechnique of environmental metabolomics, risk assessments of anthropogenic contaminants are profoundly demonstrated.
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Affiliation(s)
- Li-Juan Zhang
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Lu Qian
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Ling-Yun Ding
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Lei Wang
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Ming Hung Wong
- Consortium on Health, Environment, Education and Research (CHEER), Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong, China
| | - Hu-Chun Tao
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
- Corresponding author.
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24
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Shyp V, Dubey BN, Böhm R, Hartl J, Nesper J, Vorholt JA, Hiller S, Schirmer T, Jenal U. Reciprocal growth control by competitive binding of nucleotide second messengers to a metabolic switch in Caulobacter crescentus. Nat Microbiol 2020; 6:59-72. [PMID: 33168988 DOI: 10.1038/s41564-020-00809-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 10/02/2020] [Indexed: 12/13/2022]
Abstract
Bacteria use small signalling molecules such as (p)ppGpp or c-di-GMP to tune their physiology in response to environmental changes. It remains unclear whether these regulatory networks operate independently or whether they interact to optimize bacterial growth and survival. We report that (p)ppGpp and c-di-GMP reciprocally regulate the growth of Caulobacter crescentus by converging on a single small-molecule-binding protein, SmbA. While c-di-GMP binding inhibits SmbA, (p)ppGpp competes for the same binding site to sustain SmbA activity. We demonstrate that (p)ppGpp specifically promotes Caulobacter growth on glucose, whereas c-di-GMP inhibits glucose consumption. We find that SmbA contributes to this metabolic switch and promotes growth on glucose by quenching the associated redox stress. The identification of an effector protein that acts as a central regulatory hub for two global second messengers opens up future studies on specific crosstalk between small-molecule-based regulatory networks.
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Affiliation(s)
| | | | - Raphael Böhm
- Biozentrum, University of Basel, Basel, Switzerland
| | - Johannes Hartl
- Institute of Microbiology, ETH Zurich, Zürich, Switzerland
| | - Jutta Nesper
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | | | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland.
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Xu W, Lin J, Gao M, Chen Y, Cao J, Pu J, Huang L, Zhao J, Qian K. Rapid Computer-Aided Diagnosis of Stroke by Serum Metabolic Fingerprint Based Multi-Modal Recognition. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2002021. [PMID: 33173737 PMCID: PMC7610260 DOI: 10.1002/advs.202002021] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/30/2020] [Indexed: 05/07/2023]
Abstract
Stroke is a leading cause of mortality and disability worldwide, expected to result in 61 million disability-adjusted life-years in 2020. Rapid diagnostics is the core of stroke management for early prevention and medical treatment. Serum metabolic fingerprints (SMFs) reflect underlying disease progression, predictive of patient phenotypes. Deep learning (DL) encoding SMFs with clinical indexes outperforms single biomarkers, while posing challenges with poor prediction to interpret by feature selection. Herein, rapid computer-aided diagnosis of stroke is performed using SMF based multi-modal recognition by DL, to combine adaptive machine learning with a novel feature selection approach. SMFs are extracted by nano-assisted laser desorption/ionization mass spectrometry (LDI MS), consuming 100 nL of serum in seconds. A multi-modal recognition is constructed by integrating SMFs and clinical indexes with an enhanced area under curve (AUC) up to 0.845 for stroke screening, compared to single-modal diagnosis by only SMFs or clinical indexes. The prediction of DL is addressed by selecting 20 key metabolite features with differential regulation through a saliency map approach, shedding light on the molecular mechanisms in stroke. The approach highlights the emerging role of DL in precision medicine and suggests an expanding utility for computational analysis of SMFs in stroke screening.
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Affiliation(s)
- Wei Xu
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji HospitalSchool of MedicineShanghai Jiao Tong University160 Pujian RoadShanghai200127P. R. China
- State Key Laboratory for Oncogenes and Related GenesSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030P. R. China
| | - Jixian Lin
- Department of NeurologyMinhang HospitalFudan University170 Xinsong RoadShanghai201199P. R. China
| | - Ming Gao
- School of Management Science and EngineeringDongbei University of Finance and EconomicsDalian116025P. R. China
- Center for Post‐doctoral Studies of Computer ScienceNortheastern UniversityShenyang110819P. R. China
| | - Yuhan Chen
- School of Management Science and EngineeringDongbei University of Finance and EconomicsDalian116025P. R. China
- Center for Post‐doctoral Studies of Computer ScienceNortheastern UniversityShenyang110819P. R. China
| | - Jing Cao
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji HospitalSchool of MedicineShanghai Jiao Tong University160 Pujian RoadShanghai200127P. R. China
- State Key Laboratory for Oncogenes and Related GenesSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030P. R. China
| | - Jun Pu
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji HospitalSchool of MedicineShanghai Jiao Tong University160 Pujian RoadShanghai200127P. R. China
- State Key Laboratory for Oncogenes and Related GenesSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030P. R. China
| | - Lin Huang
- Stem Cell Research CenterRenji HospitalSchool of MedicineShanghai Jiao Tong University160 Pujian RoadShanghai200127P. R. China
| | - Jing Zhao
- Department of NeurologyMinhang HospitalFudan University170 Xinsong RoadShanghai201199P. R. China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji HospitalSchool of MedicineShanghai Jiao Tong University160 Pujian RoadShanghai200127P. R. China
- State Key Laboratory for Oncogenes and Related GenesSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030P. R. China
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26
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Bandekar AC, Subedi S, Ioerger TR, Sassetti CM. Cell-Cycle-Associated Expression Patterns Predict Gene Function in Mycobacteria. Curr Biol 2020; 30:3961-3971.e6. [PMID: 32916109 PMCID: PMC7578119 DOI: 10.1016/j.cub.2020.07.070] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/26/2020] [Accepted: 07/22/2020] [Indexed: 12/20/2022]
Abstract
Although the major events in prokaryotic cell cycle progression are likely to be coordinated with transcriptional and metabolic changes, these processes remain poorly characterized. Unlike many rapidly growing bacteria, DNA replication and cell division are temporally resolved in mycobacteria, making these slow-growing organisms a potentially useful system to investigate the prokaryotic cell cycle. To determine whether cell-cycle-dependent gene regulation occurs in mycobacteria, we characterized the temporal changes in the transcriptome of synchronously replicating populations of Mycobacterium tuberculosis (Mtb). By enriching for genes that display a sinusoidal expression pattern, we discover 485 genes that oscillate with a period consistent with the cell cycle. During cytokinesis, the timing of gene induction could be used to predict the timing of gene function, as mRNA abundance was found to correlate with the order in which proteins were recruited to the developing septum. Similarly, the expression pattern of primary metabolic genes could be used to predict the relative importance of these pathways for different cell cycle processes. Pyrimidine synthetic genes peaked during DNA replication, and their depletion caused a filamentation phenotype that phenocopied defects in this process. In contrast, the inosine monophasphate dehydrogenase dedicated to guanosine synthesis, GuaB2, displayed the opposite expression pattern and its depletion perturbed septation. Together, these data imply obligate coordination between primary metabolism and cell division and identify periodically regulated genes that can be related to specific cell biological functions.
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Affiliation(s)
- Aditya C Bandekar
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Sishir Subedi
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77843, USA.
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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27
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Pang Z, Chong J, Li S, Xia J. MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics. Metabolites 2020; 10:E186. [PMID: 32392884 PMCID: PMC7281575 DOI: 10.3390/metabo10050186] [Citation(s) in RCA: 315] [Impact Index Per Article: 78.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/30/2020] [Accepted: 05/03/2020] [Indexed: 12/26/2022] Open
Abstract
Liquid chromatography coupled to high-resolution mass spectrometry platforms are increasingly employed to comprehensively measure metabolome changes in systems biology and complex diseases. Over the past decade, several powerful computational pipelines have been developed for spectral processing, annotation, and analysis. However, significant obstacles remain with regard to parameter settings, computational efficiencies, batch effects, and functional interpretations. Here, we introduce MetaboAnalystR 3.0, a significantly improved pipeline with three key new features: (1) efficient parameter optimization for peak picking; (2) automated batch effect correction; and 3) more accurate pathway activity prediction. Our benchmark studies showed that this workflow was 20~100X faster compared to other well-established workflows and produced more biologically meaningful results. In summary, MetaboAnalystR 3.0 offers an efficient pipeline to support high-throughput global metabolomics in the open-source R environment.
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Affiliation(s)
- Zhiqiang Pang
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Ste Anne de Bellevue, QC H9X 3V9, Canada; (Z.P.); (J.C.)
| | - Jasmine Chong
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Ste Anne de Bellevue, QC H9X 3V9, Canada; (Z.P.); (J.C.)
| | - Shuzhao Li
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, Canada;
| | - Jianguo Xia
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Ste Anne de Bellevue, QC H9X 3V9, Canada; (Z.P.); (J.C.)
- Department of Animal Science, McGill University, 21111 Lakeshore Road, Ste Anne de Bellevue, QC H9X 3V9, Canada
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28
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Bergé M, Pezzatti J, González-Ruiz V, Degeorges L, Mottet-Osman G, Rudaz S, Viollier PH. Bacterial cell cycle control by citrate synthase independent of enzymatic activity. eLife 2020; 9:52272. [PMID: 32149608 PMCID: PMC7083601 DOI: 10.7554/elife.52272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 03/04/2020] [Indexed: 11/17/2022] Open
Abstract
Proliferating cells must coordinate central metabolism with the cell cycle. How central energy metabolism regulates bacterial cell cycle functions is not well understood. Our forward genetic selection unearthed the Krebs cycle enzyme citrate synthase (CitA) as a checkpoint regulator controlling the G1→S transition in the polarized alpha-proteobacterium Caulobacter crescentus, a model for cell cycle regulation and asymmetric cell division. We find that loss of CitA promotes the accumulation of active CtrA, an essential cell cycle transcriptional regulator that maintains cells in G1-phase, provided that the (p)ppGpp alarmone is present. The enzymatic activity of CitA is dispensable for CtrA control, and functional citrate synthase paralogs cannot replace CitA in promoting S-phase entry. Our evidence suggests that CitA was appropriated specifically to function as a moonlighting enzyme to link central energy metabolism with S-phase entry. Control of the G1-phase by a central metabolic enzyme may be a common mechanism of cellular regulation.
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Affiliation(s)
- Matthieu Bergé
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Julian Pezzatti
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
| | - Víctor González-Ruiz
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland.,Swiss Centre for Applied Human Toxicology (SCAHT), Basel, Switzerland
| | - Laurence Degeorges
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Geneviève Mottet-Osman
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Serge Rudaz
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland.,Swiss Centre for Applied Human Toxicology (SCAHT), Basel, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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