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Rojas VK, Winter MG, Jimenez AG, Tanner NW, Crockett SL, Spiga L, Hendrixson DR, Winter SE. Infection-associated gene regulation of L-tartrate metabolism in Salmonella enterica serovar Typhimurium. mBio 2024; 15:e0035024. [PMID: 38682906 DOI: 10.1128/mbio.00350-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/28/2024] [Indexed: 05/01/2024] Open
Abstract
Enteric pathogens such as Salmonella enterica serovar Typhimurium experience spatial and temporal changes to the metabolic landscape throughout infection. Host reactive oxygen and nitrogen species non-enzymatically convert monosaccharides to alpha hydroxy acids, including L-tartrate. Salmonella utilizes L-tartrate early during infection to support fumarate respiration, while L-tartrate utilization ceases at later time points due to the increased availability of exogenous electron acceptors such as tetrathionate, nitrate, and oxygen. It remains unknown how Salmonella regulates its gene expression to metabolically adapt to changing nutritional environments. Here, we investigated how the transcriptional regulation for L-tartrate metabolism in Salmonella is influenced by infection-relevant cues. L-tartrate induces the transcription of ttdBAU, genes involved in L-tartrate utilization. L-tartrate metabolism is negatively regulated by two previously uncharacterized transcriptional regulators TtdV (STM3357) and TtdW (STM3358), and both TtdV and TtdW are required for the sensing of L-tartrate. The electron acceptors nitrate, tetrathionate, and oxygen repress ttdBAU transcription via the two-component system ArcAB. Furthermore, the regulation of L-tartrate metabolism is required for optimal fitness in a mouse model of Salmonella-induced colitis. TtdV, TtdW, and ArcAB allow for the integration of two cues, i.e., substrate availability and availability of exogenous electron acceptors, to control L-tartrate metabolism. Our findings provide novel insights into how Salmonella prioritizes the utilization of different electron acceptors for respiration as it experiences transitional nutrient availability throughout infection. IMPORTANCE Bacterial pathogens must adapt their gene expression profiles to cope with diverse environments encountered during infection. This coordinated process is carried out by the integration of cues that the pathogen senses to fine-tune gene expression in a spatiotemporal manner. Many studies have elucidated the regulatory mechanisms of how Salmonella sense metabolites in the gut to activate or repress its virulence program; however, our understanding of how Salmonella coordinates its gene expression to maximize the utilization of carbon and energy sources found in transitional nutrient niches is not well understood. In this study, we discovered how Salmonella integrates two infection-relevant cues, substrate availability and exogenous electron acceptors, to control L-tartrate metabolism. From our experiments, we propose a model for how L-tartrate metabolism is regulated in response to different metabolic cues in addition to characterizing two previously unknown transcriptional regulators. This study expands our understanding of how microbes combine metabolic cues to enhance fitness during infection.
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Affiliation(s)
- Vivian K Rojas
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, California, USA
| | - Maria G Winter
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, California, USA
| | - Angel G Jimenez
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Natasha W Tanner
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, California, USA
| | - Stacey L Crockett
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Luisella Spiga
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - David R Hendrixson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sebastian E Winter
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, California, USA
- Department of Medical Microbiology and Immunology, UC Davis School of Medicine, Davis, California, USA
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Hansen ZA, Schilmiller AL, Guzior DV, Rudrik JT, Quinn RA, Vasco KA, Manning SD. Shifts in the functional capacity and metabolite composition of the gut microbiome during recovery from enteric infection. Front Cell Infect Microbiol 2024; 14:1359576. [PMID: 38779558 PMCID: PMC11109446 DOI: 10.3389/fcimb.2024.1359576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
While enteric pathogens have been widely studied for their roles in causing foodborne infection, their impacts on the gut microbial community have yet to be fully characterized. Previous work has identified notable changes in the gut microbiome related to pathogen invasion, both taxonomically and genetically. Characterization of the metabolic landscape during and after enteric infection, however, has not been explored. Consequently, we investigated the metabolome of paired stools recovered from 60 patients (cases) during and after recovery from enteric bacterial infections (follow-ups). Shotgun metagenomics was applied to predict functional microbial pathways combined with untargeted metametabolomics classified by Liquid Chromatography Mass Spectrometry. Notably, cases had a greater overall metabolic capacity with significantly higher pathway richness and evenness relative to the follow-ups (p<0.05). Metabolic pathways related to central carbon metabolism, amino acid metabolism, and lipid and fatty acid biosynthesis were more highly represented in cases and distinct signatures for menaquinone production were detected. By contrast, the follow-up samples had a more diverse metabolic landscape with enhanced richness of polar metabolites (p<0.0001) and significantly greater richness, evenness, and overall diversity of nonpolar metabolites (p<0.0001). Although many metabolites could not be annotated with existing databases, a marked increase in certain clusters of metabolites was observed in the follow-up samples when compared to the case samples and vice versa. These findings suggest the importance of key metabolites in gut health and recovery and enhance understanding of metabolic fluctuations during enteric infections.
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Affiliation(s)
- Zoe A. Hansen
- Department of Microbiology, Genetics, and Immunology, Michigan State University E., Lansing, MI, United States
| | - Anthony L. Schilmiller
- Research Technology Support Facility, Mass Spectrometry and Metabolomics Core, Michigan State University E., Lansing, MI, United States
| | - Douglas V. Guzior
- Department of Microbiology, Genetics, and Immunology, Michigan State University E., Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University E., Lansing, MI, United States
| | - James T. Rudrik
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, MI, United States
| | - Robert A. Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University E., Lansing, MI, United States
| | - Karla A. Vasco
- Department of Microbiology, Genetics, and Immunology, Michigan State University E., Lansing, MI, United States
| | - Shannon D. Manning
- Department of Microbiology, Genetics, and Immunology, Michigan State University E., Lansing, MI, United States
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Rojas VK, Winter MG, Jimenez AG, Tanner NW, Crockett SL, Spiga L, Hendrixson DR, Winter SE. Gene regulation of infection-associated L-tartrate metabolism in Salmonella enterica serovar Typhimurium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.578992. [PMID: 38370731 PMCID: PMC10871181 DOI: 10.1101/2024.02.05.578992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Enteric pathogens such as Salmonella enterica serovar Typhimurium experience spatial and temporal changes to the metabolic landscape throughout infection. Host reactive oxygen and nitrogen species non-enzymatically convert monosaccharides to alpha hydroxy acids, including L-tartrate. Salmonella utilizes L-tartrate early during infection to support fumarate respiration, while L-tartrate utilization ceases at later time points due to the increased availability of exogenous electron acceptors such as tetrathionate, nitrate, and oxygen. It remains unknown how Salmonella regulates its gene expression to metabolically adapt to changing nutritional environments. Here, we investigated how the transcriptional regulation for L-tartrate metabolism in Salmonella is influenced by infection-relevant cues. L-tartrate induces the transcription of ttdBAU, genes involved in L-tartrate utilization. L-tartrate metabolism is negatively regulated by two previously uncharacterized transcriptional regulators TtdV (STM3357) and TtdW (STM3358), and both TtdV and TtdW are required for sensing of L-tartrate. The electron acceptors nitrate, tetrathionate, and oxygen repress ttdBAU transcription via the two-component system ArcAB. Furthermore, regulation of L-tartrate metabolism is required for optimal fitness in a mouse model of Salmonella-induced colitis. TtdV, TtdW, and ArcAB allow for the integration of two cues, substrate availability and availability of exogenous electron acceptors, to control L-tartrate metabolism. Our findings provide novel insights into how Salmonella prioritizes utilization of different electron acceptors for respiration as it experiences transitional nutrient availability throughout infection.
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Affiliation(s)
- Vivian K. Rojas
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, CA, USA
| | - Maria G. Winter
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, CA, USA
| | - Angel G. Jimenez
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Current address: Infectious Diseases, Genentech, South San Francisco, California, USA
| | - Natasha W. Tanner
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, CA, USA
| | - Stacey L. Crockett
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Luisella Spiga
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Current address: Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - David R. Hendrixson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sebastian E. Winter
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis School of Medicine, Davis, CA, USA
- Department of Medical Microbiology and Immunology, UC Davis School of Medicine, Davis, CA, USA
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Dawood MFA, Tahjib-Ul-Arif M, Sohag AAM, Abdel Latef AAH. Role of Acetic Acid and Nitric Oxide against Salinity and Lithium Stress in Canola ( Brassica napus L.). PLANTS (BASEL, SWITZERLAND) 2023; 13:51. [PMID: 38202358 PMCID: PMC10781170 DOI: 10.3390/plants13010051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024]
Abstract
In this study, canola (Brassica napus L.) seedlings were treated with individual and combined salinity and lithium (Li) stress, with and without acetic acid (AA) or nitric acid (NO), to investigate their possible roles against these stresses. Salinity intensified Li-induced damage, and the principal component analysis revealed that this was primarily driven by increased oxidative stress, deregulation of sodium and potassium accumulation, and an imbalance in tissue water content. However, pretreatment with AA and NO prompted growth, re-established sodium and potassium homeostasis, and enhanced the defense system against oxidative and nitrosative damage by triggering the antioxidant capacity. Combined stress negatively impacted phenylalanine ammonia lyase activity, affecting flavonoids, carotenoids, and anthocyanin levels, which were then restored in canola plants primed with AA and NO. Additionally, AA and NO helped to maintain osmotic balance by increasing trehalose and proline levels and upregulating signaling molecules such as hydrogen sulfide, γ-aminobutyric acid, and salicylic acid. Both AA and NO improved Li detoxification by increasing phytochelatins and metallothioneins, and reducing glutathione contents. Comparatively, AA exerted more effective protection against the detrimental effects of combined stress than NO. Our findings offer novel perspectives on the impacts of combining salt and Li stress.
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Affiliation(s)
- Mona F. A. Dawood
- Botany and Microbiology Department, Faculty of Science, Assiut University, Assiut 71516, Egypt;
| | - Md. Tahjib-Ul-Arif
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh;
| | - Abdullah Al Mamun Sohag
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh;
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Martínez-Alvarez L, Ramond JB, Vikram S, León-Sobrino C, Maggs-Kölling G, Cowan DA. With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities. Appl Environ Microbiol 2023; 89:e0062923. [PMID: 37971255 PMCID: PMC10734447 DOI: 10.1128/aem.00629-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/24/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE The hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.
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Affiliation(s)
- Laura Martínez-Alvarez
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | - Jean-Baptiste Ramond
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
- Extreme Ecosystem Microbiomics & Ecogenomics (E²ME) Lab., Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Surendra Vikram
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | - Carlos León-Sobrino
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | | | - Don A. Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
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Qian X, Xin K, Zhang L, Zhou J, Xu A, Dong W, Jiang M. Integration of ARTP Mutation and Adaptive Laboratory Evolution to Reveal 1,4-Butanediol Degradation in Pseudomonas putida KT2440. Microbiol Spectr 2023; 11:e0498822. [PMID: 37067433 PMCID: PMC10269461 DOI: 10.1128/spectrum.04988-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/30/2023] [Indexed: 04/18/2023] Open
Abstract
Biotransformation of plastics or their depolymerization monomers as raw materials would offer a better end-of-life solutions to the plastic waste dilemma. 1,4-butanediol (BDO) is one of the major depolymerization monomers of many plastics polymers. BDO valorization presents great significance for waste plastic up-recycling and fermenting feedstock exploitation. In the present study, atmospheric pressure room temperature plasma (ARTP)-induced mutation combined with adaptive laboratory evolution (ALE) was used to improve the BDO utilization capability of Pseudomonas putida KT2440. The excellent mutant P. putida NB10 was isolated and stored in the China Typical Culture Preservation Center (CCTCC) with the deposit number M 2021482. Whole-genome resequencing and transcriptome analysis revealed that the BDO degradation process consists of β-oxidation, glyoxylate carboligase (GCL) pathway, glyoxylate cycle and gluconeogenesis pathway. The imbalance between the two key intermediates (acetyl-CoA and glycolyl-CoA) and the accumulation of cytotoxic aldehydes resulted in the weak metabolism performance of KT2440 in the utilization of BDO. The balance of the carbon flux and enhanced tolerance to cytotoxic intermediates endow NB10 with great BDO degradation capability. This study deeply revealed the metabolic mechanism behind BDO degradation and provided an excellent chassis cell for BDO further up-cycling to high-value chemicals. IMPORTANCE Plastic waste represents not only a global pollution problem but also a carbon-rich, low-cost, globally renewable feedstock for industrial biotechnology. BDO is the basic material for polybutylene terephthalate (PBT), poly butylene adipate-co-terephthalate (PBAT), poly (butylene succinate) (PBS), etc. Herein, the construction of BDO valorization cell factory presents great significance for waste plastic up-recycling and novel fermentation feedstock exploitation. However, BDO is hard to be metabolized and its metabolic pathway is unclear. This study presents a P. putida mutant NB10, obtained through the integration of ARTP and ALE, displaying significant growth improvement with BDO as the sole carbon source. Further genome resequencing, transcriptome analysis and genetic engineering deeply revealed the metabolic mechanism behind BDO degradation in P. putida, this study offers an excellent microbial chassis and modification strategy for plastic waste up-cycling.
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Affiliation(s)
- Xiujuan Qian
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People’s Republic of China
| | - Kaiyuan Xin
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People’s Republic of China
| | - Lili Zhang
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People’s Republic of China
| | - Jie Zhou
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People’s Republic of China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, People’s Republic of China
| | - Anming Xu
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People’s Republic of China
| | - Weiliang Dong
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People’s Republic of China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, People’s Republic of China
| | - Min Jiang
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People’s Republic of China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, People’s Republic of China
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7
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Pattinson A, Bahia S, Le Gall G, Morris CJ, Harding SV, McArthur M. Using a multi-omic approach to investigate the mechanism of 12-bis-THA activity against Burkholderia thailandensis. Front Microbiol 2023; 13:1092230. [PMID: 37252207 PMCID: PMC10213367 DOI: 10.3389/fmicb.2022.1092230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/28/2022] [Indexed: 05/31/2023] Open
Abstract
Burkholderia pseudomallei is the causative agent of the tropical disease, melioidosis. It is intrinsically resistant to many antimicrobials and treatment requires an onerous regimen of intravenous and orally administered drugs. Relapse of disease and high rates of mortality following treatment are common, demonstrating the need for new anti-Burkholderia agents. The cationic bola-amphiphile, 12,12'-(dodecane-1,12-diyl) bis (9-amino-1,2,3,4-tetrahydroacridinium), referred to as 12-bis-THA, is a molecule with the potential to treat Burkholderia infections. 12-bis-THA spontaneously forms cationic nanoparticles that bind anionic phospholipids in the prokaryotic membrane and are readily internalized. In this study, we examine the antimicrobial activity of 12-bis-THA against strains of Burkholderia thailandensis. As B. pseudomallei produces a polysaccharide capsule we first examined if this extra barrier influenced the activity of 12-bis-THA which is known to act on the bacterial envelope. Therefore two strains of B. thailandensis were selected for further testing, strain E264 which does not produce a capsule and strain E555 which does produce a capsule that is chemically similar to that found in B. pseudomallei. In this study no difference in the minimum inhibitory concentration (MIC) was observed when capsulated (E555) and unencapsulated (E264) strains of B. thailandensis were compared, however time-kill analysis showed that the unencapsulated strain was more susceptible to 12-bis-THA. The presence of the capsule did not affect the membrane permeation of 12-bis-THA at MIC concentrations. Proteomic and metabolomic analyses showed that 12-bis-THA causes a shift in central metabolism away from glycolysis and glyoxylate cycle, and suppressed the production of the F1 domain of ATP synthase. In summary, we provide insight into the molecular mechanisms underpinning the activity of 12-bis-THA against B. thailandensis and discuss its potential for further development.
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Affiliation(s)
- Adam Pattinson
- Norwich Medical School, Bob Champion Building for Research and Education, University of East Anglia, Norwich, United Kingdom
| | - Sandeep Bahia
- School of Pharmacy, University of East Anglia, Norwich, United Kingdom
| | - Gwénaëlle Le Gall
- Norwich Medical School, Bob Champion Building for Research and Education, University of East Anglia, Norwich, United Kingdom
| | | | - Sarah V. Harding
- CBR Division, Defense Science and Technology Laboratory, Salisbury, United Kingdom
- Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Michael McArthur
- Norwich Medical School, Bob Champion Building for Research and Education, University of East Anglia, Norwich, United Kingdom
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8
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Moreau PL. Regulation of phosphate starvation-specific responses in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36972330 DOI: 10.1099/mic.0.001312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Toxic agents added into the medium of rapidly growing Escherichia coli induce specific stress responses through the activation of specialized transcription factors. Each transcription factor and downstream regulon (e.g. SoxR) are linked to a unique stress (e.g. superoxide stress). Cells starved of phosphate induce several specific stress regulons during the transition to stationary phase when the growth rate is steadily declining. Whereas the regulatory cascades leading to the expression of specific stress regulons are well known in rapidly growing cells stressed by toxic products, they are poorly understood in cells starved of phosphate. The intent of this review is to both describe the unique mechanisms of activation of specialized transcription factors and discuss signalling cascades leading to the induction of specific stress regulons in phosphate-starved cells. Finally, I discuss unique defence mechanisms that could be induced in cells starved of ammonium and glucose.
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Affiliation(s)
- Patrice L Moreau
- Laboratoire Chimie Bactérienne, LCB-UMR 7283, Institut Microbiologie Méditerranée, CNRS/Université Aix-Marseille, Marseille, France
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9
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Castronovo S, Helmholz L, Wolff D, Poulsen JS, Nielsen JL, Ternes TA, Schmidt TC, Wick A. Protein fractionation and shotgun proteomics analysis of enriched bacterial cultures shed new light on the enzymatically catalyzed degradation of acesulfame. WATER RESEARCH 2023; 230:119535. [PMID: 36610183 DOI: 10.1016/j.watres.2022.119535] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/08/2022] [Accepted: 12/25/2022] [Indexed: 06/17/2023]
Abstract
The removal of organic micropollutants in municipal wastewater treatment is an extensively studied field of research, but the underlying enzymatic processes have only been elucidated to a small extent so far. In order to shed more light on the enzymatic degradation of the artificial sweetener acesulfame (ACE) in this context, we enriched two bacterial taxa which were not yet described to be involved in the degradation of ACE, an unknown Chelatococcus species and Ensifer adhaerens, by incubating activated sludge in chemically defined media containing ACE as sole carbon source. Cell-free lysates were extracted, spiked with ACE and analyzed via target LC-MS/MS, demonstrating for the first time enzymatically catalyzed ACE degradation outside of living cells. Fractionation of the lysate via two-dimensional fast protein liquid chromatography (FPLC) succeeded in a partial separation of the enzymes catalyzing the initial transformation reaction of ACE from those catalyzing the further transformation pathway. Thereby, an accumulation of the intermediate transformation product acetoacetamide-n-sulfonic acid (ANSA) in the ACE-degrading fractions was achieved, providing first quantitative evidence that the cleavage of the sulfuric ester moiety of ACE is the initial transformation step. The metaproteome of the enrichments was analyzed in the FPLC fractions and in the unfractionated lysate, using shotgun proteomics via UHPLC-HRMS/MS and label-free quantification. The comparison of protein abundances in the FPLC fractions to the corresponding ACE degradation rates revealed a metallo-β-lactamase fold metallo-hydrolase as most probable candidate for the enzyme catalyzing the initial transformation from ACE to ANSA. This enzyme was by far the most abundant of all detected proteins and amounted to a relative protein abundance of 91% in the most active fraction after the second fractionation step. Moreover, the analysis of the unfractionated lysate resulted in a list of further proteins possibly involved in the transformation of ACE, most striking a highly abundant amidase likely catalyzing the further transformation of ANSA, and an ABC transporter substrate-binding protein that may be involved in the uptake of ACE into the cell.
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Affiliation(s)
- Sandro Castronovo
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany; Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany.
| | - Lissa Helmholz
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - David Wolff
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany
| | | | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg East, Denmark
| | - Thomas A Ternes
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Torsten C Schmidt
- Instrumental Analytical Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany; Centre for Water and Environmental Research, University of Duisburg-Essen, Universitätsstr. 2, 45141 Essen, Germany
| | - Arne Wick
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany
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10
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Qiu Y, Ozturk S, Cui X, Qin W, Wu Q, Liu S. Increased heat tolerance and transcriptome analysis of Salmonella enterica Enteritidis PT 30 heat-shocked at 42 ℃. Food Res Int 2023; 167:112636. [PMID: 37087231 DOI: 10.1016/j.foodres.2023.112636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
In this study, we compared the heat tolerance parameter (D65℃) values of Salmonella enterica serovar Enteritidis PT 30 (S. Enteritidis ) heat adapted at different degrees (at 42 ℃ for 20-180 min) and cultivated using two methods. The treated group with the highest D65℃ value (LP-42 ℃-60 min) and the untreated groups (Control-TSB and Control-TSA) were subjected to transcriptome analysis. Heat-adaptation increased the D65℃ values of S. Enteritidis by 24.5-60.8%. The D65℃ values of the LP-42 ℃-60 min group (1.85 ± 0.13 min, 7.7% higher) was comparable to that of the Control-TSA. A total of 483 up- and 443 downregulated genes of S. enteritidis were identified in the LP-42 ℃-60 min group (log2fold change > 1, adjusted p-value < 0.05). Among these genes, 5 co-expressed and 15 differentially expressed genes in the LP-42 ℃-60 min and Control-TSA grops possibly contributed to the high D65℃ values of S. Enteritidis . The Rpo regulon was involved in the heat adaptation of S. Enteritidis , as evidenced by the significant upregulation of rpoS, rpoN, and rpoE. KEGG enrichment pathways, such as biosynthesis of secondary metabolites, tricarboxylic acid, and ribosomes were identified and mapped to reveal the molecular mechanisms of S. enteritidis during heat adaptation. This study quantified the enhanced heat tolerance of S. Enteritidis heat adapted at different degrees of heat-adaptation. The results of this study may serve as a basis for elucidating the molecular mechanisms underlying the enhanced heat tolerance at the transcriptome level.
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Affiliation(s)
- Yan Qiu
- College of Food Science, Sichuan Agricultural University, Ya'an, China
| | - Samet Ozturk
- Department of Food Engineering, Gümüşhane University, Gümüşhane, Turkey
| | - Xinyao Cui
- College of Food Science, Sichuan Agricultural University, Ya'an, China
| | - Wen Qin
- College of Food Science, Sichuan Agricultural University, Ya'an, China; Food Processing and Safety Institute, Sichuan Agricultural University, Ya'an, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Shuxiang Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, China; Food Processing and Safety Institute, Sichuan Agricultural University, Ya'an, China; State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou 510070, China.
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11
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Schubert C, Unden G. Fumarate, a central electron acceptor for Enterobacteriaceae beyond fumarate respiration and energy conservation. Adv Microb Physiol 2023; 82:267-299. [PMID: 36948656 DOI: 10.1016/bs.ampbs.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
C4-dicarboxylates (C4-DCs) such as fumarate, l-malate and l-aspartate are key substrates for Enterobacteria such as Escherichia coli or Salmonella typhimurium during anaerobic growth. In general, C4-DCs are oxidants during biosynthesis, e.g., of pyrimidine or heme, acceptors for redox balancing, a high-quality nitrogen source (l-aspartate) and electron acceptor for fumarate respiration. Fumarate reduction is required for efficient colonization of the murine intestine, even though the colon contains only small amounts of C4-DCs. However, fumarate can be produced endogenously by central metabolism, allowing autonomous production of an electron acceptor for biosynthesis and redox balancing. Bacteria possess a complex set of transporters for the uptake (DctA), antiport (DcuA, DcuB, TtdT) and excretion (DcuC) of C4-DCs. DctA and DcuB exert regulatory functions and link transport to metabolic control through interaction with regulatory proteins. The sensor kinase DcuS of the C4-DC two-component system DcuS-DcuR forms complexes with DctA (aerobic) or DcuB (anaerobic), representing the functional state of the sensor. Moreover, EIIAGlc from the glucose phospho-transferase system binds to DctA and presumably inhibits C4-DC uptake. Overall, the function of fumarate as an oxidant in biosynthesis and redox balancing explains the pivotal role of fumarate reductase for intestinal colonization, while the role of fumarate in energy conservation (fumarate respiration) is of minor importance.
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Affiliation(s)
- Christopher Schubert
- Institute for Molecular Physiology (IMP), Microbiology and Biotechnology; Johannes Gutenberg-University, Mainz, Germany; Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
| | - Gottfried Unden
- Institute for Molecular Physiology (IMP), Microbiology and Biotechnology; Johannes Gutenberg-University, Mainz, Germany.
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12
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Diehl C, Gerlinger PD, Paczia N, Erb TJ. Synthetic anaplerotic modules for the direct synthesis of complex molecules from CO 2. Nat Chem Biol 2023; 19:168-175. [PMID: 36470994 PMCID: PMC9889269 DOI: 10.1038/s41589-022-01179-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 09/22/2022] [Indexed: 12/12/2022]
Abstract
Anaplerosis is an essential feature of metabolism that allows the continuous operation of natural metabolic networks, such as the citric acid cycle, by constantly replenishing drained intermediates. However, this concept has not been applied to synthetic in vitro metabolic networks, thus far. Here we used anaplerotic strategies to directly access the core sequence of the CETCH cycle, a new-to-nature in vitro CO2-fixation pathway that features several C3-C5 biosynthetic precursors. We drafted four different anaplerotic modules that use CO2 to replenish the CETCH cycle's intermediates and validated our designs by producing 6-deoxyerythronolide B (6-DEB), the C21-macrolide backbone of erythromycin. Our best design allowed the carbon-positive synthesis of 6-DEB via 54 enzymatic reactions in vitro at yields comparable to those with isolated 6-DEB polyketide synthase (DEBS). Our work showcases how new-to-nature anaplerotic modules can be designed and tailored to enhance and expand the synthetic capabilities of complex catalytic in vitro reaction networks.
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Affiliation(s)
- Christoph Diehl
- grid.419554.80000 0004 0491 8361Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Patrick D. Gerlinger
- grid.419554.80000 0004 0491 8361Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- grid.419554.80000 0004 0491 8361Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J. Erb
- grid.419554.80000 0004 0491 8361Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany ,grid.452532.7SYNMIKRO Center for Synthetic Microbiology, Marburg, Germany
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13
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Yeast Mannan-Rich Fraction Modulates Endogenous Reactive Oxygen Species Generation and Antibiotic Sensitivity in Resistant E. coli. Int J Mol Sci 2022; 24:ijms24010218. [PMID: 36613662 PMCID: PMC9820725 DOI: 10.3390/ijms24010218] [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: 11/11/2022] [Revised: 11/30/2022] [Accepted: 12/14/2022] [Indexed: 12/25/2022] Open
Abstract
Mannan-rich fraction (MRF) isolated from Saccharomyces cerevisiae has been studied for its beneficial impact on animal intestinal health. Herein, we examined how MRF affected the formation of reactive oxygen species (ROS), impacting antibiotic susceptibility in resistant Escherichia coli through the modulation of bacterial metabolism. The role of MRF in effecting proteomic change was examined using a proteomics-based approach. The results showed that MRF, when combined with bactericidal antibiotic treatment, increased ROS production in resistant E. coli by 59.29 ± 4.03% compared to the control (p ≤ 0.05). We further examined the effect of MRF alone and in combination with antibiotic treatment on E. coli growth and explored how MRF potentiates bacterial susceptibility to antibiotics via proteomic changes in key metabolic pathways. Herein we demonstrated that MRF supplementation in the growth media of ampicillin-resistant E. coli had a significant impact on the normal translational control of the central metabolic pathways, including those involved in the glycolysis-TCA cycle (p ≤ 0.05).
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14
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Longitudinal metabolomic profiles reveal sex-specific adjustments to long-duration spaceflight and return to Earth. Cell Mol Life Sci 2022; 79:578. [DOI: 10.1007/s00018-022-04566-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/05/2022] [Accepted: 09/19/2022] [Indexed: 11/05/2022]
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15
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Isocitrate binds to the itaconic acid-responsive LysR-type transcriptional regulator RipR in Salmonella pathogenesis. J Biol Chem 2022; 298:102562. [PMID: 36198361 PMCID: PMC9637912 DOI: 10.1016/j.jbc.2022.102562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/25/2022] [Accepted: 09/29/2022] [Indexed: 11/20/2022] Open
Abstract
Macrophages produce itaconic acid in phagosomes in response to bacterial cell wall component lipopolysaccharide to eliminate invading pathogenic bacteria. Itaconic acid competitively inhibits the first enzyme of the bacterial glyoxylate cycle. To overcome itaconic acid stress, bacteria employ the bacterial LysR-type transcriptional regulator RipR. However, it remains unknown which molecule activates RipR in bacterial pathogenesis. In this study, we determined the crystal structure of the regulatory domain of RipR from the intracellular pathogen Salmonella. The RipR regulatory domain structure exhibited the typical dimeric arrangement with the putative ligand-binding site between the two subdomains. Our isothermal titration calorimetry experiments identified isocitrate as the physiological ligand of RipR, whose intracellular level is increased in response to itaconic acid stress. We further found that 3-phenylpropionic acid significantly decreased the resistance of the bacteria to an itaconic acid challenge. Consistently, the complex structure revealed that the compound is antagonistically bound to the RipR ligand-binding site. This study provides the molecular basis of bacterial survival in itaconic acid stress from our immune systems. Further studies are required to reveal biochemical activity, which would elucidate how Salmonella survives in macrophage phagosomes by defending against itaconic acid inhibition of bacterial metabolism.
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16
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Degradation of Exogenous Fatty Acids in Escherichia coli. Biomolecules 2022; 12:biom12081019. [PMID: 35892328 PMCID: PMC9329746 DOI: 10.3390/biom12081019] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 12/10/2022] Open
Abstract
Many bacteria possess all the machineries required to grow on fatty acids (FA) as a unique source of carbon and energy. FA degradation proceeds through the β-oxidation cycle that produces acetyl-CoA and reduced NADH and FADH cofactors. In addition to all the enzymes required for β-oxidation, FA degradation also depends on sophisticated systems for its genetic regulation and for FA transport. The fact that these machineries are conserved in bacteria suggests a crucial role in environmental conditions, especially for enterobacteria. Bacteria also possess specific enzymes required for the degradation of FAs from their environment, again showing the importance of this metabolism for bacterial adaptation. In this review, we mainly describe FA degradation in the Escherichia coli model, and along the way, we highlight and discuss important aspects of this metabolism that are still unclear. We do not detail exhaustively the diversity of the machineries found in other bacteria, but we mention them if they bring additional information or enlightenment on specific aspects.
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17
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Metabolomics Analysis Coupled with Weighted Gene Co-Expression Network Analysis Unravels the Associations of Tricarboxylic Acid Cycle-Intermediates with Edible Pigments Produced by Monascus purpureus (Hong Qu). Foods 2022; 11:foods11142168. [PMID: 35885410 PMCID: PMC9320606 DOI: 10.3390/foods11142168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
Monascus azaphilones pigments (MonAzPs) produced by microbial fermentation are widely used as food chemicals for coloring and supplying beneficial biological attributes. In this study, a fermentation perturbation strategy was implemented by separately adding different amino acids, and detecting the intracellular metabolome via UHPLC-Q-Orbitrap HRMS. With the aid of weighted gene co-expression network analysis, two metabolic intermediates, fumarate and malate, involved in the tricarboxylic acid cycle, were identified as the hub metabolites. Moreover, exogenous addition of fumarate or malate significantly promoted red pigment production, and reduced orange/yellow pigment production. The importance of the tricarboxylic acid cycle was further emphasized by detecting intracellular levels of ATP, NAD(P)H, and expression of oxidoreductase-coding genes located in the MonAzPs synthetic gene cluster, suggesting a considerable effect of the energy supply on MonAzPs synthesis. Collectively, metabolomics is a powerful approach to position the crucial metabolic regulatory factors, and facilitate the development of engineering strategies for targeted regulation, lower trial-and-error cost, and advance safe and controllable processes for fermented food chemistry industries.
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18
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Chen J, Tong T, Yang Y, Ke Y, Chen X, Xie S. In-situ active Bisphenol A-degrading microorganisms in mangrove sediments. ENVIRONMENTAL RESEARCH 2022; 206:112251. [PMID: 34695429 DOI: 10.1016/j.envres.2021.112251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Bisphenol A (BPA), as both an endocrine disrupting compound and an important industrial material, is broadly distributed in coastal regions and may cause adverse effects on mangrove ecosystems. Although many BPA degraders have been isolated from various environments, the in-situ active BPA-degrading microorganisms in mangrove ecosystem are still unknown. In this study, DNA-based stable isotope probing in combination with high-throughput sequencing was adopted to pinpoint the microbes actually involved in BPA metabolism in mangrove sediments. Five bacterial genera were speculated to be associated with BPA degradation based on linear discriminant analysis (LDA) effect size (LEfSe) analysis, including Truepera, Methylobacterium, Novosphingobium, Rhodococcus and Rhodobacter. The in-situ BPA degraders were different between mudflat and forest sediments. The Shannon index of microbes in heavy fractions was significantly lower than that in light fractions. Besides, phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) demonstrated that the functional genes relevant to cytochrome P450, benzoate degradation, bisphenol degradation and citrate cycle were up-regulated significantly in in-situ BPA-degrading microbes. These findings greatly expanded the knowledge of indigenous BPA metabolic microorganisms in mangrove ecosystems.
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Affiliation(s)
- Jianfei Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Tianli Tong
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Yuyin Yang
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou, 510655, China
| | - Yanchu Ke
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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19
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Ponath F, Hör J, Vogel J. An overview of gene regulation in bacteria by small RNAs derived from mRNA 3' ends. FEMS Microbiol Rev 2022; 46:6564598. [PMID: 35388892 PMCID: PMC9438474 DOI: 10.1093/femsre/fuac017] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/30/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Over the past two decades, small noncoding RNAs (sRNAs) that regulate mRNAs by short base pairing have gone from a curiosity to a major class of post-transcriptional regulators in bacteria. They are integral to many stress responses and regulatory circuits, affecting almost all aspects of bacterial life. Following pioneering sRNA searches in the early 2000s, the field quickly focused on conserved sRNA genes in the intergenic regions of bacterial chromosomes. Yet, it soon emerged that there might be another rich source of bacterial sRNAs—processed 3′ end fragments of mRNAs. Several such 3′ end-derived sRNAs have now been characterized, often revealing unexpected, conserved functions in diverse cellular processes. Here, we review our current knowledge of these 3′ end-derived sRNAs—their biogenesis through ribonucleases, their molecular mechanisms, their interactions with RNA-binding proteins such as Hfq or ProQ and their functional scope, which ranges from acting as specialized regulators of single metabolic genes to constituting entire noncoding arms in global stress responses. Recent global RNA interactome studies suggest that the importance of functional 3′ end-derived sRNAs has been vastly underestimated and that this type of cross-regulation between genes at the mRNA level is more pervasive in bacteria than currently appreciated.
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Affiliation(s)
- Falk Ponath
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Jens Hör
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany.,Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
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20
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Glyoxylate protects against cyanide toxicity through metabolic modulation. Sci Rep 2022; 12:4982. [PMID: 35322094 PMCID: PMC8943054 DOI: 10.1038/s41598-022-08803-y] [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: 08/09/2021] [Accepted: 03/04/2022] [Indexed: 11/09/2022] Open
Abstract
Although cyanide's biological effects are pleiotropic, its most obvious effects are as a metabolic poison. Cyanide potently inhibits cytochrome c oxidase and potentially other metabolic enzymes, thereby unleashing a cascade of metabolic perturbations that are believed to cause lethality. From systematic screens of human metabolites using a zebrafish model of cyanide toxicity, we have identified the TCA-derived small molecule glyoxylate as a potential cyanide countermeasure. Following cyanide exposure, treatment with glyoxylate in both mammalian and non-mammalian animal models confers resistance to cyanide toxicity with greater efficacy and faster kinetics than known cyanide scavengers. Glyoxylate-mediated cyanide resistance is accompanied by rapid pyruvate consumption without an accompanying increase in lactate concentration. Lactate dehydrogenase is required for this effect which distinguishes the mechanism of glyoxylate rescue as distinct from countermeasures based solely on chemical cyanide scavenging. Our metabolic data together support the hypothesis that glyoxylate confers survival at least in part by reversing the cyanide-induced redox imbalances in the cytosol and mitochondria. The data presented herein represent the identification of a potential cyanide countermeasure operating through a novel mechanism of metabolic modulation.
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21
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C4-dicarboxylates as growth substrates and signaling molecules for commensal and pathogenic enteric bacteria in mammalian intestine. J Bacteriol 2022; 204:e0054521. [PMID: 34978458 DOI: 10.1128/jb.00545-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The C4-dicarboxylates (C4-DC) L-aspartate and L-malate have been identified as playing an important role in the colonization of mammalian intestine by enteric bacteria, such as Escherichia coli and Salmonella Typhimurium, and succinate as a signaling molecule for host-enteric bacteria interaction. Thus, endogenous and exogenous fumarate respiration and related functions are required for efficient initial growth of the bacteria. L-aspartate represents a major substrate for fumarate respiration in the intestine and a high-quality substrate for nitrogen assimilation. During nitrogen assimilation, DcuA catalyzes an L-aspartate/fumarate antiport and serves as a nitrogen shuttle for the net uptake of ammonium only, whereas DcuB acts as a redox shuttle that catalyzes the L-malate/succinate antiport during fumarate respiration. The C4-DC two-component system DcuS-DcuR is active in the intestine and responds to intestinal C4-DC levels. Moreover, in macrophages and in mice, succinate is a signal that promotes virulence and survival of S. Tm and pathogenic E. coli. On the other hand, intestinal succinate is an important signaling molecule for the host and activates response and protective programs. Therefore, C4-DCs play a major role in supporting colonization of enteric bacteria and as signaling molecules for the adaptation of host physiology.
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22
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Jie YK, Cheng CH, Wang LC, Ma HL, Deng YQ, Liu GX, Feng J, Guo ZX, Ye LT. Hypoxia-induced oxidative stress and transcriptome changes in the mud crab (Scylla paramamosain). Comp Biochem Physiol C Toxicol Pharmacol 2021; 245:109039. [PMID: 33785424 DOI: 10.1016/j.cbpc.2021.109039] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/04/2021] [Accepted: 03/20/2021] [Indexed: 02/08/2023]
Abstract
Mud crab (Scylla paramamosain) is an economically important cultured species in China. Hypoxia is a major environmental stressor during mud crab culture. In the present study, we investigated the oxidative stress and transcriptome changes in the gills of mud crab after intermediate hypoxia stress with dissolved oxygen (DO) 3.0 ± 0.2 mg/L (named as "DO3") and acute hypoxia stress with DO 1.0 ± 0.2 mg/L (named as "DO1") for 0, 3, 6, 12 and 24 h. The superoxide dismutase (SOD) activity of DO1 increased significantly at 3, 6 and 24 h after hypoxia stress, while SOD activity of DO3 increased significantly at 6 and 24 h. The total antioxidant capacity (T-AOC) increased significantly at 6, 12 and 24 h after hypoxia stress. The malondialdehyde (MDA) concentration of DO1 increased significantly at 6, 12 and 24 h after hypoxia stress, while MDA concentration of DO3 only increased significantly at 6 h. The lactate dehydrogenase (LDH) activity of DO1 increased significantly at 3, 6, 12 and 24 h after hypoxia stress, while LDH activity of DO3 increased significantly at 12 and 24 h. Transcriptomic analysis was conducted at 24 h of gill tissues after hypoxia stress. A total of 1052 differentially expressed genes (DEGs) were obtained, including 394 DEGs between DO1 and DO3, 481 DEGs between DO1 and control group, 177 DEGs between DO3 and control group. DEGs were enriched in the pathways related to metabolism, immune functions, ion transport, and signal transduction. Transcriptional analysis showed that glycolysis and tricarboxylic acid cycle genes were the key factors in regulating the adaptation of mud crab to hypoxia stress.
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Affiliation(s)
- Yu-Kun Jie
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510300, China
| | - Chang-Hong Cheng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510300, China.
| | - Li-Cang Wang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510300, China
| | - Hong-Ling Ma
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510300, China
| | - Yi-Qin Deng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510300, China
| | - Guang-Xin Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510300, China
| | - Juan Feng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510300, China
| | - Zhi-Xun Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510300, China.
| | - Ling-Tong Ye
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510300, China
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23
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Guo S, Asset T, Atanassov P. Catalytic Hybrid Electrocatalytic/Biocatalytic Cascades for Carbon Dioxide Reduction and Valorization. ACS Catal 2021. [DOI: 10.1021/acscatal.0c04862] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Shengyuan Guo
- Department of Chemical and Biomolecular Engineering, National Fuel Cell Research Center, University of California Irvine, Irvine, California 92697, United States
| | - Tristan Asset
- Department of Chemical and Biomolecular Engineering, National Fuel Cell Research Center, University of California Irvine, Irvine, California 92697, United States
| | - Plamen Atanassov
- Department of Chemical and Biomolecular Engineering, National Fuel Cell Research Center, University of California Irvine, Irvine, California 92697, United States
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24
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Jaswal K, Shrivastava M, Chaba R. Revisiting long-chain fatty acid metabolism in Escherichia coli: integration with stress responses. Curr Genet 2021; 67:573-582. [PMID: 33740112 DOI: 10.1007/s00294-021-01178-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 12/29/2022]
Abstract
Long-chain fatty acids (LCFAs) are a tremendous source of metabolic energy, an essential component of membranes, and important effector molecules that regulate a myriad of cellular processes. As an energy-rich nutrient source, the role of LCFAs in promoting bacterial survival and infectivity is well appreciated. LCFA degradation generates a large number of reduced cofactors that may confer redox stress; therefore, it is imperative to understand how bacteria deal with this paradoxical situation. Although the LCFA utilization pathway has been studied in great detail, especially in Escherichia coli, where the earliest studies date back to the 1960s, the interconnection of LCFA degradation with bacterial stress responses remained largely unexplored. Recent work in E. coli shows that LCFA degradation induces oxidative stress and also impedes oxidative protein folding. Importantly, both issues arise due to the insufficiency of ubiquinone, a lipid-soluble electron carrier in the electron transport chain. However, to maintain redox homeostasis, bacteria induce sophisticated cellular responses. Here, we review these findings in light of our current knowledge of the LCFA metabolic pathway, metabolism-induced oxidative stress, the process of oxidative protein folding, and stress combat mechanisms. We discuss probable mechanisms for the activation of defense players during LCFA metabolism and the likely feedback imparted by them. We suggest that besides defending against intrinsic stresses, LCFA-mediated upregulation of stress response pathways primes bacteria to adapt to harsh external environments. Collectively, the interplay between LCFA metabolism and stress responses is likely an important factor that underlies the success of LCFA-utilizing bacteria in the host.
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Affiliation(s)
- Kanchan Jaswal
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Megha Shrivastava
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Rachna Chaba
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India.
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25
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Cyrino LAR, Delwing-de Lima D, Ullmann OM, Maia TP. Concepts of Neuroinflammation and Their Relationship With Impaired Mitochondrial Functions in Bipolar Disorder. Front Behav Neurosci 2021; 15:609487. [PMID: 33732117 PMCID: PMC7959852 DOI: 10.3389/fnbeh.2021.609487] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/18/2021] [Indexed: 12/24/2022] Open
Abstract
Bipolar disorder (BD) is a chronic psychiatric disease, characterized by frequent behavioral episodes of depression and mania, and neurologically by dysregulated neurotransmission, neuroplasticity, growth factor signaling, and metabolism, as well as oxidative stress, and neuronal apoptosis, contributing to chronic neuroinflammation. These abnormalities result from complex interactions between multiple susceptibility genes and environmental factors such as stress. The neurocellular abnormalities of BD can result in gross morphological changes, such as reduced prefrontal and hippocampal volume, and circuit reorganization resulting in cognitive and emotional deficits. The term "neuroprogression" is used to denote the progressive changes from early to late stages, as BD severity and loss of treatment response correlate with the number of past episodes. In addition to circuit and cellular abnormalities, BD is associated with dysfunctional mitochondria, leading to severe metabolic disruption in high energy-demanding neurons and glia. Indeed, mitochondrial dysfunction involving electron transport chain (ETC) disruption is considered the primary cause of chronic oxidative stress in BD. The ensuing damage to membrane lipids, proteins, and DNA further perpetuates oxidative stress and neuroinflammation, creating a perpetuating pathogenic cycle. A deeper understanding of BD pathophysiology and identification of associated biomarkers of neuroinflammation are needed to facilitate early diagnosis and treatment of this debilitating disorder.
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Affiliation(s)
- Luiz Arthur Rangel Cyrino
- Programa de Pós-Graduação em Saúde e Meio Ambiente, Laboratório de Práticas Farmacêuticas of Department of Pharmacy, University of Joinville Region—UNIVILLE, Joinville, Brazil
- Department of Psychology, University of Joinville—UNIVILLE, Joinville, Brazil
- Department of Pharmacy, University of Joinville—UNIVILLE, Joinville, Brazil
| | - Daniela Delwing-de Lima
- Programa de Pós-Graduação em Saúde e Meio Ambiente, Laboratório de Práticas Farmacêuticas of Department of Pharmacy, University of Joinville Region—UNIVILLE, Joinville, Brazil
- Department of Pharmacy, University of Joinville—UNIVILLE, Joinville, Brazil
- Department of Medicine, University of Joinville—UNIVILLE, Joinville, Brazil
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Durall C, Kukil K, Hawkes JA, Albergati A, Lindblad P, Lindberg P. Production of succinate by engineered strains of Synechocystis PCC 6803 overexpressing phosphoenolpyruvate carboxylase and a glyoxylate shunt. Microb Cell Fact 2021; 20:39. [PMID: 33557832 PMCID: PMC7871529 DOI: 10.1186/s12934-021-01529-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/25/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Cyanobacteria are promising hosts for the production of various industrially important compounds such as succinate. This study focuses on introduction of the glyoxylate shunt, which is naturally present in only a few cyanobacteria, into Synechocystis PCC 6803. In order to test its impact on cell metabolism, engineered strains were evaluated for succinate accumulation under conditions of light, darkness and anoxic darkness. Each condition was complemented by treatments with 2-thenoyltrifluoroacetone, an inhibitor of succinate dehydrogenase enzyme, and acetate, both in nitrogen replete and deplete medium. RESULTS We were able to introduce genes encoding the glyoxylate shunt, aceA and aceB, encoding isocitrate lyase and malate synthase respectively, into a strain of Synechocystis PCC 6803 engineered to overexpress phosphoenolpyruvate carboxylase. Our results show that complete expression of the glyoxylate shunt results in higher extracellular succinate accumulation compared to the wild type control strain after incubation of cells in darkness and anoxic darkness in the presence of nitrate. Addition of the inhibitor 2-thenoyltrifluoroacetone increased succinate titers in all the conditions tested when nitrate was available. Addition of acetate in the presence of the inhibitor further increased the succinate accumulation, resulting in high levels when phosphoenolpyruvate carboxylase was overexpressed, compared to control strain. However, the highest succinate titer was obtained after dark incubation of an engineered strain with a partial glyoxylate shunt overexpressing isocitrate lyase in addition to phosphoenolpyruvate carboxylase, with only 2-thenoyltrifluoroacetone supplementation to the medium. CONCLUSIONS Heterologous expression of the glyoxylate shunt with its central link to the tricarboxylic acid cycle (TCA) for acetate assimilation provides insight on the coordination of the carbon metabolism in the cell. Phosphoenolpyruvate carboxylase plays an important role in directing carbon flux towards the TCA cycle.
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Affiliation(s)
- Claudia Durall
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Kateryna Kukil
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Jeffrey A Hawkes
- Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, Box 599, 751 20, Uppsala, Sweden
| | - Alessia Albergati
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Pia Lindberg
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden.
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Pan L, Tian Y, Sun H, Wang Y, Liu G. TMT-based proteomics analysis reveals the efficacy of jiangzhuo formula in improving the lipid profiles of dyslipidemia rats. JOURNAL OF ETHNOPHARMACOLOGY 2021; 264:113390. [PMID: 32931881 DOI: 10.1016/j.jep.2020.113390] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/17/2020] [Accepted: 09/09/2020] [Indexed: 06/11/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Jiangzhuo Formula (JZF) is a traditional Chinese herbal prescription that is clinically applied to treat dyslipidemia. However, the mechanism underlying its efficacy remains unexplored. AIM OF THE STUDY This study aims to elucidate the underlying mechanisms, explore potential pathways, and identify the key proteins of JZF for the treatment of dyslipidemia. METHODS In this work, Q-Orbitrap high-resolution liquid chromatography mass spectrometry was used to identify the natural ingredients in JZF, rats with dyslipidemia were established via a high-fat diet for four weeks, then the dyslipidemia rats were treated with high-dose JZF (9 g/d) and low-dose JZF (4.5 g/d) for four weeks. After treatment, serum lipid detection and Oil-red-O staining were conducted to assess the efficacy of JZF in ameliorating dyslipidemia. Tandem mass tag (TMT) -based quantitative proteomics technology was then used to evaluate the roles and importance of proteins from the extracted hepatic tissue. The differentially expressed proteins were assessed by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, Gene Ontology (GO), and protein-protein interaction (PPI) networks. Western blot and PCR analysis were used to validate the potential targets regulated by JZF. RESULTS JZF could significantly improve the blood lipid profiles of serum and fat deposits of the liver. A total of 123 differentially expressed proteins were detected after JZF intervention, comprising 65 up-regulated proteins and 58 down-regulated proteins. The KEGG pathway analysis revealed that cholesterol metabolism, the PPAR signaling pathway, and bile secretion were the principal pathways involved in the disordered lipid metabolism, while GO analysis suggested that proteins that are located in the cell, regulate cellular processes, and show binding activity contribute to reductions in lipids. The combination of proteomics, Western blot, and PCR suggested that Apolipoprotein B (APOB), Apolipoprotein E (APOE), cholesterol 7 alpha-hydroxylase A1 (CYP7A1), and Hydroxymethylglutaryl-CoA synthase 1 (HMGCS1) might play critical roles in JZF's lipid-lowering network. CONCLUSION JZF can effectively improve lipid profiles via multiple pathways involved in cholesterol metabolism, the PPAR signaling pathway, and bile secretion. Generally, the proteomics techniques used in this research show that JZF could be a promising drug for the treatment of dyslipidemia.
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Affiliation(s)
- Linlin Pan
- Department of Chinese Medicine Literature and Culture, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China.
| | - Yuan Tian
- Department of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China.
| | - Haiyang Sun
- Department of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China.
| | - Yao Wang
- Department of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China.
| | - Guirong Liu
- Department of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China.
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28
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Shahriar S, Ahsan T, Khan A, Akhteruzzaman S, Shehreen S, Sajib AA. Aspartame, acesulfame K and sucralose- influence on the metabolism of Escherichia coli. Metabol Open 2020; 8:100072. [PMID: 33336183 PMCID: PMC7732866 DOI: 10.1016/j.metop.2020.100072] [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: 10/25/2020] [Revised: 11/18/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Gut microbes play a crucial role in the maintenance of human health. Components in the diet of the host affect their metabolism and diversity. Here, we investigated the influences of three commonly used non-caloric artificial sweeteners-aspartame, acesulfame K and sucralose-on the growth and metabolism of an omnipresent gut microbe Escherichia coli K-12. Methods: Growth of E. coli in the presence of aspartame, acesulfame K and sucralose in media was assessed and the influences of these artificial sweeteners on metabolism were investigated by relative expression analysis of genes encoding the rate limiting steps of important metabolic pathways as well as their global metabolomic profiles. Results: As a whole, E. coli growth was inhibited by aspartame and induced by acesulfame potassium, while the effect of sucralose on growth was less prominent. Although the expressions of multiple key enzymes that regulate important metabolic pathways were significantly altered by all three sweeteners, acesulfame K caused the most notable changes in this regard. In multivariate analysis with the metabolite profiles, the sucralose-treated cells clustered the closest to the untreated cells, while the acesulfame potassium treated cells were the most distant. These sweeteners affect multiple metabolic pathways in E. coli, which include propanoate, phosphonate, phosphinate and fatty acid metabolism, pentose phosphate pathway, and biosynthesis of several amino acids including lysine and the aromatic amino acids. Similar to the gene expression pattern, acesulfame potassium treated E. coli showed the largest deviation in their metabolite profiles compared to the untreated cells.
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Affiliation(s)
- Shayan Shahriar
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Tamim Ahsan
- Department of Genetic Engineering & Biotechnology, Bangabandhu Sheikh Mujibur Rahman Maritime University, Dhaka, Bangladesh
| | - Abira Khan
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Sharif Akhteruzzaman
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Saadlee Shehreen
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Abu Ashfaqur Sajib
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
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29
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Mu Y, Li W, Wei Z, He L, Zhang W, Chen X. Transcriptome analysis reveals molecular strategies in gills and heart of large yellow croaker (Larimichthys crocea) under hypoxia stress. FISH & SHELLFISH IMMUNOLOGY 2020; 104:304-313. [PMID: 32544557 DOI: 10.1016/j.fsi.2020.06.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/07/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
The gills and heart are two major targets of hypoxia in fish. However, the molecular responses in fish gills and heart to hypoxia challenge remain unclear. Here, RNA-Seq technology was used to study the gene expression profiles in gills and heart of large yellow croaker (Larimichthys crocea) at 6, 24, and 48 h after hypoxia stress. A total of 1,546 and 2,746 differentially expressed genes (DEGs) were identified in gills and heart, respectively. Expression changes of nine genes in each tissue were further validated by the qPCR. Based on KEGG and Gene ontology enrichments, we found that various innate immunity-related genes, such as complement components (C1qs, C2, C3, C6, and C7), chemokines (CCL3, CCL17, CCL19, CCL25, and CXCL8_L3), chemokine receptors (CCR9, CXCR1, and CXCR3), and nitric oxide synthase (NOS), were significantly down-regulated in gills and/or heart, suggesting that innate immune processes mediated by these genes may be inhibited by hypoxia. The genes involved in both glycolysis pathway (LDHA) and tricarboxylic acid cycle (IDH2 and OGDH) were up-regulated in gills and heart of hypoxic large yellow croakers, possibly because gill and heart tissues need enough energy to accelerate gas exchange and blood circulation. Hypoxia also affected the ion transport in gills of large yellow croaker, through down-regulating the expression levels of numerous classical ion transporters, including HVCN1, SLC20A2, SLC4A4, RHBG, RHCG, and SCN4A, suggesting an energy conservation strategy to hypoxia stress. All these results indicate that the immune processes, glycolytic pathways, and ion transport were significantly altered in gills and/or heart of large yellow croaker under hypoxia, possibly contributing to maintain cellular energy balance during hypoxia. Our data, therefore, afford new information to understand the tissue-specific molecular responses of bony fish to hypoxia stress.
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Affiliation(s)
- Yinnan Mu
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Wanru Li
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Zuyun Wei
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Lianghua He
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Weini Zhang
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Xinhua Chen
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, PR China.
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30
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Silveira CB, Luque A, Roach TN, Villela H, Barno A, Green K, Reyes B, Rubio-Portillo E, Le T, Mead S, Hatay M, Vermeij MJ, Takeshita Y, Haas A, Bailey B, Rohwer F. Biophysical and physiological processes causing oxygen loss from coral reefs. eLife 2019; 8:49114. [PMID: 31793432 PMCID: PMC6890468 DOI: 10.7554/elife.49114] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/27/2019] [Indexed: 12/25/2022] Open
Abstract
The microbialization of coral reefs predicts that microbial oxygen consumption will cause reef deoxygenation. Here we tested this hypothesis by analyzing reef microbial and primary producer oxygen metabolisms. Metagenomic data and in vitro incubations of bacteria with primary producer exudates showed that fleshy algae stimulate incomplete carbon oxidation metabolisms in heterotrophic bacteria. These metabolisms lead to increased cell sizes and abundances, resulting in bacteria consuming 10 times more oxygen than in coral incubations. Experiments probing the dissolved and gaseous oxygen with primary producers and bacteria together indicated the loss of oxygen through ebullition caused by heterogenous nucleation on algae surfaces. A model incorporating experimental production and loss rates predicted that microbes and ebullition can cause the loss of up to 67% of gross benthic oxygen production. This study indicates that microbial respiration and ebullition are increasingly relevant to reef deoxygenation as reefs become dominated by fleshy algae. Rising water temperatures, pollution and other factors are increasingly threatening corals and the entire reef ecosystems they build. The potential for corals to resist and recover from the stress these factors cause ultimately depends on their ability to compete against fast-growing fleshy algae that can rapidly take over the reefs. Living on the fleshy algae, the coral and in the surrounding water are communities of bacteria and other microbes that help maintain the health of the coral reef. Both corals and algae modify the chemical and physical environment of the reef to alter the composition of the microbial communities for their own benefit. Algae, for instance, release large amounts of sugars and other molecules of organic carbon into the water. These carbon molecules are then taken up by the bacteria, along with oxygen, to produce chemical energy via a process called respiration. This could cause the levels of oxygen in the water to decrease, potentially damaging the corals and creating more open space for the algae. Previous studies have revealed how communities of microbes on coral reefs use organic carbon, but it remains unclear how they affect the levels of oxygen in the reefs. To address this question, Silveira et al. used an approach called metagenomics to analyze the bacteria in samples of water from 87 reefs across the Pacific and the Caribbean, and also performed experiments with reef bacteria grown in the laboratory. The experiments showed that bacteria growing in the presence of fleshy algae became larger and more abundant than bacteria growing near corals, resulting in the water containing lower levels of oxygen. Furthermore, the fleshy algae produced bubbles of oxygen that were released from the water. Silveira et al. developed a mathematical model that predicted that these bubbles, combined with the respiration of bacteria that live near algae, caused the loss of 67% of the oxygen in the water surrounding the reef. These findings represent a fundamental step towards understanding how changes in the levels of oxygen in water affect the ability of coral reefs to resist and recover from stress.
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Affiliation(s)
- Cynthia B Silveira
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
| | - Antoni Luque
- Viral Information Institute, San Diego State University, San Diego, United States.,Computational Science Research Center, San Diego State University, San Diego, United States.,Department of Mathematics and Statistics, San Diego State University, San Diego, United States
| | - Ty Nf Roach
- Hawaii Institute of Marine Biology, University of Hawaii at Mānoa, Kāneohe, United States
| | - Helena Villela
- Department of Microbiology, Rio de Janeiro Federal University, Rio de Janeiro, Brazil
| | - Adam Barno
- Department of Microbiology, Rio de Janeiro Federal University, Rio de Janeiro, Brazil
| | - Kevin Green
- Department of Biology, San Diego State University, San Diego, United States
| | - Brandon Reyes
- Department of Biology, San Diego State University, San Diego, United States
| | - Esther Rubio-Portillo
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Tram Le
- Department of Biology, San Diego State University, San Diego, United States
| | - Spencer Mead
- Department of Biology, San Diego State University, San Diego, United States
| | - Mark Hatay
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
| | - Mark Ja Vermeij
- CARMABI Foundation, Willemstad, Curaçao.,Department of Freshwater and Marine Ecology, Institute for Biodiversity andEcosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | | | - Andreas Haas
- NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Barbara Bailey
- Department of Mathematics and Statistics, San Diego State University, San Diego, United States
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
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31
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Panyushkina AE, Babenko VV, Nikitina AS, Selezneva OV, Tsaplina IA, Letarova MA, Kostryukova ES, Letarov AV. Sulfobacillus thermotolerans: new insights into resistance and metabolic capacities of acidophilic chemolithotrophs. Sci Rep 2019; 9:15069. [PMID: 31636299 PMCID: PMC6803676 DOI: 10.1038/s41598-019-51486-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 09/23/2019] [Indexed: 11/09/2022] Open
Abstract
The first complete genome of the biotechnologically important species Sulfobacillus thermotolerans has been sequenced. Its 3 317 203-bp chromosome contains an 83 269-bp plasmid-like region, which carries heavy metal resistance determinants and the rusticyanin gene. Plasmid-mediated metal resistance is unusual for acidophilic chemolithotrophs. Moreover, most of their plasmids are cryptic and do not contribute to the phenotype of the host cells. A polyphosphate-based mechanism of metal resistance, which has been previously unknown in the genus Sulfobacillus or other Gram-positive chemolithotrophs, potentially operates in two Sulfobacillus species. The methylcitrate cycle typical for pathogens and identified in the genus Sulfobacillus for the first time can fulfill the energy and/or protective function in S. thermotolerans Kr1 and two other Sulfobacillus species, which have incomplete glyoxylate cycles. It is notable that the TCA cycle, disrupted in all Sulfobacillus isolates under optimal growth conditions, proved to be complete in the cells enduring temperature stress. An efficient antioxidant defense system gives S. thermotolerans another competitive advantage in the microbial communities inhabiting acidic metal-rich environments. The genomic comparisons revealed 80 unique genes in the strain Kr1, including those involved in lactose/galactose catabolism. The results provide new insights into metabolism and resistance mechanisms in the Sulfobacillus genus and other acidophiles.
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Affiliation(s)
- Anna E Panyushkina
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia.
| | - Vladislav V Babenko
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Anastasia S Nikitina
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Oksana V Selezneva
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Iraida A Tsaplina
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
| | - Maria A Letarova
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
| | - Elena S Kostryukova
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Andrey V Letarov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
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32
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Chen JJ, Xie J, Li WW, Bai SJ, Wang W, Zheng P, Xie P. Age-specific urinary metabolite signatures and functions in patients with major depressive disorder. Aging (Albany NY) 2019; 11:6626-6637. [PMID: 31493765 PMCID: PMC6756884 DOI: 10.18632/aging.102133] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/26/2019] [Indexed: 12/11/2022]
Abstract
Major depressive disorder (MDD) patients in different age ranges might have different urinary metabolic phenotypes, because age could significantly affect the physiological and psychological status of person. Therefore, it was very important to take age into consideration when studying MDD. Here, a dual platform metabolomic approach was performed to profile urine samples from young and middle-aged MDD patients. In total, 18 and 15 differential metabolites that separately discriminated young and middle-aged MDD patients, respectively, from their respective HC were identified. Only ten metabolites were significantly disturbed in both young and middle-aged MDD patients. Meanwhile, two different biomarker panels for diagnosing young and middle-aged MDD patients, respectively, were identified. Additionally, the TCA cycle was significantly affected in both young and middle-aged MDD patients, but the Glyoxylate and dicarboxylate metabolism and phenylalanine metabolism were only significantly affected in young and middle-aged MDD patients, respectively. Our results would be helpful for developing age-specific diagnostic method for MDD and further investigating the pathogenesis of this disease.
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Affiliation(s)
- Jian-Jun Chen
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Jing Xie
- Department of Endocrinology and Nephrology, Chongqing University Central Hospital, Chongqing Emergency Medical Center, Chongqing 400014, China
| | - Wen-Wen Li
- Department of Pathology, Faculty of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Shun-Jie Bai
- Department of Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Wei Wang
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing 400016, China
| | - Peng Zheng
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing 400016, China
| | - Peng Xie
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing 400016, China.,Department of Neurology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.,Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing 400016, China
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Miyakoshi M, Matera G, Maki K, Sone Y, Vogel J. Functional expansion of a TCA cycle operon mRNA by a 3' end-derived small RNA. Nucleic Acids Res 2019; 47:2075-2088. [PMID: 30541135 PMCID: PMC6393394 DOI: 10.1093/nar/gky1243] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/13/2018] [Accepted: 12/01/2018] [Indexed: 01/24/2023] Open
Abstract
Global RNA profiling studies in bacteria have predicted the existence of many of small noncoding RNAs (sRNAs) that are processed off mRNA 3′ ends to regulate other mRNAs via the RNA chaperones Hfq and ProQ. Here, we present targets of SdhX (RybD), an Hfq-dependent sRNA that is generated by RNase E mediated 3′ processing of the ∼10 000-nt mRNA of the TCA cycle operon sdhCDAB-sucABCD in enteric bacteria. An in silico search predicted ackA mRNA, which encodes acetate kinase, as a conserved primary target of SdhX. Through base pairing, SdhX represses AckA synthesis during growth of Salmonella on acetate. Repression can be achieved by a naturally occurring 38-nucleotide SdhX variant, revealing the shortest functional Hfq-associated sRNA yet. Salmonella SdhX also targets the mRNAs of fumB (anaerobic fumarase) and yfbV, a gene of unknown function adjacent to ackA. Instead, through a slightly different seed sequence, SdhX can repress other targets in Escherichia coli, namely katG (catalase) and fdoG (aerobic formate dehydrogenase). This study illustrates how a key operon from central metabolism is functionally connected to other metabolic pathways through a 3′ appended sRNA, and supports the notion that mRNA 3′UTRs are a playground for the evolution of regulatory RNA networks in bacteria.
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Affiliation(s)
- Masatoshi Miyakoshi
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 305-8575 Tsukuba, Japan.,Department of Biotechnology, Akita Prefectural University, 010-0195 Akita, Japan.,Center for Food Science and Wellness, Gunma University, 371-8510 Maebashi, Japan.,RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Gianluca Matera
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Kanako Maki
- Department of Biotechnology, Akita Prefectural University, 010-0195 Akita, Japan
| | - Yasuhiro Sone
- Department of Biotechnology, Akita Prefectural University, 010-0195 Akita, Japan
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research, D-97080 Würzburg, Germany
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34
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Gottesman S. Trouble is coming: Signaling pathways that regulate general stress responses in bacteria. J Biol Chem 2019; 294:11685-11700. [PMID: 31197038 DOI: 10.1074/jbc.rev119.005593] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteria can rapidly and reversibly respond to changing environments via complex transcriptional and post-transcriptional regulatory mechanisms. Many of these adaptations are specific, with the regulatory output tailored to the inducing signal (for instance, repairing damage to cell components or improving acquisition and use of growth-limiting nutrients). However, the general stress response, activated in bacterial cells entering stationary phase or subjected to nutrient depletion or cellular damage, is unique in that its common, broad output is induced in response to many different signals. In many different bacteria, the key regulator for the general stress response is a specialized sigma factor, the promoter specificity subunit of RNA polymerase. The availability or activity of the sigma factor is regulated by complex regulatory circuits, the majority of which are post-transcriptional. In Escherichia coli, multiple small regulatory RNAs, each made in response to a different signal, positively regulate translation of the general stress response sigma factor RpoS. Stability of RpoS is regulated by multiple anti-adaptor proteins that are also synthesized in response to different signals. In this review, the modes of signaling to and levels of regulation of the E. coli general stress response are discussed. They are also used as a basis for comparison with the general stress response in other bacteria with the aim of extracting key principles that are common among different species and highlighting important unanswered questions.
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Affiliation(s)
- Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
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35
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Spietz RL, Lundeen RA, Zhao X, Nicastro D, Ingalls AE, Morris RM. Heterotrophic carbon metabolism and energy acquisition in Candidatus Thioglobus singularis strain PS1, a member of the SUP05 clade of marine Gammaproteobacteria. Environ Microbiol 2019; 21:2391-2401. [PMID: 30951247 DOI: 10.1111/1462-2920.14623] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 11/30/2022]
Abstract
A hallmark of the SUP05 clade of marine Gammaproteobacteria is the ability to use energy obtained from reduced inorganic sulfur to fuel autotrophic fixation of carbon using RuBisCo. However, some SUP05 also have the genetic potential for heterotrophic growth, raising questions about the roles of SUP05 in the marine carbon cycle. We used genomic reconstructions, physiological growth experiments and proteomics to characterize central carbon and energy metabolism in Candidatus Thioglobus singularis strain PS1, a representative from the SUP05 clade that has the genetic potential for autotrophy and heterotrophy. Here, we show that the addition of individual organic compounds and 0.2 μm filtered diatom lysate significantly enhanced the growth of this bacterium. This positive growth response to organic substrates, combined with expression of a complete TCA cycle, heterotrophic pathways for carbon assimilation, and methylotrophic pathways for energy conversion demonstrate strain PS1's capacity for heterotrophic growth. Further, our inability to verify the expression of RuBisCO suggests that carbon fixation was not critical for growth. These results highlight the metabolic diversity of the SUP05 clade that harbours both primary producers and consumers of organic carbon in the oceans and expand our understanding of specific pathways of organic matter oxidation by the heterotrophic SUP05.
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Affiliation(s)
- Rachel L Spietz
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Rachel A Lundeen
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Xiaowei Zhao
- Department of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Daniela Nicastro
- Department of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Robert M Morris
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
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Amato P, Besaury L, Joly M, Penaud B, Deguillaume L, Delort AM. Metatranscriptomic exploration of microbial functioning in clouds. Sci Rep 2019; 9:4383. [PMID: 30867542 PMCID: PMC6416334 DOI: 10.1038/s41598-019-41032-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/27/2019] [Indexed: 01/19/2023] Open
Abstract
Clouds constitute the uppermost layer of the biosphere. They host diverse communities whose functioning remains obscure, although biological activity potentially participates to atmospheric chemical and physical processes. In order to gain information on the metabolic functioning of microbial communities in clouds, we conducted coordinated metagenomics/metatranscriptomics profiling of cloud water microbial communities. Samples were collected from a high altitude atmospheric station in France and examined for biological content after untargeted amplification of nucleic acids. Living microorganisms, essentially bacteria, maintained transcriptional and translational activities and expressed many known complementary physiological responses intended to fight oxidants, osmotic variations and cold. These included activities of oxidant detoxification and regulation, synthesis of osmoprotectants/cryoprotectants, modifications of membranes, iron uptake. Consistently these energy-demanding processes were fueled by central metabolic routes involved in oxidative stress response and redox homeostasis management, such as pentose phosphate and glyoxylate pathways. Elevated binding and transmembrane ion transports demonstrated important interactions between cells and their cloud droplet chemical environments. In addition, polysaccharides, potentially beneficial for survival like exopolysaccharides, biosurfactants and adhesins, were synthesized. Our results support a biological influence on cloud physical and chemical processes, acting notably on the oxidant capacity, iron speciation and availability, amino-acids distribution and carbon and nitrogen fates.
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Affiliation(s)
- Pierre Amato
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000, Clermont-Ferrand, France.
| | - Ludovic Besaury
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000, Clermont-Ferrand, France
| | - Muriel Joly
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000, Clermont-Ferrand, France
| | - Benjamin Penaud
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000, Clermont-Ferrand, France
| | | | - Anne-Marie Delort
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000, Clermont-Ferrand, France
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Nitta K, Laviña WA, Pontrelli S, Liao JC, Putri SP, Fukusaki E. Metabolome analysis revealed the knockout of glyoxylate shunt as an effective strategy for improvement of 1-butanol production in transgenic Escherichia coli. J Biosci Bioeng 2019; 127:301-308. [DOI: 10.1016/j.jbiosc.2018.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 08/27/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022]
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Thommes M, Wang T, Zhao Q, Paschalidis IC, Segrè D. Designing Metabolic Division of Labor in Microbial Communities. mSystems 2019; 4:e00263-18. [PMID: 30984871 PMCID: PMC6456671 DOI: 10.1128/msystems.00263-18] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/15/2019] [Indexed: 12/19/2022] Open
Abstract
Microbes face a trade-off between being metabolically independent and relying on neighboring organisms for the supply of some essential metabolites. This balance of conflicting strategies affects microbial community structure and dynamics, with important implications for microbiome research and synthetic ecology. A "gedanken" (thought) experiment to investigate this trade-off would involve monitoring the rise of mutual dependence as the number of metabolic reactions allowed in an organism is increasingly constrained. The expectation is that below a certain number of reactions, no individual organism would be able to grow in isolation and cross-feeding partnerships and division of labor would emerge. We implemented this idealized experiment using in silico genome-scale models. In particular, we used mixed-integer linear programming to identify trade-off solutions in communities of Escherichia coli strains. The strategies that we found revealed a large space of opportunities in nuanced and nonintuitive metabolic division of labor, including, for example, splitting the tricarboxylic acid (TCA) cycle into two separate halves. The systematic computation of possible solutions in division of labor for 1-, 2-, and 3-strain consortia resulted in a rich and complex landscape. This landscape displayed a nonlinear boundary, indicating that the loss of an intracellular reaction was not necessarily compensated for by a single imported metabolite. Different regions in this landscape were associated with specific solutions and patterns of exchanged metabolites. Our approach also predicts the existence of regions in this landscape where independent bacteria are viable but are outcompeted by cross-feeding pairs, providing a possible incentive for the rise of division of labor. IMPORTANCE Understanding how microbes assemble into communities is a fundamental open issue in biology, relevant to human health, metabolic engineering, and environmental sustainability. A possible mechanism for interactions of microbes is through cross-feeding, i.e., the exchange of small molecules. These metabolic exchanges may allow different microbes to specialize in distinct tasks and evolve division of labor. To systematically explore the space of possible strategies for division of labor, we applied advanced optimization algorithms to computational models of cellular metabolism. Specifically, we searched for communities able to survive under constraints (such as a limited number of reactions) that would not be sustainable by individual species. We found that predicted consortia partition metabolic pathways in ways that would be difficult to identify manually, possibly providing a competitive advantage over individual organisms. In addition to helping understand diversity in natural microbial communities, our approach could assist in the design of synthetic consortia.
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Affiliation(s)
- Meghan Thommes
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Taiyao Wang
- Division of Systems Engineering, Boston University, Boston, Massachusetts, USA
| | - Qi Zhao
- Division of Systems Engineering, Boston University, Boston, Massachusetts, USA
| | - Ioannis C. Paschalidis
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, USA
- Division of Systems Engineering, Boston University, Boston, Massachusetts, USA
| | - Daniel Segrè
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biology, Boston University, Boston, Massachusetts, USA
- Department of Physics, Boston University, Boston, Massachusetts, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
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Boerboom G, van Kempen T, Navarro-Villa A, Pérez-Bonilla A. Unraveling the cause of white striping in broilers using metabolomics. Poult Sci 2018; 97:3977-3986. [PMID: 29931266 PMCID: PMC6162359 DOI: 10.3382/ps/pey266] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/28/2018] [Indexed: 01/10/2023] Open
Abstract
White striping (WS) is a major problem affecting the broiler industry. Fillets affected by this myopathy present pathologies that compromise the quality of the meat, and most importantly, make the fillets more prone to rejection by the consumer. The exact etiology is still unknown, which is why a metabolomics analysis was performed on breast samples of broilers. The overall objective was to identify biological pathways involved in the pathogenesis of WS. The analysis was performed on a total of 51 muscle samples and distinction was made between normal (n = 19), moderately affected (n = 24) and severely affected (n = 8) breast fillets. Samples were analyzed using gas chromatographic mass spectral analysis and liquid chromatography quadrupole time-of-flight mass spectrometry. Data were subsequently standardized, normalized and analyzed using various multivariate statistical procedures. Metabolomics allowed for the identification of several pathways that were altered in white striped breast fillets. The tricarboxylic acid cycle exhibited opposing directionalities. This is described in literature as the backflux and enables the TCA cycle to produce high-energy phosphates through matrix-level phosphorylation and, therefore, produce energy under conditions of hypoxia. Mitochondrial fatty acid oxidation was limited due to disturbances in especially cis-5–14:1 carnitine (log2 FC of 2, P < 0.01). Because of this, accumulation of harmful fatty acids took place, especially long-chain ones, which damages cell structures. Conversion of arginine to citrulline increased presumably to produce nitric oxide, which enhances blood flow under conditions of hypoxia. Nitric oxide however also increases oxidative damage. Increases in taurine (log2 FC of 1.2, P < 0.05) suggests stabilization of the sarcolemma under hypoxic conditions. Lastly, organic osmolytes (sorbitol, taurine, and alanine) increased (P < 0.05) in severely affected birds; likely this disrupts cell volume maintenance. Based on the results of this study, hypoxia was the most likely cause/initiator of WS in broilers. We speculate that birds suffering from WS have a vascular support system in muscle that is borderline adequate to support growth, but triggers like activity results in local hypoxia that damages tissue.
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Affiliation(s)
- Gavin Boerboom
- Trouw Nutrition R&D Amersfoort, 3811 MH, The Netherlands
| | - Theo van Kempen
- Trouw Nutrition R&D Amersfoort, 3811 MH, The Netherlands.,Department of Animal Science, North Carolina State University, Raleigh, 27695, NC, USA
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Strecker A, Schubert C, Zedler S, Steinmetz P, Unden G. DcuA of aerobically grownEscherichia coliserves as a nitrogen shuttle (L‐aspartate/fumarate) for nitrogen uptake. Mol Microbiol 2018; 109:801-811. [DOI: 10.1111/mmi.14074] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/27/2018] [Accepted: 07/02/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Alexander Strecker
- Microbiology and Wine Research, Institute of Molecular Physiology (IMP) Johannes Gutenberg‐University Mainz Mainz 55099Germany
| | - Christopher Schubert
- Microbiology and Wine Research, Institute of Molecular Physiology (IMP) Johannes Gutenberg‐University Mainz Mainz 55099Germany
| | - Sandra Zedler
- Microbiology and Wine Research, Institute of Molecular Physiology (IMP) Johannes Gutenberg‐University Mainz Mainz 55099Germany
| | - Philipp Steinmetz
- Microbiology and Wine Research, Institute of Molecular Physiology (IMP) Johannes Gutenberg‐University Mainz Mainz 55099Germany
| | - Gottfried Unden
- Microbiology and Wine Research, Institute of Molecular Physiology (IMP) Johannes Gutenberg‐University Mainz Mainz 55099Germany
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Mekuchi M, Asakura T, Sakata K, Yamaguchi T, Teruya K, Kikuchi J. Intestinal microbiota composition is altered according to nutritional biorhythms in the leopard coral grouper (Plectropomus leopardus). PLoS One 2018; 13:e0197256. [PMID: 29856743 PMCID: PMC5983564 DOI: 10.1371/journal.pone.0197256] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/30/2018] [Indexed: 12/20/2022] Open
Abstract
Aquaculture is currently a major source of fish and has the potential to become a major source of protein in the future. These demands require efficient aquaculture. The intestinal microbiota plays an integral role that benefits the host, providing nutrition and modulating the immune system. Although our understanding of microbiota in fish gut has increased, comprehensive studies examining fish microbiota and host metabolism remain limited. Here, we investigated the microbiota and host metabolism in the coral leopard grouper, which is traded in Asian markets as a superior fish and has begun to be produced via aquaculture. We initially examined the structural changes of the gut microbiota using next-generation sequencing and found that the composition of microbiota changed between fasting and feeding conditions. The dominant phyla were Proteobacteria in fasting and Firmicutes in feeding; interchanging the dominant bacteria required 12 hours. Moreover, microbiota diversity was higher under feeding conditions than under fasting conditions. Multivariate analysis revealed that Proteobacteria are the key bacteria in fasting and Firmicutes and Fusobacteria are the key bacteria in feeding. Subsequently, we estimated microbiota functional capacity. Microbiota functional structure was relatively stable throughout the experiment; however, individual function activity changed according to feeding conditions. Taken together, these findings indicate that the gut microbiota could be a key factor to understanding fish feeding conditions and play a role in interactions with host metabolism. In addition, the composition of microbiota in ambient seawater directly affects the fish; therefore, it is important to monitor the microbiota in rearing tanks and seawater circulating systems.
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Affiliation(s)
- Miyuki Mekuchi
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
- National Fishery Research Institute of Fishery Sciences, Fishery Research and Education Organization, Kanazawa-ku, Yokohama, Japan
| | - Taiga Asakura
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Kenji Sakata
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | | | | | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, Aichi, Japan
- * E-mail:
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Li CF, Ma JQ, Huang DJ, Ma CL, Jin JQ, Yao MZ, Chen L. Comprehensive Dissection of Metabolic Changes in Albino and Green Tea Cultivars. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:2040-2048. [PMID: 29397711 DOI: 10.1021/acs.jafc.7b05623] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Albino tea cultivars are special mutants of tea plants with white or yellow leaf color. In this study, three albino tea cultivars, including 'Anji Baicha', 'Huangjinya', and 'Baijiguan', and two green tea cultivars, 'Longjing 43' and 'Fuding Dabaicha', were applied to metabolite profiling by gas chromatography-mass spectrometry and ultraperformance liquid chromatography-mass spectrometry. Multivariate analyses revealed significantly different metabolite phenotypes in leaves among albino cultivars and green cultivars. The differential metabolite-related pathways included galactose metabolism, tryptophan metabolism, phenylpropanoid biosynthesis, and flavonoid biosynthesis. For the young leaves of albino cultivars, the sugar (sorbitol and erythrose) and amino acid (mainly proline, isoleucine, ornithine, aspartic acid, threonine, and valine) concentrations increased, whereas gallocatechin and epigallocatechin gallate concentrations decreased. These results reveal the divergence in metabolic profiling between tea plant cultivars with different leaf colors. With the development of leaves, the concentrations of flavonoids increased largely in the older leaves of albino cultivars.
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Affiliation(s)
- Chun-Fang Li
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute of the Chinese Academy of Agricultural Sciences , Hangzhou, Zhejiang 310008, People's Republic of China
- School of Agriculture and Food Science, Zhejiang Agriculture and Forestry University , Lin'an, Hangzhou, Zhejiang 311300, People's Republic of China
| | - Jian-Qiang Ma
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute of the Chinese Academy of Agricultural Sciences , Hangzhou, Zhejiang 310008, People's Republic of China
| | - Dan-Juan Huang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute of the Chinese Academy of Agricultural Sciences , Hangzhou, Zhejiang 310008, People's Republic of China
| | - Chun-Lei Ma
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute of the Chinese Academy of Agricultural Sciences , Hangzhou, Zhejiang 310008, People's Republic of China
| | - Ji-Qiang Jin
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute of the Chinese Academy of Agricultural Sciences , Hangzhou, Zhejiang 310008, People's Republic of China
| | - Ming-Zhe Yao
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute of the Chinese Academy of Agricultural Sciences , Hangzhou, Zhejiang 310008, People's Republic of China
| | - Liang Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute of the Chinese Academy of Agricultural Sciences , Hangzhou, Zhejiang 310008, People's Republic of China
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Engineering Escherichia coli for glycolic acid production from D-xylose through the Dahms pathway and glyoxylate bypass. Appl Microbiol Biotechnol 2018; 102:2179-2189. [DOI: 10.1007/s00253-018-8744-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/20/2017] [Accepted: 12/26/2017] [Indexed: 11/25/2022]
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Cellular Concentrations of the Transporters DctA and DcuB and the Sensor DcuS of Escherichia coli and the Contributions of Free and Complexed DcuS to Transcriptional Regulation by DcuR. J Bacteriol 2018; 200:JB.00612-17. [PMID: 29203472 DOI: 10.1128/jb.00612-17] [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] [Accepted: 11/27/2017] [Indexed: 11/20/2022] Open
Abstract
In Escherichia coli, the catabolism of C4-dicarboxylates is regulated by the DcuS-DcuR two-component system. The functional state of the sensor kinase DcuS is controlled by C4-dicarboxylates (like fumarate) and complexation with the C4-dicarboxylate transporters DctA and DcuB, respectively. Free DcuS (DcuSF) is known to be constantly active even in the absence of fumarate, whereas the DcuB-DcuS and DctA-DcuS complexes require fumarate for activation. To elucidate the impact of the transporters on the functional state of DcuS and the concentrations of DcuSF and DcuB-DcuS (or DctA-DcuS), the absolute levels of DcuS, DcuB, and DctA were determined in aerobically or anaerobically grown cells by mass spectrometry. DcuS was present at a constant very low level (10 to 20 molecules DcuS/cell), whereas the levels of DcuB and DctA were higher (minimum, 200 molecules/cell) and further increased with fumarate (12.7- and 2.7-fold, respectively). Relating DcuS and DcuB contents with the functional state of DcuS allowed an estimation of the proportions of DcuS in the free (DcuSF) and the complexed (DcuB-DcuS) states. Unexpectedly, DcuSF levels were always low (<2% of total DcuS), ruling out earlier models that show DcuSF as the major species under noninducing conditions. In the absence of fumarate, when DcuSF is responsible for basal dcuB expression, up to 8% of the maximal DcuB levels are formed. These suffice for DcuB-DcuS complex formation and basal transport activity. In the presence of fumarate (>100 μM), the DcuB-DcuS complex drives the majority of dcuB expression and is thus responsible for induction.IMPORTANCE Two-component systems (TCS) are major devices for sensing by bacteria and adaptation to environmental cues. Membrane-bound sensor kinases of TCS often use accessory proteins of unknown function. The DcuS-DcuR TCS responds to C4-dicarboxylates and requires formation of the complex of DcuS with C4-dicarboxylate transporters DctA or DcuB. Free DcuS (DcuSF) is constitutively active in autophosphorylation and was supposed to have a major role under specific conditions. Here, absolute concentrations of DcuS, DcuB, and DctA were determined under activating and nonactivating conditions by mass spectrometry. The relationship of their absolute contents to the functional state of DcuS revealed their contribution to the control of DcuS-DcuR in vivo, which was not accessible by other approaches, leading to a revision of previous models.
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Spiga L, Winter MG, Furtado de Carvalho T, Zhu W, Hughes ER, Gillis CC, Behrendt CL, Kim J, Chessa D, Andrews-Polymenis HL, Beiting DP, Santos RL, Hooper LV, Winter SE. An Oxidative Central Metabolism Enables Salmonella to Utilize Microbiota-Derived Succinate. Cell Host Microbe 2017; 22:291-301.e6. [PMID: 28844888 DOI: 10.1016/j.chom.2017.07.018] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 06/23/2017] [Accepted: 07/28/2017] [Indexed: 12/31/2022]
Abstract
The mucosal inflammatory response induced by Salmonella serovar Typhimurium creates a favorable niche for this gut pathogen. Conventional wisdom holds that S. Typhimurium undergoes an incomplete tricarboxylic acid (TCA) cycle in the anaerobic mammalian gut. One change during S. Typhimurium-induced inflammation is the production of oxidized compounds by infiltrating neutrophils. We show that inflammation-derived electron acceptors induce a complete, oxidative TCA cycle in S. Typhimurium, allowing the bacteria to compete with the microbiota for colonization. A complete TCA cycle facilitates utilization of the microbiota-derived fermentation product succinate as a carbon source. S. Typhimurium succinate utilization genes contribute to efficient colonization in conventionally raised mice, but provide no growth advantage in germ-free mice. Mono-association of gnotobiotic mice with Bacteroides, a major succinate producer, restores succinate utilization in S. Typhimurium. Thus, oxidative central metabolism enables S. Typhimurium to utilize a variety of carbon sources, including microbiota-derived succinate.
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Affiliation(s)
- Luisella Spiga
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maria G Winter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tatiane Furtado de Carvalho
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Wenhan Zhu
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elizabeth R Hughes
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Caroline C Gillis
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cassie L Behrendt
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiwoong Kim
- Department of Clinical Science, Quantitative Biomedical Research Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Daniela Chessa
- Department of Biomedical Science, School of Medicine, University of Sassari, Sassari, Italy
| | - Helene L Andrews-Polymenis
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University System Health Science Center, Bryan, TX 77807, USA
| | - Daniel P Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Renato L Santos
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Lora V Hooper
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sebastian E Winter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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Tao L, Zhang Y, Fan S, Nobile CJ, Guan G, Huang G. Integration of the tricarboxylic acid (TCA) cycle with cAMP signaling and Sfl2 pathways in the regulation of CO2 sensing and hyphal development in Candida albicans. PLoS Genet 2017; 13:e1006949. [PMID: 28787458 PMCID: PMC5567665 DOI: 10.1371/journal.pgen.1006949] [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: 06/19/2017] [Revised: 08/22/2017] [Accepted: 07/28/2017] [Indexed: 11/23/2022] Open
Abstract
Morphological transitions and metabolic regulation are critical for the human fungal pathogen Candida albicans to adapt to the changing host environment. In this study, we generated a library of central metabolic pathway mutants in the tricarboxylic acid (TCA) cycle, and investigated the functional consequences of these gene deletions on C. albicans biology. Inactivation of the TCA cycle impairs the ability of C. albicans to utilize non-fermentable carbon sources and dramatically attenuates cell growth rates under several culture conditions. By integrating the Ras1-cAMP signaling pathway and the heat shock factor-type transcription regulator Sfl2, we found that the TCA cycle plays fundamental roles in the regulation of CO2 sensing and hyphal development. The TCA cycle and cAMP signaling pathways coordinately regulate hyphal growth through the molecular linkers ATP and CO2. Inactivation of the TCA cycle leads to lowered intracellular ATP and cAMP levels and thus affects the activation of the Ras1-regulated cAMP signaling pathway. In turn, the Ras1-cAMP signaling pathway controls the TCA cycle through both Efg1- and Sfl2-mediated transcriptional regulation in response to elevated CO2 levels. The protein kinase A (PKA) catalytic subunit Tpk1, but not Tpk2, may play a major role in this regulation. Sfl2 specifically binds to several TCA cycle and hypha-associated genes under high CO2 conditions. Global transcriptional profiling experiments indicate that Sfl2 is indeed required for the gene expression changes occurring in response to these elevated CO2 levels. Our study reveals the regulatory role of the TCA cycle in CO2 sensing and hyphal development and establishes a novel link between the TCA cycle and Ras1-cAMP signaling pathways. Energy metabolism through the TCA cycle and mitochondrial electron transport are critical for the human fungal pathogen Candida albicans to survive and propagate in the host. This is, in part, due to the fact that C. albicans is a Crabtree-negative species, and thus exclusively uses respiration when oxygen is available. Here, we investigate the roles of the TCA cycle in hyphal development and CO2 sensing in C. albicans. Through the use of ATP and the cellular signaling molecule CO2, the TCA cycle integrates with the Ras1-cAMP signaling pathway, which is a central regulator of hyphal growth, to govern basic cellular biological processes. Together with Efg1, a downstream transcription factor of the cAMP signaling pathway, the heat shock factor-type transcription regulator Sfl2 controls CO2-induced hyphal growth in C. albicans. Deletion of SFL2 results in the loss of global transcriptional responses under elevated CO2 levels. Our study indicates that the TCA cycle not only occupies the central position of cellular metabolism but also regulates other biological processes such as CO2 sensing and hyphal development through integration with the Ras1-cAMP signaling pathway in C. albicans.
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Affiliation(s)
- Li Tao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yulong Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuru Fan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Clarissa J. Nobile
- Department of Molecular and Cell Biology, University of California, Merced, California, United States of America
| | - Guobo Guan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Guanghua Huang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail:
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Bouvet O, Bourdelier E, Glodt J, Clermont O, Denamur E. Diversity of the auxotrophic requirements in natural isolates of Escherichia coli. MICROBIOLOGY-SGM 2017; 163:891-899. [PMID: 28651684 DOI: 10.1099/mic.0.000482] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Isolates of Escherichia coli, except Shigella, are generally prototrophic; they do not require any growth factors to grow in mineral medium. However, a nicotinic acid requirement is common among B2 phylogroup STc95 O18 E. coli clone strains. Nicotinic acid is a precursor of nicotinamide adenine dinucleotide (NAD), an essential molecule that plays central role in cellular metabolism. The defect in NAD synthesis of these strains is due to alterations in de novo biosynthesis pathway nadB gene. Here, by studying growth on minimal medium with glycolytic (glucose) or gluconeogenic (pyruvate or succinate) substrates as the carbon supply in a large panel of E. coli natural isolates representative of the species diversity, we identify an absolute nicotinic acid requirement in non-STc95 strains due in one case to a nadA inactivation. The growth on glucose medium of some extraintestinal pathogenic E. coli strains belonging to various non-O18 B2 phylogroup STc95 clones is restored either by aspartate or nicotinate, demonstrating that the nicotinic acid requirement can also be due to an intracellular aspartate depletion. The auxotrophic requirements depend on the carbon source available in the environment. Moreover, some strains prototrophic in glucose medium become auxotrophic in succinate medium, and conversely, some strainsauxotrophic in glucose medium become prototrophic in succinate medium. Finally, a partial depletion of intracellular aspartate can be observed in some prototrophic strains belonging to various phylogroups. The observed more or less significant depletion according to isolates may be due to differences in tricarboxylic acid cycle enzyme activities. These metabolic defects could be involved in the adaptation of E. coli to its various niches.
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Affiliation(s)
- Odile Bouvet
- IAME, UMR 1137, INSERM, Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France
| | - Emmanuelle Bourdelier
- IAME, UMR 1137, INSERM, Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France
| | - Jeremy Glodt
- IAME, UMR 1137, INSERM, Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France
| | - Olivier Clermont
- IAME, UMR 1137, INSERM, Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France
| | - Erick Denamur
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, F-75018, Paris, France.,IAME, UMR 1137, INSERM, Univ Paris Diderot, Sorbonne Paris Cité, F-75018, Paris, France
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Lethal Consequences of Overcoming Metabolic Restrictions Imposed on a Cooperative Bacterial Population. mBio 2017; 8:mBio.00042-17. [PMID: 28246357 PMCID: PMC5347341 DOI: 10.1128/mbio.00042-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Quorum sensing (QS) controls cooperative activities in many Proteobacteria. In some species, QS-dependent specific metabolism contributes to the stability of the cooperation. However, the mechanism by which QS and metabolic networks have coevolved to support stable public good cooperation and maintenance of the cooperative group remains unknown. Here we explored the underlying mechanisms of QS-controlled central metabolism in the evolutionary aspects of cooperation. In Burkholderia glumae, the QS-dependent glyoxylate cycle plays an important role in cooperativity. A bifunctional QS-dependent transcriptional regulator, QsmR, rewired central metabolism to utilize the glyoxylate cycle rather than the tricarboxylic acid cycle. Defects in the glyoxylate cycle caused metabolic imbalance and triggered high expression of the stress-responsive chaperonin GroEL. High-level expression of GroEL in glyoxylate cycle mutants interfered with the biosynthesis of a public resource, oxalate, by physically interrupting the oxalate biosynthetic enzyme ObcA. Under such destabilized cooperativity conditions, spontaneous mutations in the qsmR gene in glyoxylate cycle mutants occurred to relieve metabolic stresses, but these mutants lost QsmR-mediated pleiotropy. Overcoming the metabolic restrictions imposed on the population of cooperators among glyoxylate cycle mutants resulted in the occurrence and selection of spontaneous qsmR mutants despite the loss of other important functions. These results provide insight into how QS bacteria have evolved to maintain stable cooperation via QS-mediated metabolic coordination. We address how quorum sensing (QS) has coevolved with metabolic networks to maintain bacterial sociality. We found that QS-mediated metabolic rewiring is critical for sustainable bacterial cooperation in Burkholderia glumae. The loss of the glyoxylate cycle triggered the expression of the stress-responsive molecular chaperonin GroEL. Excessive biosynthesis of GroEL physically hampered biosynthesis of a public good, oxalate. This is one good example of how molecular chaperones play critical roles in bacterial cooperation. In addition, we showed that metabolic restrictions in the glyoxylate cycle acted as a selection pressure on metabolic networks; there were spontaneous mutations in the qsmR gene to relieve such stresses. However, the presence of spontaneous qsmR mutants had tragic consequences for a cooperative population of B. glumae due to failure of qsmR-dependent activation of public good biosynthesis. These results provide a good example of a bacterial strategy for robust cooperation via QS-mediated metabolic rewiring.
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Lim JC, Thevarajoo S, Selvaratnam C, Goh KM, Shamsir MS, Ibrahim Z, Chong CS. Global transcriptomic response of Anoxybacillus sp. SK 3-4 to aluminum exposure. J Basic Microbiol 2016; 57:151-161. [PMID: 27859397 DOI: 10.1002/jobm.201600494] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/23/2016] [Indexed: 01/15/2023]
Abstract
Anoxybacillus sp. SK 3-4 is a Gram-positive, rod-shaped bacterium and a member of family Bacillaceae. We had previously reported that the strain is an aluminum resistant thermophilic bacterium. This is the first report to provide a detailed analysis of the global transcriptional response of Anoxybacillus when the cells were exposed to 600 mg L-1 of aluminum. The transcriptome was sequenced using Illumina MiSeq sequencer. Total of 708 genes were differentially expressed (fold change >2.00) with 316 genes were up-regulated while 347 genes were down-regulated, in comparing to control with no aluminum added in the culture. Based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the majority of genes encoding for cell metabolism such as glycolysis, sulfur metabolism, cysteine and methionine metabolism were up-regulated; while most of the gene associated with tricarboxylic acid cycle (TCA cycle) and valine, leucine and isoleucine metabolism were down-regulated. In addition, a significant number of the genes encoding ABC transporters, metal ions transporters, and some stress response proteins were also differentially expressed following aluminum exposure. The findings provide further insight and help us to understand on the resistance of Anoxybacillus sp. SK 3-4 toward aluminium.
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Affiliation(s)
- Jia Chun Lim
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Suganthi Thevarajoo
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Chitra Selvaratnam
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Zaharah Ibrahim
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Chun Shiong Chong
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
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Duan X, Huang X, Wang X, Yan S, Guo S, Abdalla AE, Huang C, Xie J. l-Serine potentiates fluoroquinolone activity against Escherichia coli by enhancing endogenous reactive oxygen species production. J Antimicrob Chemother 2016; 71:2192-9. [PMID: 27118777 DOI: 10.1093/jac/dkw114] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/08/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The increase in multiple antimicrobial-resistant bacteria seriously threatens global public health. Novel effective strategies are urgently needed. l-Serine was reported as the most effective amino acid inhibitor against bacterial growth and can sensitize Escherichia coli cells to gentamicin. It is currently unknown whether l-serine affects other type of antibiotics such as β-lactams and fluoroquinolones. METHODS Using E. coli, we studied the combination of l-serine with diverse antibiotics against laboratory and clinical E. coli cultures and persisters. The intracellular NAD(+)/NADH level and ROS were determined using kits. Total cellular iron was determined by using a colorimetric ferrozine-based assay. RESULTS Exogenous l-serine sensitized E. coli ATCC 25922 and clinically isolated fluoroquinolone-resistant E. coli to fluoroquinolones. This potentiation is independent of growth phase. Addition of serine increases the production of NADH. The underlying mechanism of this strategy is that the combination of serine with ofloxacin or moxifloxacin increases the NAD(+)/NADH ratio, disrupts the Fe-S clusters and increases the production of endogenous reactive oxygen species. Furthermore, we used a serine and ofloxacin or moxifloxacin combination in vitro to combat bacterial persister cells, compared with antibiotic treatment alone; combinational treatments of persister cells with antibiotics and l-serine resulted in a significantly greater decrease in cell viability. CONCLUSIONS To our knowledge, this is the first report that l-serine can potentiate the action of ofloxacin or moxifloxacin against Gram-negative bacteria and could constitute a new strategy for the eradication of bacterial infections.
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Affiliation(s)
- Xiangke Duan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environment Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xue Huang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environment Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiaoyu Wang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environment Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Shuangquan Yan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environment Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Siyao Guo
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environment Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China Hanhong College, Southwest University, Chongqing 400715, China
| | - Abualgasim Elgaili Abdalla
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environment Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China Department of Clinical Microbiology, College of Medical Laboratory Sciences, Omdurman Islamic University, Omdurman, Khartoum, Sudan
| | - Changwu Huang
- The Fifth People's Hospital of Chongqing, Chongqing 400715, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environment Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China
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