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Menzel R, Tobias K, Fidan T, Rietz A, Ruess L. Dissection of the synthesis of polyunsaturated fatty acids in nematodes and Collembola of the soil fauna. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159541. [PMID: 39097082 DOI: 10.1016/j.bbalip.2024.159541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/10/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024]
Abstract
It is becoming increasingly clear that not only unicellular, photoautotrophic eukaryotes, plants, and fungi, but also invertebrates are capable of synthesizing ω3 long-chain polyunsaturated fatty acids (LC-PUFA) de novo. However, the distribution of this anabolic capacity among different invertebrate groups and its implementation at the gene and protein level are often still unknown. This study investigated the PUFA pathways in common soil fauna, i.e. two nematode and two Collembola species. Of these, one species each (Panagrellus redivivus, Folsomia candida) was assumed to produce ω3 LC-PUFA de novo, while the others (Acrobeloides bodenheimeri, Isotoma caerulea) were supposed to be unable to do so. A highly labeled oleic acid (99 % 13C) was supplemented and the isotopic signal was used to trace its metabolic path. All species followed the main pathway of lipid biosynthesis. However, in A. bodenheimeri this terminated at arachidonic acid (ω6 PUFA), whereas the other three species continued the pathway to eicosapentaenoic acid (ω3 PUFA), including I. caerulea. For the nematode P. redivivus the identification and functional characterization of four new fatty acid desaturase (FAD) genes was performed. These genes encode the FAD activities Δ9, Δ6, and Δ5, respectively. Additionally, the Δ12 desaturase was analyzed, yet the observed activity of an ω3 FAD could not be attributed to a coding gene. In the Collembola F. candida, 11 potential first desaturases (Δ9) and 13 front-end desaturases (Δ6 or Δ5 FADs) have been found. Further sequence analysis indicates the presence of omega FADs, specifically Δ12, which are likely derived from Δ9 FADs.
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Affiliation(s)
- Ralph Menzel
- Institute of Biology - Ecology, Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Kevin Tobias
- Institute of Biology - Ecology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Tugce Fidan
- Institute of Biology - Ecology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Alexandra Rietz
- Institute of Biology - Ecology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Liliane Ruess
- Institute of Biology - Ecology, Humboldt-Universität zu Berlin, Berlin, Germany
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2
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Eisenreich W, Leberfing J, Rudel T, Heesemann J, Goebel W. Interactions of SARS-CoV-2 with Human Target Cells-A Metabolic View. Int J Mol Sci 2024; 25:9977. [PMID: 39337465 PMCID: PMC11432161 DOI: 10.3390/ijms25189977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 09/13/2024] [Accepted: 09/13/2024] [Indexed: 09/30/2024] Open
Abstract
Viruses are obligate intracellular parasites, and they exploit the cellular pathways and resources of their respective host cells to survive and successfully multiply. The strategies of viruses concerning how to take advantage of the metabolic capabilities of host cells for their own replication can vary considerably. The most common metabolic alterations triggered by viruses affect the central carbon metabolism of infected host cells, in particular glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle. The upregulation of these processes is aimed to increase the supply of nucleotides, amino acids, and lipids since these metabolic products are crucial for efficient viral proliferation. In detail, however, this manipulation may affect multiple sites and regulatory mechanisms of host-cell metabolism, depending not only on the specific viruses but also on the type of infected host cells. In this review, we report metabolic situations and reprogramming in different human host cells, tissues, and organs that are favorable for acute and persistent SARS-CoV-2 infection. This knowledge may be fundamental for the development of host-directed therapies.
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Affiliation(s)
- Wolfgang Eisenreich
- Structural Membrane Biochemistry, Bavarian NMR Center (BNMRZ), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany;
| | - Julian Leberfing
- Structural Membrane Biochemistry, Bavarian NMR Center (BNMRZ), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany;
| | - Thomas Rudel
- Chair of Microbiology, Biocenter, University of Würzburg, 97074 Würzburg, Germany;
| | - Jürgen Heesemann
- Max von Pettenkofer Institute, Ludwig Maximilian University of Munich, 80336 München, Germany; (J.H.); (W.G.)
| | - Werner Goebel
- Max von Pettenkofer Institute, Ludwig Maximilian University of Munich, 80336 München, Germany; (J.H.); (W.G.)
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3
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Stachura DL, Kalyvas JT, Abell AD. New Potent Sulfonamide-Based Inhibitors of S. aureus Biotin Protein Ligase. ACS Med Chem Lett 2024; 15:1467-1473. [PMID: 39291019 PMCID: PMC11403734 DOI: 10.1021/acsmedchemlett.4c00325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 08/29/2024] [Accepted: 08/29/2024] [Indexed: 09/19/2024] Open
Abstract
The key regulatory metabolic enzyme, biotin protein ligase (BPL), is an attractive target for the development of novel antibiotics against multi-drug-resistant bacteria, such as Staphylococcus aureus. Here we report the synthesis and assay of a new series of inhibitors (6-9) against S. aureus BPL (SaBPL), where a component sulfonamide linker was used to mimic the acyl-phosphate group of the natural intermediate biotinyl-5'-AMP (1). A pivotal correlation between the acidity of the central NH of the sulfonamide linker of 6-9 and in vitro inhibitory activity against SaBPL was observed. Specifically, sulfonylcarbamate 8, with its highly acidic sulfonyl central NH, as evaluated by 1H NMR spectroscopy, showed exceptional potency (K i = 10.3 ± 3.8 nM). Furthermore, three inhibitors demonstrated minimum inhibitory concentrations of 16-32 μg/mL against clinical methicillin-resistant S. aureus (MRSA) strains.
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Affiliation(s)
- Damian L Stachura
- Centre for Nanoscale BioPhotonics (CNBP) and Institute of Photonics and Advanced Sensing (IPAS), Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - John T Kalyvas
- Centre for Nanoscale BioPhotonics (CNBP) and Institute of Photonics and Advanced Sensing (IPAS), Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Andrew D Abell
- Centre for Nanoscale BioPhotonics (CNBP) and Institute of Photonics and Advanced Sensing (IPAS), Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
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4
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Liu Y, Wang R, Zhang C, Huang L, Chen J, Zeng Y, Chen H, Wang G, Qian K, Huang P. Automated Diagnosis and Phenotyping of Tuberculosis Using Serum Metabolic Fingerprints. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2406233. [PMID: 39159075 DOI: 10.1002/advs.202406233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/23/2024] [Indexed: 08/21/2024]
Abstract
Tuberculosis (TB) stands as the second most fatal infectious disease after COVID-19, the effective treatment of which depends on accurate diagnosis and phenotyping. Metabolomics provides valuable insights into the identification of differential metabolites for disease diagnosis and phenotyping. However, TB diagnosis and phenotyping remain great challenges due to the lack of a satisfactory metabolic approach. Here, a metabolomics-based diagnostic method for rapid TB detection is reported. Serum metabolic fingerprints are examined via an automated nanoparticle-enhanced laser desorption/ionization mass spectrometry platform outstanding by its rapid detection speed (measured in seconds), minimal sample consumption (in nanoliters), and cost-effectiveness (approximately $3). A panel of 14 m z-1 features is identified as biomarkers for TB diagnosis and a panel of 4 m z-1 features for TB phenotyping. Based on the acquired biomarkers, TB metabolic models are constructed through advanced machine learning algorithms. The robust metabolic model yields a 97.8% (95% confidence interval (CI), 0.964-0.986) area under the curve (AUC) in TB diagnosis and an 85.7% (95% CI, 0.806-0.891) AUC in phenotyping. In this study, serum metabolic biomarker panels are revealed and develop an accurate metabolic tool with desirable diagnostic performance for TB diagnosis and phenotyping, which may expedite the effective implementation of the end-TB strategy.
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Affiliation(s)
- Yajing Liu
- Department of Ultrasound in Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, P. R. China
| | - Ruimin Wang
- State Key Laboratory for Oncogenes and Related Genes School of Biomedical Engineering Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Chao Zhang
- Department of Ultrasound in Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, P. R. China
| | - Lin Huang
- State Key Laboratory for Oncogenes and Related Genes School of Biomedical Engineering Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Jifan Chen
- Department of Ultrasound in Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, P. R. China
| | - Yiqing Zeng
- Department of Ultrasound in Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, P. R. China
| | - Hongjian Chen
- Post-Doctoral Research Center, Zhejiang SUKEAN Pharmaceutical Co., Ltd, Hangzhou, 311225, P. R. China
| | - Guowei Wang
- Department of Ultrasound in Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, P. R. China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related Genes School of Biomedical Engineering Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Pintong Huang
- Department of Ultrasound in Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, P. R. China
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, 310053, P. R. China
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5
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Saha P, Mukherjee SK, Hossain ST. Regulation of TCA cycle genes by srbA sRNA: Impacts on Pseudomonas aeruginosa virulence and survival. Biochem Biophys Res Commun 2024; 737:150520. [PMID: 39128223 DOI: 10.1016/j.bbrc.2024.150520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/25/2024] [Accepted: 08/07/2024] [Indexed: 08/13/2024]
Abstract
Pseudomonas aeruginosa, an opportunistic bacterial pathogen of public health concern, is known for its metabolic versatility, adaptability in harsh environment, and pathogenic aggressiveness. P. aeruginosa relies on various regulatory networks modulated by small non-coding RNAs, which in turn influence different physiological traits such as metabolism, stress response, and pathogenesis. In this study, srbA sRNA has been shown to play a diverse role in regulating cellular metabolism and the production of different virulence factors in P. aeruginosa. srbA was found to control the TCA cycle, a key regulatory pathway for cellular metabolism and energy production, by regulating three main enzymes: citrate synthase (gltA), isocitrate dehydrogenase (icd), and α-ketoglutarate dehydrogenase E1 subunit (sucA) at both the transcriptional and translational levels. By modulating the TCA cycle, srbA could help the bacteria to adapt nutritional stress by lowering energy consumption. Additionally, srbA has been found to differentially regulate production of various virulence factors such as rhamnolipid, elastase, LasA protease, and pyocyanin under both nutrient-rich and nutrient-limiting conditions. It could also influence motilities in P. aeruginosa, linked to biofilm formation and pathogenicity. Thus, srbA might hold a promise in the research area for identifying virulence pathways and developing novel therapeutic targets to combat the global pathogenic threat of P. aeruginosa.
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Affiliation(s)
- Piyali Saha
- Department of Microbiology, University of Kalyani, Kalyani, 741235, India
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6
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Ewald J, He Z, Dimitriew W, Schuster S. Including glutamine in a resource allocation model of energy metabolism in cancer and yeast cells. NPJ Syst Biol Appl 2024; 10:77. [PMID: 39025861 PMCID: PMC11258256 DOI: 10.1038/s41540-024-00393-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 06/10/2024] [Indexed: 07/20/2024] Open
Abstract
Energy metabolism is crucial for all living cells, especially during fast growth or stress scenarios. Many cancer and activated immune cells (Warburg effect) or yeasts (Crabtree effect) mostly rely on aerobic glucose fermentation leading to lactate or ethanol, respectively, to generate ATP. In recent years, several mathematical models have been proposed to explain the Warburg effect on theoretical grounds. Besides glucose, glutamine is a very important substrate for eukaryotic cells-not only for biosynthesis, but also for energy metabolism. Here, we present a minimal constraint-based stoichiometric model for explaining both the classical Warburg effect and the experimentally observed respirofermentation of glutamine (WarburQ effect). We consider glucose and glutamine respiration as well as the respective fermentation pathways. Our resource allocation model calculates the ATP production rate, taking into account enzyme masses and, therefore, pathway costs. While our calculation predicts glucose fermentation to be a superior energy-generating pathway in human cells, different enzyme characteristics in yeasts reduce this advantage, in some cases to such an extent that glucose respiration is preferred. The latter is observed for the fungal pathogen Candida albicans, which is a known Crabtree-negative yeast. Further, optimization results show that glutamine is a valuable energy source and important substrate under glucose limitation, in addition to its role as a carbon and nitrogen source of biomass in eukaryotic cells. In conclusion, our model provides insights that glutamine is an underestimated fuel for eukaryotic cells during fast growth and infection scenarios and explains well the observed parallel respirofermentation of glucose and glutamine in several cell types.
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Affiliation(s)
- Jan Ewald
- Department of Bioinformatics, Friedrich Schiller University of Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) Dresden/Leipzig, Leipzig University, Humboldtstraße 25, 04105, Leipzig, Germany
| | - Ziyang He
- Department of Bioinformatics, Friedrich Schiller University of Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany
| | - Wassili Dimitriew
- Department of Bioinformatics, Friedrich Schiller University of Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Friedrich Schiller University of Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany.
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7
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Lacroix M, Moreau J, Zampaloni C, Bissantz C, Shirvani H, Marchand S, Couet W, Chauzy A. Impact of nutritional factors on in vitro PK/PD modelling of polymyxin B against various strains of Acinetobacter baumannii. Int J Antimicrob Agents 2024; 64:107189. [PMID: 38697578 DOI: 10.1016/j.ijantimicag.2024.107189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/05/2024]
Abstract
The main objective of this study was to assess the effect of rich artificial cation-adjusted Mueller-Hinton broth (CAMHB) on the growth of three strains of Acinetobacter baumannii (ATCC 19606 and two clinical strains), either susceptible or resistant to polymyxin B (PMB), and on PMB bactericidal activity. A pharmacokinetic (PK)/pharmacodynamic (PD) modelling approach was used to characterize the effect of PMB in various conditions. Time-kill experiments were performed using undiluted CAMHB or CAMHB diluted to 50%, 25% and 10%, with or without Ca2+ and Mg2+ compensation (known to affect PMB activity), and with PMB concentrations ranging from 0.25 to 256 mg/L based on the strain's MIC. For each strain, time-kill replicates were modelled using NONMEM. Unexpectedly, dilution of CAMHB by up to 10-fold did not affect the growth rate of any of the three strains in the absence of PMB. However, the bactericidal activity of PMB increased with medium dilution, resulting in a reduction in the apparent bacterial regrowth of the various strains observed after a few hours. Data for each strain were well characterized by a PK/PD model, with two bacterial subpopulations with different susceptibility to PMB (more susceptible and less susceptible). The impact of medium dilution and cation compensation showed relatively high, unexplained between-strain variability. Further studies are needed to characterize the mechanism underlying the medium dilution effect.
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Affiliation(s)
- Mathilde Lacroix
- Université de Poitiers, INSERM U1070, PHAR2, Poitiers, France; Institut Roche, Boulogne-Billancourt, France
| | - Jérémy Moreau
- Université de Poitiers, INSERM U1070, PHAR2, Poitiers, France
| | - Claudia Zampaloni
- Roche Pharma Research and Early Development, Immunology, Infectious Disease and Ophthalmology, Roche Innovation Centre Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Caterina Bissantz
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Centre Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | | | - Sandrine Marchand
- Université de Poitiers, INSERM U1070, PHAR2, Poitiers, France; Département de Pharmacocinétique et Toxicologie, CHU Poitiers, Poitiers, France
| | - William Couet
- Université de Poitiers, INSERM U1070, PHAR2, Poitiers, France; Département de Pharmacocinétique et Toxicologie, CHU Poitiers, Poitiers, France
| | - Alexia Chauzy
- Université de Poitiers, INSERM U1070, PHAR2, Poitiers, France.
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8
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Shin J, Zielinski DC, Palsson BO. Deciphering nutritional stress responses via knowledge-enriched transcriptomics for microbial engineering. Metab Eng 2024; 84:34-47. [PMID: 38825177 DOI: 10.1016/j.ymben.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/27/2024] [Accepted: 05/28/2024] [Indexed: 06/04/2024]
Abstract
Understanding diverse bacterial nutritional requirements and responses is foundational in microbial research and biotechnology. In this study, we employed knowledge-enriched transcriptomic analytics to decipher complex stress responses of Vibrio natriegens to supplied nutrients, aiming to enhance microbial engineering efforts. We computed 64 independently modulated gene sets that comprise a quantitative basis for transcriptome dynamics across a comprehensive transcriptomics dataset containing a broad array of nutrient conditions. Our approach led to the i) identification of novel transporter systems for diverse substrates, ii) a detailed understanding of how trace elements affect metabolism and growth, and iii) extensive characterization of nutrient-induced stress responses, including osmotic stress, low glycolytic flux, proteostasis, and altered protein expression. By clarifying the relationship between the acetate-associated regulon and glycolytic flux status of various nutrients, we have showcased its vital role in directing optimal carbon source selection. Our findings offer deep insights into the transcriptional landscape of bacterial nutrition and underscore its significance in tailoring strain engineering strategies, thereby facilitating the development of more efficient and robust microbial systems for biotechnological applications.
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Affiliation(s)
- Jongoh Shin
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Daniel C Zielinski
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
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9
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Ahator SD, Hegstad K, Lentz CS, Johannessen M. Deciphering Staphylococcus aureus-host dynamics using dual activity-based protein profiling of ATP-interacting proteins. mSystems 2024; 9:e0017924. [PMID: 38656122 PMCID: PMC11097646 DOI: 10.1128/msystems.00179-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
The utilization of ATP within cells plays a fundamental role in cellular processes that are essential for the regulation of host-pathogen dynamics and the subsequent immune response. This study focuses on ATP-binding proteins to dissect the complex interplay between Staphylococcus aureus and human cells, particularly macrophages (THP-1) and keratinocytes (HaCaT), during an intracellular infection. A snapshot of the various protein activity and function is provided using a desthiobiotin-ATP probe, which targets ATP-interacting proteins. In S. aureus, we observe enrichment in pathways required for nutrient acquisition, biosynthesis and metabolism of amino acids, and energy metabolism when located inside human cells. Additionally, the direct profiling of the protein activity revealed specific adaptations of S. aureus to the keratinocytes and macrophages. Mapping the differentially activated proteins to biochemical pathways in the human cells with intracellular bacteria revealed cell-type-specific adaptations to bacterial challenges where THP-1 cells prioritized immune defenses, autophagic cell death, and inflammation. In contrast, HaCaT cells emphasized barrier integrity and immune activation. We also observe bacterial modulation of host processes and metabolic shifts. These findings offer valuable insights into the dynamics of S. aureus-host cell interactions, shedding light on modulating host immune responses to S. aureus, which could involve developing immunomodulatory therapies. IMPORTANCE This study uses a chemoproteomic approach to target active ATP-interacting proteins and examines the dynamic proteomic interactions between Staphylococcus aureus and human cell lines THP-1 and HaCaT. It uncovers the distinct responses of macrophages and keratinocytes during bacterial infection. S. aureus demonstrated a tailored response to the intracellular environment of each cell type and adaptation during exposure to professional and non-professional phagocytes. It also highlights strategies employed by S. aureus to persist within host cells. This study offers significant insights into the human cell response to S. aureus infection, illuminating the complex proteomic shifts that underlie the defense mechanisms of macrophages and keratinocytes. Notably, the study underscores the nuanced interplay between the host's metabolic reprogramming and immune strategy, suggesting potential therapeutic targets for enhancing host defense and inhibiting bacterial survival. The findings enhance our understanding of host-pathogen interactions and can inform the development of targeted therapies against S. aureus infections.
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Affiliation(s)
- Stephen Dela Ahator
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
| | - Kristin Hegstad
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Christian S. Lentz
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
| | - Mona Johannessen
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
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10
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Li Z, Guo X, Ma Y, Hu B, Yang Y, Tian H, Liu X, Meng N, Zhu J, Yan D, Song H, Bao B, Li X, Dai X, Zheng Y, Jin Y, Zheng H. The hidden risk: Changes in functional potentials of microbial keystone taxa under global climate change jeopardizing soil carbon storage in alpine grasslands. ENVIRONMENT INTERNATIONAL 2024; 185:108516. [PMID: 38447452 DOI: 10.1016/j.envint.2024.108516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/18/2024] [Accepted: 02/18/2024] [Indexed: 03/08/2024]
Abstract
Climate change is endangering the soil carbon stock of alpine grasslands on the Qinghai-Tibetan Plateau (QTP), but the limited comprehension regarding the mechanisms that sustain carbon storage under hydrothermal changes increases the uncertainty associated with this finding. Here, we examined the relative abundance of soil microbial keystone taxa and their functional potentials, as well as their influence on soil carbon storage with increased precipitation across alpine grasslands on the QTP, China. The findings indicate that alterations in precipitation significantly decreased the relative abundance of the carbon degradation potentials of keystone taxa, such as chemoheterotrophs. The inclusion of keystone taxa and their internal functional potentials in the two best alternative models explained 70% and 63% of the variance in soil organic carbon (SOC) density, respectively. Moreover, we found that changes in chemoheterotrophs had negative effects on SOC density as indicated by a structural equation model, suggesting that some specialized functional potentials of keystone taxa are not conducive to the accumulation of carbon sink. Our study offers valuable insights into the intricate correlation between precipitation-induced alterations in soil microbial keystone taxa and SOC storage, highlighting a rough categorization is difficult to distinguish the hidden threats and the importance of incorporating functional potentials in SOC storage prediction models in response to changing climate.
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Affiliation(s)
- Zuzheng Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Beijing Academy of Forestry and Landscape Architecture, Beijing 100044, China
| | - Xue Guo
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Ma
- Institute of Earth Environment, Chinese Academy of Sciences, Xian 710061, China
| | - Baoan Hu
- School of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Yanzheng Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Huixia Tian
- School of Environment and Resources, Taiyuan University of Science and Technology, Taiyuan 030024, China
| | - Xujun Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Nan Meng
- Department of Earth System Science, Ministry of Education Key Laboratory for Earth System Modeling, Institute for Global Change Studies, Tsinghua University, Beijing 10084, China
| | - Jinyi Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Danni Yan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hao Song
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Binqiang Bao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xuan Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xuhuan Dai
- Technical Centre for Soil, Agriculture and Rural Ecology and Environment, Ministry of Ecology and Environment, Beijing 100012, China
| | - Yi Zheng
- Beijing Academy of Forestry and Landscape Architecture, Beijing 100044, China
| | - Yingshan Jin
- Beijing Academy of Forestry and Landscape Architecture, Beijing 100044, China
| | - Hua Zheng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Bin P, Liu W, Zhang X, Liu B, Zhu G. A novel antibacterial strategy for targeting the bacterial methionine biosynthesis pathway. Int J Antimicrob Agents 2024; 63:107057. [PMID: 38072168 DOI: 10.1016/j.ijantimicag.2023.107057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 11/28/2023] [Accepted: 12/05/2023] [Indexed: 01/25/2024]
Abstract
Bacterial pathogens reprogramme their metabolic networks to support growth and establish infection at specific sites. Bacterial central metabolism has been considered attractive for developing antimicrobial drugs; however, most metabolic enzymes are conserved between humans and bacteria. This study found that blockade of methionine biosynthesis in Citrobacter rodentium and Salmonella enteritidis inhibited bacterial growth and activity of the type III secretion system, resulting in severe defects in colonization and pathogenicity. In addition, α-methyl-methionine was found to inhibit the activity of methionine biosynthetic enzyme MetA, and consequently reduce the virulence and pathogenicity of enteric pathogens. These findings highlight the crucial role of methionine in bacterial virulence, and describe a potential new drug target.
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Affiliation(s)
- Peng Bin
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Joint Laboratory of International Cooperation on Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-Innovation Centre for Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and AgriProduct Safety of Ministry of Education of China, College of Veterinary Medicine, Yangzhou University, Yangzhou, China; College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Wanyang Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Joint Laboratory of International Cooperation on Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-Innovation Centre for Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and AgriProduct Safety of Ministry of Education of China, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Xiaojie Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Joint Laboratory of International Cooperation on Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-Innovation Centre for Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and AgriProduct Safety of Ministry of Education of China, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Baobao Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Joint Laboratory of International Cooperation on Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-Innovation Centre for Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and AgriProduct Safety of Ministry of Education of China, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Joint Laboratory of International Cooperation on Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, Jiangsu, China; Jiangsu Co-Innovation Centre for Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and AgriProduct Safety of Ministry of Education of China, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.
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12
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Zou H, Zhang B, Liang H, Li C, Chen J, Wu Y. Defence mechanisms of Pinctada fucata martensii to Vibrio parahaemolyticus infection: Insights from proteomics and metabolomics. FISH & SHELLFISH IMMUNOLOGY 2023; 143:109204. [PMID: 37931889 DOI: 10.1016/j.fsi.2023.109204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/08/2023]
Abstract
Survival of pearl oysters is not only challenged by coastal pollution, but also pathogen infection that may eventually incur substantial economic losses in the pearl farming industry. Yet, whether pearl oysters can defend themselves against pathogen infection through molecular mechanisms remains largely unexplored. By using iTRAQ proteomic and metabolomic analyses, we analysed the proteins and metabolites in the serum of pearl oysters (Pinctada fucata martensii) when stimulated by pathogenic bacteria (Vibrio parahaemolyticus). Proteomic results found that a total of 2,242 proteins were identified in the experimental (i.e., Vibrio-stimulated) and control groups, where 166 of them were differentially expressed (120 upregulated and 46 downregulated in the experimental group). Regarding the immune response enrichment results, the pathway of signal transduction was significantly enriched, such as cytoskeleton and calcium signalling pathways. Proteins, including cathepsin L, heat shock protein 20, myosin and astacin-like protein, also contributed to the immune response of oysters. Pathogen stimulation also altered the metabolite profile of oysters, where 49 metabolites associated with metabolism of energy, fatty acids and amino acids were found. Integrated analysis suggests that the oysters could respond to pathogen infection by coordinating multiple cellular processes. Thus, the proteins and metabolites identified herein not only represent valuable genetic resources for developing molecular biomarkers and genetic breeding research, but also open new avenues for studies on the molecular defence mechanisms of pearl oysters to pathogen infection.
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Affiliation(s)
- Hexin Zou
- Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Bin Zhang
- Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Haiying Liang
- Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, Guangdong, 524088, China.
| | - Chaojie Li
- Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Jie Chen
- Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Yifan Wu
- Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
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13
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Upton EM, Schlievert PM, Zhang Y, Rauckhorst AJ, Taylor EB, Radoshevich L. Glycerol monolaurate inhibits Francisella novicida growth and is produced intracellularly in an ISG15-dependent manner. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000905. [PMID: 37954520 PMCID: PMC10638595 DOI: 10.17912/micropub.biology.000905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/20/2023] [Accepted: 10/22/2023] [Indexed: 11/14/2023]
Abstract
Glycerol Monolaurate (GML) is a naturally occurring fatty acid monoester with antimicrobial properties. Francisella tularensis is an agent of bioterrorism known for its unique lipopolysaccharide structure and low immunogenicity. Here we assessed whether exogenous GML would inhibit the growth of Francisella novicida . GML potently impeded Francisella growth and survival in vitro . To appraise the metabolic response to infection, we used GC-MS to survey the metabolome, and surprisingly, observed intracellular GML production following Francisella infection. Notably, the ubiquitin-like protein ISG15 was necessary for increased GML levels induced by bacterial infection, and enhanced ISG15 conjugation correlated with GML levels following serum starvation.
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Affiliation(s)
- Ellen M. Upton
- Department of Microbiology and Immunology, University of Iowa, Carver College of Medicine, Iowa City, Iowa, USA
| | - Patrick M. Schlievert
- Department of Microbiology and Immunology, University of Iowa, Carver College of Medicine, Iowa City, Iowa, USA
| | - Yifeng Zhang
- Department of Microbiology and Immunology, University of Iowa, Carver College of Medicine, Iowa City, Iowa, USA
| | - Adam J. Rauckhorst
- Department of Molecular Physiology and Biophysics, University of Iowa, Carver College of Medicine, Iowa City, Iowa, USA
- Fraternal Order of Eagles Diabetes Research Center Metabolomics Core Facility, University of Iowa, Carver College of Medicine, Iowa City, Iowa, USA
| | - Eric B. Taylor
- Department of Molecular Physiology and Biophysics, University of Iowa, Carver College of Medicine, Iowa City, Iowa, USA
- Fraternal Order of Eagles Diabetes Research Center Metabolomics Core Facility, University of Iowa, Carver College of Medicine, Iowa City, Iowa, USA
| | - Lilliana Radoshevich
- Department of Microbiology and Immunology, University of Iowa, Carver College of Medicine, Iowa City, Iowa, USA
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14
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Pokorzynski ND, Groisman EA. How Bacterial Pathogens Coordinate Appetite with Virulence. Microbiol Mol Biol Rev 2023; 87:e0019822. [PMID: 37358444 PMCID: PMC10521370 DOI: 10.1128/mmbr.00198-22] [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] [Indexed: 06/27/2023] Open
Abstract
Cells adjust growth and metabolism to nutrient availability. Having access to a variety of carbon sources during infection of their animal hosts, facultative intracellular pathogens must efficiently prioritize carbon utilization. Here, we discuss how carbon source controls bacterial virulence, with an emphasis on Salmonella enterica serovar Typhimurium, which causes gastroenteritis in immunocompetent humans and a typhoid-like disease in mice, and propose that virulence factors can regulate carbon source prioritization by modifying cellular physiology. On the one hand, bacterial regulators of carbon metabolism control virulence programs, indicating that pathogenic traits appear in response to carbon source availability. On the other hand, signals controlling virulence regulators may impact carbon source utilization, suggesting that stimuli that bacterial pathogens experience within the host can directly impinge on carbon source prioritization. In addition, pathogen-triggered intestinal inflammation can disrupt the gut microbiota and thus the availability of carbon sources. By coordinating virulence factors with carbon utilization determinants, pathogens adopt metabolic pathways that may not be the most energy efficient because such pathways promote resistance to antimicrobial agents and also because host-imposed deprivation of specific nutrients may hinder the operation of certain pathways. We propose that metabolic prioritization by bacteria underlies the pathogenic outcome of an infection.
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Affiliation(s)
- Nick D. Pokorzynski
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
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15
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Salaemae W, Thompson AP, Gaiser BI, Lee KJ, Huxley MT, Sumby CJ, Polyak SW, Abell AD, Bruning JB, Wegener KL. Fortuitous In Vitro Compound Degradation Produces a Tractable Hit against Mycobacterium tuberculosis Dethiobiotin Synthetase: A Cautionary Tale of What Goes In Does Not Always Come Out. ACS Chem Biol 2023; 18:1985-1992. [PMID: 37651626 DOI: 10.1021/acschembio.3c00215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
We previously reported potent ligands and inhibitors of Mycobacterium tuberculosis dethiobiotin synthetase (MtDTBS), a promising target for antituberculosis drug development (Schumann et al., ACS Chem Biol. 2021, 16, 2339-2347); here, the unconventional origin of the fragment compound they were derived from is described for the first time. Compound 1 (9b-hydroxy-6b,7,8,9,9a,9b-hexahydrocyclopenta[3,4]cyclobuta[1,2-c]chromen-6(6aH)-one), identified by an in silico fragment screen, was subsequently shown by surface plasmon resonance to have dose-responsive binding (KD = 0.6 mM). Clear electron density was revealed in the DAPA substrate binding pocket when 1 was soaked into MtDTBS crystals, but the density was inconsistent with the structure of 1. Here, we show that the lactone of 1 hydrolyzes to a carboxylic acid (2) under basic conditions, including those of the crystallography soak, with a subsequent ring opening of the component cyclobutane ring forming a cyclopentylacetic acid (3). Crystals soaked directly with authentic 3 produced an electron density that matched that of crystals soaked with presumed 1, confirming the identity of the bound ligand. The synthetic utility of fortuitously formed 3 enabled the subsequent compound development of nanomolar inhibitors. Our findings represent an example of chemical modification within drug discovery assays and demonstrate the value of high-resolution structural data in the fragment hit validation process.
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Affiliation(s)
- Wanisa Salaemae
- Biochemistry, Division of Health and Applied Sciences, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Andrew P Thompson
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Birgit I Gaiser
- Centre for Nanoscale BioPhotonics (CNBP), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Kwang Jun Lee
- Centre for Nanoscale BioPhotonics (CNBP), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Michael T Huxley
- Department of Chemistry, School of Physics, Chemistry and Earth Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Christopher J Sumby
- Department of Chemistry, School of Physics, Chemistry and Earth Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Steven W Polyak
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Andrew D Abell
- Centre for Nanoscale BioPhotonics (CNBP), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Department of Chemistry, School of Physics, Chemistry and Earth Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - John B Bruning
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Kate L Wegener
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
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16
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Kim J, Ahn SB, Hong S, Kim KS, Ko EHE, Jo IJ, Chang J, Kim M, Lee W, Lee H. Intracellular Dynamics-Resolved Label-Free Scattering Reveals Real-Time Metabolism of Single Bacteria. NANO LETTERS 2023; 23:8225-8232. [PMID: 37650605 DOI: 10.1021/acs.nanolett.3c02370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Nanoscopic investigation of bacterial cells is essential to reveal their physiological status, impacting all cellular functions. Currently, this requires labeled probes or targeted staining procedures. Herein, we report a new bacterial feature, intracellular dynamics-resolved Rayleigh scattering (IDRS), that visualizes spatiotemporal cytoplasmic transitions in unlabeled bacteria and characterizes their real-time physiological status in 10 s. From single-bacterium IDRS signals, we discovered unique spatial patterns and their multiple transitions in Gram-negative and Gram-positive bacteria. The magnitude of IDRS signal variation highly correlated with the metabolic status of bacteria, differentiating persistent subpopulations. This is also the first report demonstrating distinct real-time metabolic conditions of unlabeled drug-resistant bacteria that are exposed to different doses of antibiotics. Our strategy opens up a way to simultaneously trace in situ metabolic and antibiotic resistance statuses, which can be applied in single-cell level control of bacterial metabolism and efficacy with a heterogeneous nature.
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Affiliation(s)
- Jungwoo Kim
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Soo Bin Ahn
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Subin Hong
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Kwang-Sun Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Esther Ha-Eun Ko
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - I Jeong Jo
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - JuOae Chang
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Meehyein Kim
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Wonsik Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Haemi Lee
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
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17
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Pensinger DA, Gutierrez KV, Smith HB, Vincent WJB, Stevenson DS, Black KA, Perez-Medina KM, Dillard JP, Rhee KY, Amador-Noguez D, Huynh TN, Sauer JD. Listeria monocytogenes GlmR Is an Accessory Uridyltransferase Essential for Cytosolic Survival and Virulence. mBio 2023; 14:e0007323. [PMID: 36939339 PMCID: PMC10128056 DOI: 10.1128/mbio.00073-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/14/2023] [Indexed: 03/21/2023] Open
Abstract
The cytosol of eukaryotic host cells is an intrinsically hostile environment for bacteria. Understanding how cytosolic pathogens adapt to and survive in the cytosol is critical to developing novel therapeutic interventions against these pathogens. The cytosolic pathogen Listeria monocytogenes requires glmR (previously known as yvcK), a gene of unknown function, for resistance to cell-wall stress, cytosolic survival, inflammasome avoidance, and, ultimately, virulence in vivo. In this study, a genetic suppressor screen revealed that blocking utilization of UDP N-acetylglucosamine (UDP-GlcNAc) by a nonessential wall teichoic acid decoration pathway restored resistance to lysozyme and partially restored virulence of ΔglmR mutants. In parallel, metabolomic analysis revealed that ΔglmR mutants are impaired in the production of UDP-GlcNAc, an essential peptidoglycan and wall teichoic acid (WTA) precursor. We next demonstrated that purified GlmR can directly catalyze the synthesis of UDP-GlcNAc from GlcNAc-1P and UTP, suggesting that it is an accessory uridyltransferase. Biochemical analysis of GlmR orthologues suggests that uridyltransferase activity is conserved. Finally, mutational analysis resulting in a GlmR mutant with impaired catalytic activity demonstrated that uridyltransferase activity was essential to facilitate cell-wall stress responses and virulence in vivo. Taken together, these studies indicate that GlmR is an evolutionary conserved accessory uridyltransferase required for cytosolic survival and virulence of L. monocytogenes. IMPORTANCE Bacterial pathogens must adapt to their host environment in order to cause disease. The cytosolic bacterial pathogen Listeria monocytogenes requires a highly conserved protein of unknown function, GlmR (previously known as YvcK), to survive in the host cytosol. GlmR is important for resistance to some cell-wall stresses and is essential for virulence. The ΔglmR mutant is deficient in production of an essential cell-wall metabolite, UDP-GlcNAc, and suppressors that increase metabolite levels also restore virulence. Purified GlmR can directly catalyze the synthesis of UDP-GlcNAc, and this enzymatic activity is conserved in both Bacillus subtilis and Staphylococcus aureus. These results highlight the importance of accessory cell wall metabolism enzymes in responding to cell-wall stress in a variety of Gram-positive bacteria.
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Affiliation(s)
- Daniel A. Pensinger
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Kimberly V. Gutierrez
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Hans B. Smith
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - William J. B. Vincent
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - David S. Stevenson
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | - Krizia M. Perez-Medina
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Joseph P. Dillard
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Kyu Y. Rhee
- Weill Cornell Medical College, New York, New York, USA
| | - Daniel Amador-Noguez
- Microbiology Doctoral Training Program, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - TuAnh N. Huynh
- Microbiology Doctoral Training Program, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Food Science, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - John-Demian Sauer
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin—Madison, Madison, Wisconsin, USA
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18
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Carrilero L, Urwin L, Ward E, Choudhury NR, Monk IR, Turner CE, Stinear TP, Corrigan RM. Stringent Response-Mediated Control of GTP Homeostasis Is Required for Long-Term Viability of Staphylococcus aureus. Microbiol Spectr 2023; 11:e0044723. [PMID: 36877013 PMCID: PMC10101089 DOI: 10.1128/spectrum.00447-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 03/07/2023] Open
Abstract
Staphylococcus aureus is an opportunistic bacterial pathogen that often results in difficult-to-treat infections. One mechanism used by S. aureus to enhance survival during infection is the stringent response. This is a stress survival pathway that utilizes the nucleotides (p)ppGpp to reallocate bacterial resources, shutting down growth until conditions improve. Small colony variants (SCVs) of S. aureus are frequently associated with chronic infections, and this phenotype has previously been linked to a hyperactive stringent response. Here, we examine the role of (p)ppGpp in the long-term survival of S. aureus under nutrient-restricted conditions. When starved, a (p)ppGpp-null S. aureus mutant strain ((p)ppGpp0) initially had decreased viability. However, after 3 days we observed the presence and dominance of a population of small colonies. Similar to SCVs, these small colony isolates (p0-SCIs) had reduced growth but remained hemolytic and sensitive to gentamicin, phenotypes that have been tied to SCVs previously. Genomic analysis of the p0-SCIs revealed mutations arising within gmk, encoding an enzyme in the GTP synthesis pathway. We show that a (p)ppGpp0 strain has elevated levels of GTP, and that the mutations in the p0-SCIs all lower Gmk enzyme activity and consequently cellular GTP levels. We further show that in the absence of (p)ppGpp, cell viability can be rescued using the GuaA inhibitor decoyinine, which artificially lowers the intracellular GTP concentration. Our study highlights the role of (p)ppGpp in GTP homeostasis and underscores the importance of nucleotide signaling for long-term survival of S. aureus in nutrient-limiting conditions, such as those encountered during infections. IMPORTANCE Staphylococcus aureus is a human pathogen that upon invasion of a host encounters stresses, such as nutritional restriction. The bacteria respond by switching on a signaling cascade controlled by the nucleotides (p)ppGpp. These nucleotides function to shut down bacterial growth until conditions improve. Therefore, (p)ppGpp are important for bacterial survival and have been implicated in promoting chronic infections. Here, we investigate the importance of (p)ppGpp for long-term survival of bacteria in nutrient-limiting conditions similar to those in a human host. We discovered that in the absence of (p)ppGpp, bacterial viability decreases due to dysregulation of GTP homeostasis. However, the (p)ppGpp-null bacteria were able to compensate by introducing mutations in the GTP synthesis pathway that led to a reduction in GTP build-up and a rescue of viability. This study therefore highlights the importance of (p)ppGpp for the regulation of GTP levels and for long-term survival of S. aureus in restricted environments.
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Affiliation(s)
- Laura Carrilero
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Lucy Urwin
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Ezra Ward
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Naznin R. Choudhury
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Ian R. Monk
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Claire E. Turner
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Rebecca M. Corrigan
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
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19
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Ali A, Waris A, Khan MA, Asim M, Khan AU, Khan S, Zeb J. Recent advancement, immune responses, and mechanism of action of various vaccines against intracellular bacterial infections. Life Sci 2023; 314:121332. [PMID: 36584914 DOI: 10.1016/j.lfs.2022.121332] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022]
Abstract
Emerging and re-emerging bacterial infections are a serious threat to human and animal health. Extracellular bacteria are free-living, while facultative intracellular bacteria replicate inside eukaryotic host cells. Many serious human illnesses are now known to be caused by intracellular bacteria such as Salmonella enterica, Escherichia coli, Staphylococcus aureus, Rickettsia massiliae, Chlamydia species, Brucella abortus, Mycobacterium tuberculosis and Listeria monocytogenes, which result in substantial morbidity and mortality. Pathogens like Mycobacterium, Brucella, MRSA, Shigella, Listeria, and Salmonella can infiltrate and persist in mammalian host cells, particularly macrophages, where they proliferate and establish a repository, resulting in chronic and recurrent infections. The current treatment for these bacteria involves the application of narrow-spectrum antibiotics. FDA-approved vaccines against obligate intracellular bacterial infections are lacking. The development of vaccines against intracellular pathogenic bacteria are more difficult because host defense against these bacteria requires the activation of the cell-mediated pathway of the immune system, such as CD8+ T and CD4+ T. However, different types of vaccines, including live, attenuated, subunit, killed whole cell, nano-based and DNA vaccines are currently in clinical trials. Substantial development has been made in various vaccine strategies against intracellular pathogenic bacteria. This review focuses on the mechanism of intracellular bacterial infection, host immune response, and recent advancements in vaccine development strategies against various obligate intracellular bacterial infections.
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Affiliation(s)
- Asmat Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Pakistan
| | - Abdul Waris
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong.
| | - Muhammad Ajmal Khan
- Division of Life Sciences, Center for Cancer Research and State Key Laboratory of Molecular Neurosciences, The Hong Kong University of Science and Technology, Hong Kong
| | - Muhammad Asim
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong
| | - Atta Ullah Khan
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China
| | - Sahrish Khan
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Jehan Zeb
- Department of Infectious Diseases and Public Health, City University of Hong Kong, Hong Kong
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20
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Moreno R, Rojo F. The importance of understanding the regulation of bacterial metabolism. Environ Microbiol 2023; 25:54-58. [PMID: 35859345 PMCID: PMC10084369 DOI: 10.1111/1462-2920.16123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 06/30/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Renata Moreno
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Fernando Rojo
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
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21
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Metabolomic approaches for the detection of Listeria monocytogenes and Staphylococcus aureus in culture media. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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22
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Nikitushkin V, Shleeva M, Loginov D, Dyčka F. F, Sterba J, Kaprelyants A. Shotgun proteomic profiling of dormant, ‘non-culturable’ Mycobacterium tuberculosis. PLoS One 2022; 17:e0269847. [PMID: 35944020 PMCID: PMC9362914 DOI: 10.1371/journal.pone.0269847] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 05/27/2022] [Indexed: 11/19/2022] Open
Abstract
Dormant cells of Mycobacterium tuberculosis, in addition to low metabolic activity and a high level of drug resistance, are characterized by ‘non-culturability’–a specific reversible state of the inability of the cells to grow on solid media. The biochemical characterization of this physiological state of the pathogen is only superficial, pending clarification of the metabolic processes that may exist in such cells. In this study, applying LC-MS proteomic profiling, we report the analysis of proteins accumulated in dormant, ‘non-culturable’ M. tuberculosis cells in an in vitro model of self-acidification of mycobacteria in the post-stationary phase, simulating the in vivo persistence conditions—the raw data are available via ProteomeXchange with identifier PXD028849. This approach revealed the preservation of 1379 proteins in cells after 5 months of storage in dormancy; among them, 468 proteins were statistically different from those in the actively growing cells and bore a positive fold change (FC). Differential analysis revealed the proteins of the pH-dependent regulatory system PhoP and allowed the reconstruction of the reactions of central carbon/glycerol metabolism, as well as revealing the salvaged pathways of mycothiol and UMP biosynthesis, establishing the cohort of survival enzymes of dormancy. The annotated pathways mirror the adaptation of the mycobacterial metabolic machinery to life within lipid-rich macrophages: especially the involvement of the methyl citrate and glyoxylate pathways. Thus, the current in vitro model of M. tuberculosis self-acidification reflects the biochemical adaptation of these bacteria to persistence in vivo. Comparative analysis with published proteins displaying antigenic properties makes it possible to distinguish immunoreactive proteins among the proteins bearing a positive FC in dormancy, which may include specific antigens of latent tuberculosis. Additionally, the biotransformatory enzymes (oxidoreductases and hydrolases) capable of prodrug activation and stored up in the dormant state were annotated. These findings may potentially lead to the discovery of immunodiagnostic tests for early latent tuberculosis and trigger the discovery of efficient drugs/prodrugs with potency against non-replicating, dormant populations of mycobacteria.
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Affiliation(s)
- Vadim Nikitushkin
- A.N. Bach Institute of Biochemistry, Federal Research Centre ‘Fundamentals of Biotechnology’ of the Russian Academy of Sciences, Moscow, Russia
- * E-mail: (VN); (FDF)
| | - Margarita Shleeva
- A.N. Bach Institute of Biochemistry, Federal Research Centre ‘Fundamentals of Biotechnology’ of the Russian Academy of Sciences, Moscow, Russia
| | - Dmitry Loginov
- Faculty of Science, University of South Bohemia, Branišovská, Czech Republic
- BioCeV—Institute of Microbiology of the CAS, Vestec, Czech Republic
- Orekhovich Institute of Biomedical Chemistry, Moscow, Russia
| | - Filip Dyčka F.
- Faculty of Science, University of South Bohemia, Branišovská, Czech Republic
- * E-mail: (VN); (FDF)
| | - Jan Sterba
- Faculty of Science, University of South Bohemia, Branišovská, Czech Republic
| | - Arseny Kaprelyants
- A.N. Bach Institute of Biochemistry, Federal Research Centre ‘Fundamentals of Biotechnology’ of the Russian Academy of Sciences, Moscow, Russia
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23
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Sugihara K, Kitamoto S, Saraithong P, Nagao-Kitamoto H, Hoostal M, McCarthy C, Rosevelt A, Muraleedharan CK, Gillilland MG, Imai J, Omi M, Bishu S, Kao JY, Alteri CJ, Barnich N, Schmidt TM, Nusrat A, Inohara N, Golob JL, Kamada N. Mucolytic bacteria license pathobionts to acquire host-derived nutrients during dietary nutrient restriction. Cell Rep 2022; 40:111093. [PMID: 35858565 PMCID: PMC10903618 DOI: 10.1016/j.celrep.2022.111093] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/26/2022] [Accepted: 06/21/2022] [Indexed: 12/26/2022] Open
Abstract
Pathobionts employ unique metabolic adaptation mechanisms to maximize their growth in disease conditions. Adherent-invasive Escherichia coli (AIEC), a pathobiont enriched in the gut mucosa of patients with inflammatory bowel disease (IBD), utilizes diet-derived L-serine to adapt to the inflamed gut. Therefore, the restriction of dietary L-serine starves AIEC and limits its fitness advantage. Here, we find that AIEC can overcome this nutrient limitation by switching the nutrient source from the diet to the host cells in the presence of mucolytic bacteria. During diet-derived L-serine restriction, the mucolytic symbiont Akkermansia muciniphila promotes the encroachment of AIEC to the epithelial niche by degrading the mucus layer. In the epithelial niche, AIEC acquires L-serine from the colonic epithelium and thus proliferates. Our work suggests that the indirect metabolic network between pathobionts and commensal symbionts enables pathobionts to overcome nutritional restriction and thrive in the gut.
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Affiliation(s)
- Kohei Sugihara
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Sho Kitamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Prakaimuk Saraithong
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Hiroko Nagao-Kitamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Matthew Hoostal
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Caroline McCarthy
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Alexandra Rosevelt
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Merritt G Gillilland
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jin Imai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Maiko Omi
- Department of Biologic and Materials Sciences and Prosthodontics, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | - Shrinivas Bishu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - John Y Kao
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Nicolas Barnich
- M2iSH, UMR1071 Inserm/University Clermont Auvergne, Clermont-Ferrand, France
| | - Thomas M Schmidt
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Asma Nusrat
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Naohiro Inohara
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan L Golob
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.
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24
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Chung CH, Chandrasekaran S. A flux-based machine learning model to simulate the impact of pathogen metabolic heterogeneity on drug interactions. PNAS NEXUS 2022; 1:pgac132. [PMID: 36016709 PMCID: PMC9396445 DOI: 10.1093/pnasnexus/pgac132] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023]
Abstract
Drug combinations are a promising strategy to counter antibiotic resistance. However, current experimental and computational approaches do not account for the entire complexity involved in combination therapy design, such as the effect of pathogen metabolic heterogeneity, changes in the growth environment, drug treatment order, and time interval. To address these limitations, we present a comprehensive approach that uses genome-scale metabolic modeling and machine learning to guide combination therapy design. Our mechanistic approach (a) accommodates diverse data types, (b) accounts for time- and order-specific interactions, and (c) accurately predicts drug interactions in various growth conditions and their robustness to pathogen metabolic heterogeneity. Our approach achieved high accuracy (area under the receiver operating curve (AUROC) = 0.83 for synergy, AUROC = 0.98 for antagonism) in predicting drug interactions for Escherichia coli cultured in 57 metabolic conditions based on experimental validation. The entropy in bacterial metabolic response was predictive of combination therapy outcomes across time scales and growth conditions. Simulation of metabolic heterogeneity using population FBA identified two subpopulations of E. coli cells defined by the levels of three proteins (eno, fadB, and fabD) in glycolysis and lipid metabolism that influence cell tolerance to a broad range of antibiotic combinations. Analysis of the vast landscape of condition-specific drug interactions revealed a set of 24 robustly synergistic drug combinations with potential for clinical use.
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Affiliation(s)
- Carolina H Chung
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Center for Bioinformatics and Computational Medicine, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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25
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Leseigneur C, Boucontet L, Duchateau M, Pizarro-Cerda J, Matondo M, Colucci-Guyon E, Dussurget O. NAD kinase promotes Staphylococcus aureus pathogenesis by supporting production of virulence factors and protective enzymes. eLife 2022; 11:e79941. [PMID: 35723663 PMCID: PMC9208755 DOI: 10.7554/elife.79941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Nicotinamide adenine dinucleotide phosphate (NADPH) is the primary electron donor for reductive reactions that are essential for the biosynthesis of major cell components in all organisms. Nicotinamide adenine dinucleotide kinase (NADK) is the only enzyme that catalyzes the synthesis of NADP(H) from NAD(H). While the enzymatic properties and physiological functions of NADK have been thoroughly studied, the role of NADK in bacterial pathogenesis remains unknown. Here, we used CRISPR interference to knock down NADK gene expression to address the role of this enzyme in Staphylococcus aureus pathogenic potential. We find that NADK inhibition drastically decreases mortality of zebrafish infected with S. aureus. Furthermore, we show that NADK promotes S. aureus survival in infected macrophages by protecting bacteria from antimicrobial defense mechanisms. Proteome-wide data analysis revealed that production of major virulence-associated factors is sustained by NADK. We demonstrate that NADK is required for expression of the quorum-sensing response regulator AgrA, which controls critical S. aureus virulence determinants. These findings support a key role for NADK in bacteria survival within innate immune cells and the host during infection.
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Affiliation(s)
- Clarisse Leseigneur
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité de Recherche YersiniaParisFrance
| | - Laurent Boucontet
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Unité Macrophages et Développement de l’ImmunitéParisFrance
| | - Magalie Duchateau
- Institut Pasteur, Université Paris Cité, CNRS USR2000, Unité de Spectrométrie de Masse pour la Biologie, Plateforme de protéomiqueParisFrance
| | - Javier Pizarro-Cerda
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité de Recherche YersiniaParisFrance
| | - Mariette Matondo
- Institut Pasteur, Université Paris Cité, CNRS USR2000, Unité de Spectrométrie de Masse pour la Biologie, Plateforme de protéomiqueParisFrance
| | - Emma Colucci-Guyon
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Unité Macrophages et Développement de l’ImmunitéParisFrance
| | - Olivier Dussurget
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité de Recherche YersiniaParisFrance
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26
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Djahanschiri B, Di Venanzio G, Distel JS, Breisch J, Dieckmann MA, Goesmann A, Averhoff B, Göttig S, Wilharm G, Feldman MF, Ebersberger I. Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex. PLoS Genet 2022; 18:e1010020. [PMID: 35653398 PMCID: PMC9162365 DOI: 10.1371/journal.pgen.1010020] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/04/2022] [Indexed: 11/19/2022] Open
Abstract
Nosocomial pathogens of the Acinetobacter calcoaceticus-baumannii (ACB) complex are a cautionary example for the world-wide spread of multi- and pan-drug resistant bacteria. Aiding the urgent demand for novel therapeutic targets, comparative genomics studies between pathogens and their apathogenic relatives shed light on the genetic basis of human-pathogen interaction. Yet, existing studies are limited in taxonomic scope, sensing of the phylogenetic signal, and resolution by largely analyzing genes independent of their organization in functional gene clusters. Here, we explored more than 3,000 Acinetobacter genomes in a phylogenomic framework integrating orthology-based phylogenetic profiling and microsynteny conservation analyses. We delineate gene clusters in the type strain A. baumannii ATCC 19606 whose evolutionary conservation indicates a functional integration of the subsumed genes. These evolutionarily stable gene clusters (ESGCs) reveal metabolic pathways, transcriptional regulators residing next to their targets but also tie together sub-clusters with distinct functions to form higher-order functional modules. We shortlisted 150 ESGCs that either co-emerged with the pathogenic ACB clade or are preferentially found therein. They provide a high-resolution picture of genetic and functional changes that coincide with the manifestation of the pathogenic phenotype in the ACB clade. Key innovations are the remodeling of the regulatory-effector cascade connecting LuxR/LuxI quorum sensing via an intermediate messenger to biofilm formation, the extension of micronutrient scavenging systems, and the increase of metabolic flexibility by exploiting carbon sources that are provided by the human host. We could show experimentally that only members of the ACB clade use kynurenine as a sole carbon and energy source, a substance produced by humans to fine-tune the antimicrobial innate immune response. In summary, this study provides a rich and unbiased set of novel testable hypotheses on how pathogenic Acinetobacter interact with and ultimately infect their human host. It is a comprehensive resource for future research into novel therapeutic strategies. The spread of multi- and pan-drug resistant bacterial pathogens is a worldwide threat to human health. Understanding the genetics of host colonization and infection can substantially help in devising novel ways of treatment. Acinetobacter baumannii, a nosocomial pathogen ranked top by the World Health Organization in the list of bacteria for which novel therapeutic approaches are needed, is a prime example. Here, we have carved out the genetic make-up that distinguishes A. baumannii and its pathogenic next relatives from other and mostly apathogenic Acinetobacter species. We found a rich spectrum of pathways and regulatory modules that reveal how the pathogens have modified biofilm formation, iron scavenging, and their carbohydrate metabolism to adapt to their human host. Among these, the capability to metabolize kynurenine is particularly intriguing. Humans produce this substance to contain bacterial invaders and to fine-tune the innate immune response. But A. baumannii and closely related pathogens found a way to feed on kynurenine. This suggests that the pathogens might be able to dysregulate the human immune response. In summary, our study substantially deepens the understanding of how a highly critical pathogen interacts with its host, which substantially eases the identification of novel targets for innovative therapeutic strategies.
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Affiliation(s)
- Bardya Djahanschiri
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gisela Di Venanzio
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Jesus S. Distel
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Jennifer Breisch
- Inst. of Molecular Biosciences, Department of Molecular Microbiology and Bioenergetics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Gießen, Gießen, Germany
| | - Beate Averhoff
- Inst. of Molecular Biosciences, Department of Molecular Microbiology and Bioenergetics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stephan Göttig
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University, Frankfurt, Germany
| | | | - Mario F. Feldman
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIKF), Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
- * E-mail:
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27
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Sauvage S, Gaviard C, Tahrioui A, Coquet L, Le H, Alexandre S, Ben Abdelkrim A, Bouffartigues E, Lesouhaitier O, Chevalier S, Jouenne T, Hardouin J. Impact of Carbon Source Supplementations on Pseudomonas aeruginosa Physiology. J Proteome Res 2022; 21:1392-1407. [PMID: 35482949 DOI: 10.1021/acs.jproteome.1c00936] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen highly resistant to a wide range of antimicrobial agents, making its infections very difficult to treat. Since microorganisms need to perpetually adapt to their surrounding environment, understanding the effect of carbon sources on P. aeruginosa physiology is therefore essential to avoid increasing drug-resistance and better fight this pathogen. By a global proteomic approach and phenotypic assays, we investigated the impact of various carbon source supplementations (glucose, glutamate, succinate, and citrate) on the physiology of the P. aeruginosa PA14 strain. A total of 581 proteins were identified as differentially expressed in the 4 conditions. Most of them were more abundant in citrate supplementation and were involved in virulence, motility, biofilm development, and antibiotic resistance. Phenotypic assays were performed to check these hypotheses. By coupling all this data, we highlight the importance of the environment in which the bacterium evolves on its metabolism, and thus the necessity to better understand the metabolic pathways implied in its adaptative response according to the nutrient availability.
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Affiliation(s)
- Salomé Sauvage
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
| | - Charlotte Gaviard
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
| | - Ali Tahrioui
- Laboratoire de microbiologie signaux et microenvironnement, LMSM EA4312, 55 rue Saint-Germain, 27000 Evreux, France
| | - Laurent Coquet
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
| | - Hung Le
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France
| | - Stéphane Alexandre
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France
| | - Ahmed Ben Abdelkrim
- Lactanet, Valacta, 555 Boul des Anciens-Combattants, Sainte-Anne-de-Bellevue, Québec H9X 3R4, Canada
| | - Emeline Bouffartigues
- Laboratoire de microbiologie signaux et microenvironnement, LMSM EA4312, 55 rue Saint-Germain, 27000 Evreux, France
| | - Olivier Lesouhaitier
- Laboratoire de microbiologie signaux et microenvironnement, LMSM EA4312, 55 rue Saint-Germain, 27000 Evreux, France
| | - Sylvie Chevalier
- Laboratoire de microbiologie signaux et microenvironnement, LMSM EA4312, 55 rue Saint-Germain, 27000 Evreux, France
| | - Thierry Jouenne
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
| | - Julie Hardouin
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
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28
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Glover G, Voliotis M, Łapińska U, Invergo BM, Soanes D, O'Neill P, Moore K, Nikolic N, Petrov PG, Milner DS, Roy S, Heesom K, Richards TA, Tsaneva-Atanasova K, Pagliara S. Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells. Commun Biol 2022; 5:385. [PMID: 35444215 PMCID: PMC9021252 DOI: 10.1038/s42003-022-03336-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/30/2022] [Indexed: 12/16/2022] Open
Abstract
The interaction between a cell and its environment shapes fundamental intracellular processes such as cellular metabolism. In most cases growth rate is treated as a proximal metric for understanding the cellular metabolic status. However, changes in growth rate might not reflect metabolic variations in individuals responding to environmental fluctuations. Here we use single-cell microfluidics-microscopy combined with transcriptomics, proteomics and mathematical modelling to quantify the accumulation of glucose within Escherichia coli cells. In contrast to the current consensus, we reveal that environmental conditions which are comparatively unfavourable for growth, where both nutrients and salinity are depleted, increase glucose accumulation rates in individual bacteria and population subsets. We find that these changes in metabolic function are underpinned by variations at the translational and posttranslational level but not at the transcriptional level and are not dictated by changes in cell size. The metabolic response-characteristics identified greatly advance our fundamental understanding of the interactions between bacteria and their environment and have important ramifications when investigating cellular processes where salinity plays an important role.
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Affiliation(s)
- Georgina Glover
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Department of Physics and Astronomy, University of Exeter, Stocker Road, Exeter, EX4 4QL, UK
| | - Margaritis Voliotis
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Department of Mathematics, University of Exeter, Stocker Road, Exeter, UK
| | - Urszula Łapińska
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK
| | - Brandon M Invergo
- Translational Research Exchange at Exeter, University of Exeter, Exeter, UK
| | - Darren Soanes
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK
| | - Paul O'Neill
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK
| | - Karen Moore
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK
| | - Nela Nikolic
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Institute of Science and Technology Austria, 3400, Klosterneuburg, Austria
| | - Peter G Petrov
- Department of Physics and Astronomy, University of Exeter, Stocker Road, Exeter, EX4 4QL, UK
| | - David S Milner
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Sumita Roy
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK
| | - Kate Heesom
- University of Bristol Proteomics Facility, University Walk, Bristol, BS8 1TD, UK
| | - Thomas A Richards
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Krasimira Tsaneva-Atanasova
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Department of Mathematics, University of Exeter, Stocker Road, Exeter, UK
- Department of Bioinformatics and Mathematical Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 105 Acad. G. Bonchev Str., 1113, Sofia, Bulgaria
| | - Stefano Pagliara
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK.
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29
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Liu X, Wang X, Sun B, Sun L. The Involvement of Thiamine Uptake in the Virulence of Edwardsiella piscicida. Pathogens 2022; 11:464. [PMID: 35456139 PMCID: PMC9026889 DOI: 10.3390/pathogens11040464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 11/16/2022] Open
Abstract
Edwardsiella piscicida is a pathogenic bacterium, which can infect a number of fish species and cause a disease termed edwardsiellosis, threatening global fish farming with high prevalence and mortality. Thiamine (Vitamin B1), functioning in the form of thiamine pyrophosphate (TPP), is essential for almost all organisms. Bacteria acquire TPP by biosynthesis or by transportation of exogenous thiamine. TPP availability has been associated with bacterial pathogenicity, but the underlying mechanisms remain to be discovered. The role of thiamine in the pathogenicity of E. piscicida is unknown. In this study, we characterized a thiamine transporter (TT) operon in E. piscicida. The deletion of the TT operon resulted in an intracellular TPP lacking situation, which led to attenuated overall pathogenicity, impaired abilities associated with motility and host cell adhesion, as well as decreased expression of certain flagellar and adhesion genes. Moreover, TPP starvation led to intracellular c-di-GMP reduction, and introducing into the TPP-suppressed mutant strain an exogenous diguanylate cyclase for c-di-GMP synthesis restored the virulence loss. Taken together, this work reveals the involvement of thiamine uptake in the virulence regulation of E. piscicida, with c-di-GMP implicated in the process. These finding could be employed to explore potential drug targets against E. piscicida.
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Affiliation(s)
- Xin Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, CAS Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; (X.L.); (X.W.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266003, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinhui Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, CAS Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; (X.L.); (X.W.)
| | - Boguang Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, CAS Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; (X.L.); (X.W.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Li Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, CAS Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; (X.L.); (X.W.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266003, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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30
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Cohen H, Hoede C, Scharte F, Coluzzi C, Cohen E, Shomer I, Mallet L, Holbert S, Serre RF, Schiex T, Virlogeux-Payant I, Grassl GA, Hensel M, Chiapello H, Gal-Mor O. Intracellular Salmonella Paratyphi A is motile and differs in the expression of flagella-chemotaxis, SPI-1 and carbon utilization pathways in comparison to intracellular S. Typhimurium. PLoS Pathog 2022; 18:e1010425. [PMID: 35381053 PMCID: PMC9012535 DOI: 10.1371/journal.ppat.1010425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 04/15/2022] [Accepted: 03/09/2022] [Indexed: 12/21/2022] Open
Abstract
Although Salmonella Typhimurium (STM) and Salmonella Paratyphi A (SPA) belong to the same phylogenetic species, share large portions of their genome and express many common virulence factors, they differ vastly in their host specificity, the immune response they elicit, and the clinical manifestations they cause. In this work, we compared their intracellular transcriptomic architecture and cellular phenotypes during human epithelial cell infection. While transcription induction of many metal transport systems, purines, biotin, PhoPQ and SPI-2 regulons was similar in both intracellular SPA and STM, we identified 234 differentially expressed genes that showed distinct expression patterns in intracellular SPA vs. STM. Surprisingly, clear expression differences were found in SPI-1, motility and chemotaxis, and carbon (mainly citrate, galactonate and ethanolamine) utilization pathways, indicating that these pathways are regulated differently during their intracellular phase. Concurring, on the cellular level, we show that while the majority of STM are non-motile and reside within Salmonella-Containing Vacuoles (SCV), a significant proportion of intracellular SPA cells are motile and compartmentalized in the cytosol. Moreover, we found that the elevated expression of SPI-1 and motility genes by intracellular SPA results in increased invasiveness of SPA, following exit from host cells. These findings demonstrate unexpected flagellum-dependent intracellular motility of a typhoidal Salmonella serovar and intriguing differences in intracellular localization between typhoidal and non-typhoidal salmonellae. We propose that these differences facilitate new cycles of host cell infection by SPA and may contribute to the ability of SPA to disseminate beyond the intestinal lamina propria of the human host during enteric fever. Salmonella enterica is a ubiquitous, facultative intracellular animal and human pathogen. Although non-typhoidal Salmonella (NTS) and typhoidal Salmonella serovars belong to the same phylogenetic species and share many virulence factors, the disease they cause in humans is very different. While the underlying mechanisms for these differences are not fully understood, one possible reason expected to contribute to their different pathogenicity is a distinct expression pattern of genes involved in host-pathogen interactions. Here, we compared the global gene expression and intracellular phenotypes, during human epithelial cell infection of S. Paratyphi A (SPA) and S. Typhimurium (STM), as prototypical serovars of typhoidal and NTS, respectively. Interestingly, we identified different expression patterns in key virulence and metabolic pathways, cytosolic motility and increased reinvasion of SPA, following exit from infected cells. We hypothesize that these differences contribute to the invasive and systemic disease developed following SPA infection in humans.
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Affiliation(s)
- Helit Cohen
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Claire Hoede
- Université Fédérale de Toulouse, INRAE, BioinfOmics, UR MIAT, GenoToul Bioinformatics facility, 31326, Castanet-Tolosan, France
| | - Felix Scharte
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Charles Coluzzi
- INRAE, Université Paris-Saclay, MaIAGE, Jouy-en-Josas, France
| | - Emiliano Cohen
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Inna Shomer
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ludovic Mallet
- Université Fédérale de Toulouse, INRAE, BioinfOmics, UR MIAT, GenoToul Bioinformatics facility, 31326, Castanet-Tolosan, France
| | | | | | - Thomas Schiex
- Université Fédérale de Toulouse, ANITI, INRAE, Toulouse, France
| | | | - Guntram A. Grassl
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School and German Center for Infection Research (DZIF), Hanover, Germany
| | - Michael Hensel
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
- CellNanOs–Center of Cellular Nanoanalytics Osnabrück, Universität Osnabrück, Osnabrück, Germany
- * E-mail: (MH); (HC); (OG-M)
| | - Hélène Chiapello
- Université Fédérale de Toulouse, INRAE, BioinfOmics, UR MIAT, GenoToul Bioinformatics facility, 31326, Castanet-Tolosan, France
- INRAE, Université Paris-Saclay, MaIAGE, Jouy-en-Josas, France
- * E-mail: (MH); (HC); (OG-M)
| | - Ohad Gal-Mor
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- * E-mail: (MH); (HC); (OG-M)
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31
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Environment dependent expression of mycobacterium hormone sensitive lipases: expression pattern under ex-vivo and individual in-vitro stress conditions in M. tuberculosis H37Ra. Mol Biol Rep 2022; 49:4583-4593. [PMID: 35301657 DOI: 10.1007/s11033-022-07305-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/27/2022] [Accepted: 02/24/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Hormone-sensitive lipase (HSL) is a neutral lipase capable of hydrolysing various kinds of lipids. In comparison to single human Hormone Sensitive Lipase (hHSL), that is induced under nutritional stress, twelve serine hydrolases are annotated as HSL in Mycobacterium tuberculosis (mHSL). Mycobacterium is exposed to multiple stresses inside the host. Therefore, the present study was carried out to investigate if mHSL are also expressed under stress condition and if there is any correlation between various stress conditions and expression pattern of mHSL. METHODS AND RESULTS The expression pattern of mHSL under different environmental conditions (in-vitro and ex-vivo) were studied using qRT-PCR in M. tuberculosis H37Ra strain with 16 S rRNA as internal control. Out of 12, only two genes (lipU and lipY) were expressed at very low level in mid log phase culture under aerobic conditions, while 9 genes were expressed at stationary phase of growth. Ten mHSLs were expressed post-infection under ex-vivo conditions in time dependent manner. LipH and lipQ did not express at any time point under ex-vivo condition. The relative expression of most of the genes under individual stress was much higher than observed in ex-vivo conditions. The expression pattern of genes varied with change in stress condition. CONCLUSIONS Different sets of mHSL genes were expressed under different individual stress conditions pointing towards the requirement of different mHSL to combat different stress conditions. Overall, most of the mHSLs have demonstrated stress dependent expression pointing towards their role in intracellular survival of mycobacteria.
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Yin L, Shen X, Zhang D, Zhao R, Dai Y, Hu X, Wang J, Hou H, Pan X, Qi K. Transcriptome response of a new serotype of avian type Klebsiella varicella strain to chicken sera. Res Vet Sci 2022; 145:222-228. [PMID: 35278892 DOI: 10.1016/j.rvsc.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/16/2022] [Accepted: 03/03/2022] [Indexed: 11/17/2022]
Abstract
Klebsiella variicola is a newly discovered pathogen of zoonotic importance, commonly causing serious systemic infection via the bloodstream route. However, the mechanism by which K. variicola survives and grows in the bloodstream is poorly understood. In a previous study, a strain of Klebsiella causing chicken bloodstream infection was obtained, and whole genome sequencing showed that it was a new ST174 type K. variicola. Therefore, the present study aimed to determine the molecular mechanism underlying the survival and development of K. variicola in host serum. First, we compared the transcriptomes of K. variicola grown in Luria-Bertani broth and chicken serum. We sequenced six RNA libraries from the two groups, each library had three repeats. A total of 1046 differentially expressed genes were identified. Functional annotation analysis showed that the differentially expressed genes are mainly involved in adaptive metabolism, biosynthesis pathways (including biosynthesis of siderophore group nonribosomal peptides and lipopolysaccharide (LPS) biosynthesis), stress resistance, and several known virulence regulatory systems (including the ABC transporter system, the two-component signal transduction system and the quorum sensing system). These genes are expected to contribute to the adaptation and growth of K. variicola in host birds. This analysis provides a new insight into the pathogenesis of K. variicola.
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Affiliation(s)
- Lei Yin
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Xuehuai Shen
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Danjun Zhang
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Ruihong Zhao
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Yin Dai
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Xiaomiao Hu
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Jieru Wang
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Hongyan Hou
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Xiaocheng Pan
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China.
| | - Kezong Qi
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China.
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Hosmer J, Nasreen M, Dhouib R, Essilfie AT, Schirra HJ, Henningham A, Fantino E, Sly P, McEwan AG, Kappler U. Access to highly specialized growth substrates and production of epithelial immunomodulatory metabolites determine survival of Haemophilus influenzae in human airway epithelial cells. PLoS Pathog 2022; 18:e1010209. [PMID: 35085362 PMCID: PMC8794153 DOI: 10.1371/journal.ppat.1010209] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 12/14/2021] [Indexed: 11/18/2022] Open
Abstract
Haemophilus influenzae (Hi) infections are associated with recurring acute exacerbations of chronic respiratory diseases in children and adults including otitis media, pneumonia, chronic obstructive pulmonary disease and asthma. Here, we show that persistence and recurrence of Hi infections are closely linked to Hi metabolic properties, where preferred growth substrates are aligned to the metabolome of human airway epithelial surfaces and include lactate, pentoses, and nucleosides, but not glucose that is typically used for studies of Hi growth in vitro. Enzymatic and physiological investigations revealed that utilization of lactate, the preferred Hi carbon source, required the LldD L-lactate dehydrogenase (conservation: 98.8% of strains), but not the two redox-balancing D-lactate dehydrogenases Dld and LdhA. Utilization of preferred substrates was directly linked to Hi infection and persistence. When unable to utilize L-lactate or forced to rely on salvaged guanine, Hi showed reduced extra- and intra-cellular persistence in a murine model of lung infection and in primary normal human nasal epithelia, with up to 3000-fold attenuation observed in competitive infections. In contrast, D-lactate dehydrogenase mutants only showed a very slight reduction compared to the wild-type strain. Interestingly, acetate, the major Hi metabolic end-product, had anti-inflammatory effects on cultured human tissue cells in the presence of live but not heat-killed Hi, suggesting that metabolic endproducts also influence HI-host interactions. Our work provides significant new insights into the critical role of metabolism for Hi persistence in contact with host cells and reveals for the first time the immunomodulatory potential of Hi metabolites.
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Affiliation(s)
- Jennifer Hosmer
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Australia
| | - Marufa Nasreen
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Australia
| | - Rabeb Dhouib
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Australia
| | | | | | - Anna Henningham
- Child Health Research Centre, The University of Queensland, South Brisbane, Australia
| | - Emmanuelle Fantino
- Child Health Research Centre, The University of Queensland, South Brisbane, Australia
| | - Peter Sly
- Child Health Research Centre, The University of Queensland, South Brisbane, Australia
| | - Alastair G. McEwan
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Australia
| | - Ulrike Kappler
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Australia
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34
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Han ML, Nang SC, Lin YW, Zhu Y, Yu HH, Wickremasinghe H, Barlow CK, Creek DJ, Crawford S, Rao G, Dai C, Barr JJ, Chan K, Turner Schooley R, Velkov T, Li J. Comparative metabolomics revealed key pathways associated with the synergistic killing of multidrug-resistant Klebsiella pneumoniae by a bacteriophage-polymyxin combination. Comput Struct Biotechnol J 2022; 20:485-495. [PMID: 35070170 PMCID: PMC8760530 DOI: 10.1016/j.csbj.2021.12.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 01/21/2023] Open
Abstract
Resistance to the last-line polymyxins is emerging in multidrug-resistant Klebsiella pneumoniae and phage therapy is a promising alternative. However, phage monotherapy often rapidly causes resistance and few studies have examined antibiotic-phage combinations against K. pneumoniae. Here, we investigated the combination of polymyxin B with a novel phage pK8 against an mcr-1-carrying polymyxin-resistant clinical isolate Kp II-503 (polymyxin B MIC, 8 mg/L). The phage genome was sequenced and bacterial metabolomes were analysed at 4 and 24 h following the treatment with polymyxin B (16 mg/L), phage pK8 (102 PFU/mL) and their combination. Minimal metabolic changes across 24 h were observed with polymyxin B alone; whereas a significant inhibition of the citrate cycle, pentose phosphate pathway, amino acid and nucleotide metabolism occurred with the phage-polymyxin combination at both 4 and 24 h, but with phage alone only at 4 h. The development of resistance to phage alone was associated with enhanced membrane lipid and decreased amino acid biosynthesis in Kp II-503. Notably, cAMP, cGMP and cCMP were significantly enriched (3.1–6.6 log2fold) by phage alone and the combination only at 4 h. This is the first systems pharmacology study to investigate the enhanced bacterial killing by polymyxin-phage combination and provides important mechanistic information on phage killing, resistance and antibiotic-phage combination in K. pneumoniae.
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35
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Zulkefli NJ, Teh CSJ, Mariappan V, Ngoi ST, Vadivelu J, Ponnampalavanar S, Chai LC, Chong CW, Yap IKS, Vellasamy KM. Genomic comparison and phenotypic profiling of small colony variants of Burkholderia pseudomallei. PLoS One 2021; 16:e0261382. [PMID: 34910764 PMCID: PMC8673655 DOI: 10.1371/journal.pone.0261382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/30/2021] [Indexed: 11/18/2022] Open
Abstract
Burkholderia pseudomallei (B. pseudomallei) is an intracellular pathogen that causes melioidosis, a life-threatening infection in humans. The bacterium is able to form small colony variants (SCVs) as part of the adaptive features in response to environmental stress. In this study, we characterize the genomic characteristics, antimicrobial resistance (AMR), and metabolic phenotypes of B. pseudomallei SCV and wild type (WT) strains. Whole-genome sequence analysis was performed to characterize the genomic features of two SCVs (CS and OS) and their respective parental WT strains (CB and OB). Phylogenetic relationship between the four draft genomes in this study and 19 publicly available genomes from various countries was determined. The four draft genomes showed a close phylogenetic relationship with other genomes from Southeast Asia. Broth microdilution and phenotype microarray were conducted to determine the AMR profiles and metabolic features (carbon utilization, osmolytes sensitivity, and pH conditions) of all strains. The SCV strains exhibited identical AMR phenotype with their parental WT strains. A limited number of AMR-conferring genes were identified in the B. pseudomallei genomes. The SCVs and their respective parental WT strains generally shared similar carbon-utilization profiles, except for D,L-carnitine (CS), g-hydroxybutyric acid (OS), and succinamic acid (OS) which were utilized by the SCVs only. No difference was observed in the osmolytes sensitivity of all strains. In comparison, WT strains were more resistant to alkaline condition, while SCVs showed variable growth responses at higher acidity. Overall, the genomes of the colony morphology variants of B. pseudomallei were largely identical, and the phenotypic variations observed among the different morphotypes were strain-specific.
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Affiliation(s)
- Noorfatin Jihan Zulkefli
- Faculty of Medicine, Department of Medical Microbiology, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Cindy Shuan Ju Teh
- Faculty of Medicine, Department of Medical Microbiology, Universiti Malaya, Kuala Lumpur, Malaysia
- * E-mail: (CSJT); (KMV)
| | - Vanitha Mariappan
- Faculty of Health Sciences, Centre of Toxicology and Health Risk Studies (CORE), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Soo Tein Ngoi
- Faculty of Medicine, Department of Medical Microbiology, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Jamuna Vadivelu
- Faculty of Medicine, Department of Medical Microbiology, Universiti Malaya, Kuala Lumpur, Malaysia
| | | | - Lay Ching Chai
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Chun Wie Chong
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
- Institute for Research, Development & Innovation, International Medical University, Kuala Lumpur, Malaysia
| | - Ivan Kok Seng Yap
- Sarawak Research and Development Council, Kuching, Sarawak, Malaysia
| | - Kumutha Malar Vellasamy
- Faculty of Medicine, Department of Medical Microbiology, Universiti Malaya, Kuala Lumpur, Malaysia
- * E-mail: (CSJT); (KMV)
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Fuji N, Pichichero M, Ehrlich RL, Mell JC, Ehrlich GD, Kaur R. Transition of Serotype 35B Pneumococci From Commensal to Prevalent Virulent Strain in Children. Front Cell Infect Microbiol 2021; 11:744742. [PMID: 34765566 PMCID: PMC8577857 DOI: 10.3389/fcimb.2021.744742] [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: 07/20/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
In our community-based prospective cohort study in young children, we observed a significant increase in pneumococcal serotype 35B nasopharyngeal (NP) commensal colonization during the 2011–2014 timeframe, but these strains were not associated with disease. Beginning in 2015 and continuing through to the present, the serotype 35B virulence changed, and it became the dominant bacteria isolated and associated with pneumococcal acute otitis-media (AOM) in our cohort. We performed comparative analyses of 250 35B isolates obtained from 140 children collected between 2006 and 2019. Changes in prevalence, clonal-complex composition, and antibiotic resistance were analyzed. Seventy-two (29%) of 35B isolates underwent whole-genome sequencing to investigate genomic changes associated with the shift in virulence that resulted in increased rates of 35B-associated AOM disease. 35B strains that were commensals and AOM disease-causing were mainly associated with sequence type (ST) 558. Antibiotic concentrations of β-lactams and ofloxacin necessary to inhibit growth of 35B strains rose significantly (2006–2019) (p<0.005). However, only isolates from the 35B/ST558 showed significant increases in MIC50 of penicillin and ofloxacin between the years 2006–2014 and 2015–2019 (p=0.007 and p<0.0001). One hundred thirty-eight SNPs located in 34 different genes were significantly associated with post-2015 strains. SNPs were found in nrdG (metal binding, 10%); metP and metN (ABC transporter, 9%); corA (Mg2+ transporter, 6%); priA (DNA replication, 5%); and on the enzymic gene ldcB (LD-carboxypeptidase, 3%). Pneumococcal serotype 35B strains was a common NP commensal during 2010–2014. In 2015, a shift in increasing number of AOM cases occurred in young children caused by 35B, that was associated with changes in genetic composition and antibiotic susceptibility.
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Affiliation(s)
- Naoko Fuji
- Center for Infectious Diseases and Immunology, Rochester General Hospital Research Institute, Rochester, NY, United States
| | - Michael Pichichero
- Center for Infectious Diseases and Immunology, Rochester General Hospital Research Institute, Rochester, NY, United States
| | - Rachel L Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, and Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Philadelphia, PA, United States
| | - Joshua Chang Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, and Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Philadelphia, PA, United States
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, and Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Philadelphia, PA, United States.,Department of Otolaryngology-Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Ravinder Kaur
- Center for Infectious Diseases and Immunology, Rochester General Hospital Research Institute, Rochester, NY, United States
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37
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Wei W, Lan F, Liu Y, Wu L, Hassan BH, Wang S. Characterization of the Bifunctional Enzyme BioDA Involved in Biotin Synthesis and Pathogenicity in Aspergillus flavus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11971-11981. [PMID: 34591470 DOI: 10.1021/acs.jafc.1c03248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biotin is an important enzyme cofactor that plays a key role in all three domains. The classical bifunctional enzyme BioDA in eukaryotes (such as Aspergillus flavus and Arabidopsis thaliana) is involved in the antepenultimate and penultimate steps of biotin biosynthesis. In this study, we identified a A. flavus bifunctional gene bioDA which could complement both Escherichia coli ΔEcbioD and ΔEcbioA mutants. Interestingly, the separated domain of AfBioD and AfBioA could, respectively, fuse with EcBioA and EcBioD well and work together. What is more, we found that BioDA was almost localized to the mitochondria in A. flavus, as shown by N-terminal red fluorescent protein tag fusion. Noteworthy, the subcellular localization of AfBioDA is never affected by common environmental stresses (such as hyperosmotic stress or oxidative stress). The knockout strategy demonstrated that the deletion of AfbioDA gene from the chromosome impaired the biotin de novo synthesis pathway in A. flavus. Importantly, this A. flavus mutant blocked biotin production and decreased its pathogenicity to infect peanuts. Based on the structural comparison, we found that two inhibitors (amiclenomycin and gemcitabine) could be candidates for antifungal drugs. Taken together, our findings identified the bifunctional AfbioDA gene and shed light on biotin biosynthesis in A. flavus.
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Affiliation(s)
- Wenhui Wei
- School of Life Sciences, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Faxiu Lan
- School of Life Sciences, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yinghang Liu
- School of Life Sciences, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lianghuan Wu
- School of Life Sciences, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Bachar H Hassan
- Health Sciences Center, Stony Brook University, Stony Brook, New York, New York 11794, United States
| | - Shihua Wang
- School of Life Sciences, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Venkat K, Hoyos M, Haycocks JR, Cassidy L, Engelmann B, Rolle-Kampczyk U, von Bergen M, Tholey A, Grainger DC, Papenfort K. A dual-function RNA balances carbon uptake and central metabolism in Vibrio cholerae. EMBO J 2021; 40:e108542. [PMID: 34612526 PMCID: PMC8672173 DOI: 10.15252/embj.2021108542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 11/22/2022] Open
Abstract
Bacterial small RNAs (sRNAs) are well known to modulate gene expression by base pairing with trans‐encoded transcripts and are typically non‐coding. However, several sRNAs have been reported to also contain an open reading frame and thus are considered dual‐function RNAs. In this study, we discovered a dual‐function RNA from Vibrio cholerae, called VcdRP, harboring a 29 amino acid small protein (VcdP), as well as a base‐pairing sequence. Using a forward genetic screen, we identified VcdRP as a repressor of cholera toxin production and link this phenotype to the inhibition of carbon transport by the base‐pairing segment of the regulator. By contrast, we demonstrate that the VcdP small protein acts downstream of carbon transport by binding to citrate synthase (GltA), the first enzyme of the citric acid cycle. Interaction of VcdP with GltA results in increased enzyme activity and together VcdR and VcdP reroute carbon metabolism. We further show that transcription of vcdRP is repressed by CRP allowing us to provide a model in which VcdRP employs two different molecular mechanisms to synchronize central metabolism in V. cholerae.
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Affiliation(s)
- Kavyaa Venkat
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Mona Hoyos
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - James Rj Haycocks
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Liam Cassidy
- Systematic Proteome Research & Bioanalytics, University of Kiel, Kiel, Germany
| | | | | | | | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, University of Kiel, Kiel, Germany
| | - David C Grainger
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Kai Papenfort
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany.,Microverse Cluster, Friedrich Schiller University Jena, Jena, Germany
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Powers TR, Haeberle AL, Predeus AV, Hammarlöf DL, Cundiff JA, Saldaña-Ahuactzi Z, Hokamp K, Hinton JCD, Knodler LA. Intracellular niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica. PLoS Pathog 2021; 17:e1009280. [PMID: 34460873 PMCID: PMC8432900 DOI: 10.1371/journal.ppat.1009280] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 09/10/2021] [Accepted: 08/06/2021] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a zoonotic pathogen that causes diarrheal disease in humans and animals. During salmonellosis, S. Typhimurium colonizes epithelial cells lining the gastrointestinal tract. S. Typhimurium has an unusual lifestyle in epithelial cells that begins within an endocytic-derived Salmonella-containing vacuole (SCV), followed by escape into the cytosol, epithelial cell lysis and bacterial release. The cytosol is a more permissive environment than the SCV and supports rapid bacterial growth. The physicochemical conditions encountered by S. Typhimurium within the epithelial cytosol, and the bacterial genes required for cytosolic colonization, remain largely unknown. Here we have exploited the parallel colonization strategies of S. Typhimurium in epithelial cells to decipher the two niche-specific bacterial virulence programs. By combining a population-based RNA-seq approach with single-cell microscopic analysis, we identified bacterial genes with cytosol-induced or vacuole-induced expression signatures. Using these genes as environmental biosensors, we defined that Salmonella is exposed to oxidative stress and iron and manganese deprivation in the cytosol and zinc and magnesium deprivation in the SCV. Furthermore, iron availability was critical for optimal S. Typhimurium replication in the cytosol, as well as entC, fepB, soxS, mntH and sitA. Virulence genes that are typically associated with extracellular bacteria, namely Salmonella pathogenicity island 1 (SPI1) and SPI4, showed increased expression in the cytosol compared to vacuole. Our study reveals that the cytosolic and vacuolar S. Typhimurium virulence gene programs are unique to, and tailored for, residence within distinct intracellular compartments. This archetypical vacuole-adapted pathogen therefore requires extensive transcriptional reprogramming to successfully colonize the mammalian cytosol.
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Affiliation(s)
- TuShun R. Powers
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Amanda L. Haeberle
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Alexander V. Predeus
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Disa L. Hammarlöf
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jennifer A. Cundiff
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Zeus Saldaña-Ahuactzi
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Karsten Hokamp
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Jay C. D. Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Leigh A. Knodler
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
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Mirzaei R, Sholeh M, Jalalifar S, Zafari E, Kazemi S, Rasouli-Saravani A, Karampoor S, Yousefimashouf R. Immunometabolism in human brucellosis: An emerging field of investigation. Microb Pathog 2021; 158:105115. [PMID: 34332069 DOI: 10.1016/j.micpath.2021.105115] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 07/19/2021] [Accepted: 07/27/2021] [Indexed: 01/16/2023]
Abstract
In recent years, extreme attention has been focused on the role of immunometabolism in the regulation of immune cell responses in healthy individuals during infection, autoimmunity, and cancer. In the infection biology area, it has been shown that there is a close relationship between the immune system and the host metabolic changes. Brucella species is an intracellular coccobacillus that infects humans and mammals, which led to brucellosis. Brucella species with host-specific evolutionary mechanisms allow it to hide from or manipulate cellular immunity and achieve intracellular persistence. Intracellular bacterial pathogens such as Brucella species also employ host cell resources to replicate and persist inside the host. Targeting these host systems is one promising strategy for developing novel antimicrobials to tackle intracellular infections. This study will summarize the role of metabolic reprogramming in immune cells and their relationship to brucellosis.
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Affiliation(s)
- Rasoul Mirzaei
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Mohammad Sholeh
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Saba Jalalifar
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ehsan Zafari
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Sima Kazemi
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ashkan Rasouli-Saravani
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Rasoul Yousefimashouf
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
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XRE-Type Regulator BioX Acts as a Negative Transcriptional Factor of Biotin Metabolism in Riemerella anatipestifer. J Bacteriol 2021; 203:e0018121. [PMID: 33972354 DOI: 10.1128/jb.00181-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biotin is essential for the growth and pathogenicity of microorganisms. Damage to biotin biosynthesis results in impaired bacterial growth and decreased virulence in vivo. However, the mechanisms of biotin biosynthesis in Riemerella anatipestifer remain unclear. In this study, two R. anatipestifer genes associated with biotin biosynthesis were identified. AS87_RS05840 encoded a BirA protein lacking the N-terminal winged helix-turn-helix DNA binding domain, identifying it as a group I biotin protein ligase, and AS87_RS09325 encoded a BioX protein, which was in the helix-turn-helix xenobiotic response element family of transcription factors. Electrophoretic mobility shift assays demonstrated that BioX bound to the promoter region of bioF. In addition, the R. anatipestifer genes bioF (encoding 7-keto-8-aminopelargonic acid synthase), bioD (encoding dethiobiotin synthase), and bioA (encoding 7,8-diaminopelargonic acid synthase) were in an operon and were regulated by BioX. Quantitative reverse transcription-PCR showed that transcription of the bioFDA operon increased in the mutant Yb2ΔbioX in the presence of excessive biotin, compared with that in the wild-type strain Yb2, suggesting that BioX acted as a repressor of biotin biosynthesis. Streptavidin blot analysis showed that BirA caused biotinylation of BioX, indicating that biotinylated BioX was involved in metabolic pathways. Moreover, as determined by the median lethal dose, the virulence of Yb2ΔbioX was attenuated 500-fold compared with that of Yb2. To summarize, the genes birA and bioX were identified in R. anatipestifer, and BioX was found to act as a repressor of the bioFDA operon involved in the biotin biosynthesis pathway and identified as a bacterial virulence factor. IMPORTANCE Riemerella anatipestifer is a causative agent of diseases in ducks, geese, turkeys, and various other domestic and wild birds. Our study reveals that biotin synthesis of R. anatipestifer is regulated by the BioX through binding to the promoter region of the bioF gene to inhibit transcription of the bioFDA operon. Moreover, bioX is required for R. anatipestifer pathogenicity, suggesting that BioX is a potential target for treatment of the pathogen. R. anatipestifer BioX has thus been identified as a novel negative regulator involved in biotin metabolism and associated with bacterial virulence in this study.
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He W, Zheng Z, Bai H, Xiong LH, Wang L, Li Y, Kwok RTK, Lam JWY, Hu Q, Cheng J, Tang BZ. A biocompatible dual-AIEgen system without spectral overlap for quantitation of microbial viability and monitoring of biofilm formation. MATERIALS HORIZONS 2021; 8:1816-1824. [PMID: 34846510 DOI: 10.1039/d1mh00149c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The lack of rapid and reliable microbial detection and sensing platforms and insufficient understanding of microbial behavior may delay precautions that could be made, which is a great threat to human life and increases the heavy financial burden on society. In this contribution, a dual-aggregation-induced emission luminogen (AIEgen) system is successfully developed for microbial imaging and metabolic status sensing. This system consists of two AIEgens (DCQA and TPE-2BA) that bear positively charged groups or boronic acid groups, providing universal microbial staining ability and specific affinity for dead microbes, respectively. Based on the distinctive fluorescence response produced by the diverse interaction of AIEgens with live or dead microbes, this dual-AIEgen system can detect all the microbes and identify their viabilities. Furthermore, the morphology and metabolic status of a sessile biofilm can also be imaged and monitored. The system exhibits rapid labelling properties that suitable for various microbes, and good biocompatibilities.
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Affiliation(s)
- Wei He
- Department of Chemistry, Department of Chemical and Biological Engineering, Hong Kong Branch of Chinese Nation-al Engineering Research Center for Tissue Restoration and Reconstruction, Institute of Advanced Study and Division of Life Science The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
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43
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Sakata N, Ishiga T, Ishiga Y. Pseudmonas cannabina pv. alisalensis TrpA Is Required for Virulence in Multiple Host Plants. Front Microbiol 2021; 12:659734. [PMID: 33959115 PMCID: PMC8093880 DOI: 10.3389/fmicb.2021.659734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas cannabina pv. alisalensis (Pcal) causes bacterial leaf spot and blight of Brassicaceae and Poaceae. We previously identified several potential Pcal virulence factors with transposon mutagenesis. Among these a trpA mutant disrupted the tryptophan synthase alpha chain, and had an effect on disease symptom development and bacterial multiplication. To assess the importance of TrpA in Pcal virulence, we characterized the trpA mutant based on inoculation test and Pcal gene expression profiles. The trpA mutant showed reduced virulence when dip- and syringe-inoculated on cabbage and oat. Moreover, epiphytic bacterial populations of the trpA mutant were also reduced compared to the wild-type (WT). These results suggest that TrpA contributes to bacterial multiplication on the leaf surface and in the apoplast, and disease development. Additionally, several Brassicaceae (including Japanese radish, broccoli, and Chinese cabbage) also exhibited reduced symptom development when inoculated with the trpA mutant. Moreover, trpA disruption led to downregulation of bacterial virulence genes, including type three effectors (T3Es) and the phytotoxin coronatine (COR), and to upregulation of tryptophan biosynthesis genes. These results indicate that a trade-off between virulence factor production and Pcal multiplication with tryptophan might be regulated in the infection processes.
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Affiliation(s)
- Nanami Sakata
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Takako Ishiga
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yasuhiro Ishiga
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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44
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He Y, Chen R, Qi Y, Salazar JK, Zhang S, Tortorello ML, Deng X, Zhang W. Survival and transcriptomic response of Salmonella enterica on fresh-cut fruits. Int J Food Microbiol 2021; 348:109201. [PMID: 33930836 DOI: 10.1016/j.ijfoodmicro.2021.109201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 03/26/2021] [Accepted: 04/13/2021] [Indexed: 01/21/2023]
Abstract
Salmonella enterica is frequently implicated in foodborne disease outbreaks associated with fresh-cut fruits. In the U.S., more than one third of fruit-related outbreaks have been linked to two S. enterica serotypes Newport and Typhimurium. Approximately 80% of fruit-related human salmonellosis cases were associated with tomatoes, cantaloupes and cucumbers. In this study, we investigated the population dynamics of S. Newport and S. Typhimurium on fresh-cut tomato, cantaloupe, cucumber and apple under short-term storage conditions. We further compared the transcriptomic profiles of a S. Newport strain on fresh-cut tomato and cantaloupe using high-throughput RNA-seq. We demonstrated that both S. enterica Newport and Typhimurium survived well on various fresh-cut fruit items under refrigeration storage conditions, independent of inoculation levels. However, S. enterica displayed variable survival behaviors on different types of fruits. For example, at 7 d storage, the population of S. enterica reduced less than 0.2 log (p > 0.05) on fresh-cut tomato and cantaloupe, in contrast to ~0.5 log (p < 0.05) on cucumber and apple. RNA-seq analysis suggested that S. enterica mediates its survival on fresh-cut fruits through differentially regulating genes involved in specific carbon utilization and metabolic pathways. Several known bacterial virulence factors (e.g., pag gene) were found to be differentially regulated on fresh-cut tomato and cantaloupe, suggesting a link between the events of food contamination and subsequent human infection. Findings from this study contribute to a better understanding of S. enterica survival mechanisms on fresh-cut produce.
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Affiliation(s)
- Yingshu He
- Department of Food Science and Nutrition & Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA; Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, GA, USA.
| | - Ruixi Chen
- Department of Food Science and Nutrition & Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
| | - Yan Qi
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, GA, USA
| | - Joelle K Salazar
- Division of Food Processing Science and Technology, U. S. Food and Drug Administration, Bedford Park, IL, USA
| | - Shimei Zhang
- Department of Food Science and Nutrition & Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
| | - Mary Lou Tortorello
- Division of Food Processing Science and Technology, U. S. Food and Drug Administration, Bedford Park, IL, USA
| | - Xiangyu Deng
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, GA, USA
| | - Wei Zhang
- Department of Food Science and Nutrition & Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
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45
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Alternative σ Factors Regulate Overlapping as Well as Distinct Stress Response and Metabolic Functions in Listeria monocytogenes under Stationary Phase Stress Condition. Pathogens 2021; 10:pathogens10040411. [PMID: 33915780 PMCID: PMC8066629 DOI: 10.3390/pathogens10040411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 12/13/2022] Open
Abstract
Listeria monocytogenes can regulate and fine-tune gene expression, to adapt to diverse stress conditions encountered during foodborne transmission. To further understand the contributions of alternative sigma (σ) factors to the regulation of L. monocytogenes gene expression, RNA-Seq was performed on L. monocytogenes strain 10403S and five isogenic mutants (four strains bearing in-frame null mutations in three out of four alternative σ factor genes, ΔCHL, ΔBHL, ΔBCL, and ΔBCH, and one strain bearing null mutations in all four genes, ΔBCHL), grown to stationary phase. Our data showed that 184, 35, 34, and 20 genes were positively regulated by σB, σL, σH, and σC (posterior probability > 0.9 and Fold Change (FC) > 5.0), respectively. Moreover, σB-dependent genes showed the highest FC (based on comparisons between the ΔCHL and the ΔBCHL strain), with 44 genes showing an FC > 100; only four σL-dependent, and no σH- or σC-dependent genes showed FC >100. While σB-regulated genes identified in this study are involved in stress-associated functions and metabolic pathways, σL appears to largely regulate genes involved in a few specific metabolic pathways, including positive regulation of operons encoding phosphoenolpyruvate (PEP)-dependent phosphotransferase systems (PTSs). Overall, our data show that (i) σB and σL directly and indirectly regulate genes involved in several energy metabolism-related functions; (ii) alternative σ factors are involved in complex regulatory networks and appear to have epistatic effects in stationary phase cells; and (iii) σB regulates multiple stress response pathways, while σL and σH positively regulate a smaller number of specific pathways.
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46
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Roop RM, Barton IS, Hopersberger D, Martin DW. Uncovering the Hidden Credentials of Brucella Virulence. Microbiol Mol Biol Rev 2021; 85:e00021-19. [PMID: 33568459 PMCID: PMC8549849 DOI: 10.1128/mmbr.00021-19] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Bacteria in the genus Brucella are important human and veterinary pathogens. The abortion and infertility they cause in food animals produce economic hardships in areas where the disease has not been controlled, and human brucellosis is one of the world's most common zoonoses. Brucella strains have also been isolated from wildlife, but we know much less about the pathobiology and epidemiology of these infections than we do about brucellosis in domestic animals. The brucellae maintain predominantly an intracellular lifestyle in their mammalian hosts, and their ability to subvert the host immune response and survive and replicate in macrophages and placental trophoblasts underlies their success as pathogens. We are just beginning to understand how these bacteria evolved from a progenitor alphaproteobacterium with an environmental niche and diverged to become highly host-adapted and host-specific pathogens. Two important virulence determinants played critical roles in this evolution: (i) a type IV secretion system that secretes effector molecules into the host cell cytoplasm that direct the intracellular trafficking of the brucellae and modulate host immune responses and (ii) a lipopolysaccharide moiety which poorly stimulates host inflammatory responses. This review highlights what we presently know about how these and other virulence determinants contribute to Brucella pathogenesis. Gaining a better understanding of how the brucellae produce disease will provide us with information that can be used to design better strategies for preventing brucellosis in animals and for preventing and treating this disease in humans.
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Affiliation(s)
- R Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Ian S Barton
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Dariel Hopersberger
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Daniel W Martin
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
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47
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Ng E, Tay JRH, Balan P, Ong MMA, Bostanci N, Belibasakis GN, Seneviratne CJ. Metagenomic sequencing provides new insights into the subgingival bacteriome and aetiopathology of periodontitis. J Periodontal Res 2021; 56:205-218. [PMID: 33410172 DOI: 10.1111/jre.12811] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/29/2020] [Accepted: 09/30/2020] [Indexed: 12/17/2022]
Abstract
"Open-ended" molecular techniques such as 16S rRNA sequencing have revealed that the oral bacteriome of subgingival plaque is more diverse than originally thought. 16S rRNA analysis has demonstrated that constituents of the overall bacterial community are qualitatively similar in health and disease, differing mainly in their relative proportions with respect to each other. Species in low abundance can also act as critical species, leading to the concept of global community dysbiosis which relates to shifts in community structure, rather than shifts in membership. Correlation analysis suggests that coordinated interactions in the community are essential for incipient dysbiosis and disease pathogenesis. The subgingival bacteriome also provides biomarkers that are useful for disease detection and management. Combined with clinical and biological parameters, these may assist clinicians in developing and implementing effective treatment strategies to restore microbial homeostasis and monitor disease. Identification of higher risk groups or poor responders to treatment using unique subgingival bacteriome signatures may also lead to early intervention.
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Affiliation(s)
- Ethan Ng
- Department of Restorative Dentistry, National Dental Centre Singapore, Singapore, Singapore
| | - John R H Tay
- Department of Restorative Dentistry, National Dental Centre Singapore, Singapore, Singapore
| | - P Balan
- Singapore Oral Microbiomics Initiative, National Dental Research Institute Singapore, SingHealth, Singapore, Singapore
| | - Marianne M A Ong
- Department of Restorative Dentistry, National Dental Centre Singapore, Singapore, Singapore.,Oral Health Academic Clinical Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Nagihan Bostanci
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Georgios N Belibasakis
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Chaminda J Seneviratne
- Singapore Oral Microbiomics Initiative, National Dental Research Institute Singapore, SingHealth, Singapore, Singapore.,Oral Health Academic Clinical Programme, Duke-NUS Medical School, Singapore, Singapore
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48
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Stincone P, Comerlato CB, Brandelli A. Proteomic analysis of Listeria monocytogenes exposed to free and nanostructured antimicrobial lipopeptides. Mol Omics 2021; 17:426-437. [PMID: 33735358 DOI: 10.1039/d0mo00178c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this work, the effect of antimicrobial lipopeptide P34 on Listeria monocytogenes was evaluated for the first time through a proteomics approach. Bacteria were treated with sub-lethal doses of peptide P34 (F-P34) and P34 encapsulated into nanoliposomes (N-P34), while empty nanoliposomes (NE) and fresh buffer were used as controls. The proteomic analysis allowed the detection of one group of proteins commonly differentially represented in response to free and encapsulated P34 exposure. A second group of proteins was found to be exclusively differentially represented after exposure with encapsulated P34 only. The antimicrobial peptide P34 caused a significant downregulation of proteins associated with the transport of manganese and the over-representation of proteins related with iron transport in L. monocytogenes. In addition, reduction of stress tolerance proteins related to the σB and VirR regulons, together with the modulation of phosphoenolpyruvate phosphotransferase systems (PTS) for sugar transport were observed. The sugar and oligopeptide transporters regulated by antimicrobial action may influence the key virulence factor PrfA, reducing the pathogenicity of this microorganism.
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Affiliation(s)
- Paolo Stincone
- Laboratório de Bioquímica e Microbiologia Aplicada, Instituto de Ciência e Tecnologia de Alimentos, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, Brazil.
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49
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Chen Z. Astragaloside iv inhibits salmonella-induced meningitis via modulation of bacterial virulence and host response. Pharmacogn Mag 2021. [DOI: 10.4103/pm.pm_55_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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50
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DebRoy S, Aliaga-Tobar V, Galvez G, Arora S, Liang X, Horstmann N, Maracaja-Coutinho V, Latorre M, Hook M, Flores AR, Shelburne SA. Genome-wide analysis of in vivo CcpA binding with and without its key co-factor HPr in the major human pathogen group A Streptococcus. Mol Microbiol 2020; 115:1207-1228. [PMID: 33325565 PMCID: PMC8359418 DOI: 10.1111/mmi.14667] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/02/2020] [Accepted: 12/11/2020] [Indexed: 01/01/2023]
Abstract
Catabolite control protein A (CcpA) is a master regulator of carbon source utilization and contributes to the virulence of numerous medically important Gram‐positive bacteria. Most functional assessments of CcpA, including interaction with its key co‐factor HPr, have been performed in nonpathogenic bacteria. In this study we aimed to identify the in vivo DNA binding profile of CcpA and assess the extent to which HPr is required for CcpA‐mediated regulation and DNA binding in the major human pathogen group A Streptococcus (GAS). Using a combination RNAseq/ChIP‐seq approach, we found that CcpA affects transcript levels of 514 of 1667 GAS genes (31%) whereas direct DNA binding was identified for 105 GAS genes. Three of the directly regulated genes encode the key GAS virulence factors Streptolysin S, PrtS (IL‐8 degrading proteinase), and SpeB (cysteine protease). Mutating CcpA Val301 to Ala (strain 2221‐CcpA‐V301A) abolished interaction between CcpA and HPr and impacted the transcript levels of 205 genes (40%) in the total CcpA regulon. By ChIP‐seq analysis, CcpAV301A bound to DNA from 74% of genes bound by wild‐type CcpA, but generally with lower affinity. These data delineate the direct CcpA regulon and clarify the HPr‐dependent and independent activities of CcpA in a key pathogenic bacterium.
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Affiliation(s)
- Sruti DebRoy
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Victor Aliaga-Tobar
- Facultad de Ciencias Químicas y Farmacéuticas, Advanced Center for Chronic Diseases-ACCDiS, Universidad de Chile, Independencia, Chile.,Laboratorio de Bioingeniería, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
| | - Gabriel Galvez
- Laboratorio de Bioingeniería, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
| | - Srishtee Arora
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, USA
| | - Xiaowen Liang
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, USA
| | - Nicola Horstmann
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vinicius Maracaja-Coutinho
- Facultad de Ciencias Químicas y Farmacéuticas, Advanced Center for Chronic Diseases-ACCDiS, Universidad de Chile, Independencia, Chile.,Centro de Modelamiento Molecular, Biofísica y Bioinformática (CM2B2), Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Mauricio Latorre
- Laboratorio de Bioingeniería, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile.,Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile.,Mathomics, Center for Mathematical Modeling, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Santiago, Chile
| | - Magnus Hook
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, USA
| | - Anthony R Flores
- Division of Infectious Diseases, Department of Pediatrics, University of Texas Health Science Center McGovern Medical School, Houston, TX, USA.,Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center McGovern Medical School, Houston, TX, USA
| | - Samuel A Shelburne
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center McGovern Medical School, Houston, TX, USA.,Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston TX, USA
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