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Hsieh YYP, Sun W, Young JM, Cheung R, Hogan DA, Dandekar AA, Malik HS. Widespread fungal-bacterial competition for magnesium lowers bacterial susceptibility to polymyxin antibiotics. PLoS Biol 2024; 22:e3002694. [PMID: 38900845 PMCID: PMC11218974 DOI: 10.1371/journal.pbio.3002694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/02/2024] [Accepted: 05/29/2024] [Indexed: 06/22/2024] Open
Abstract
Fungi and bacteria coexist in many polymicrobial communities, yet the molecular basis of their interactions remains poorly understood. Here, we show that the fungus Candida albicans sequesters essential magnesium ions from the bacterium Pseudomonas aeruginosa. To counteract fungal Mg2+ sequestration, P. aeruginosa expresses the Mg2+ transporter MgtA when Mg2+ levels are low. Thus, loss of MgtA specifically impairs P. aeruginosa in co-culture with C. albicans, but fitness can be restored by supplementing Mg2+. Using a panel of fungi and bacteria, we show that Mg2+ sequestration is a general mechanism of fungal antagonism against gram-negative bacteria. Mg2+ limitation enhances bacterial resistance to polymyxin antibiotics like colistin, which target gram-negative bacterial membranes. Indeed, experimental evolution reveals that P. aeruginosa evolves C. albicans-dependent colistin resistance via non-canonical means; antifungal treatment renders resistant bacteria colistin-sensitive. Our work suggests that fungal-bacterial competition could profoundly impact polymicrobial infection treatment with antibiotics of last resort.
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Affiliation(s)
- Yu-Ying Phoebe Hsieh
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Wanting Sun
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Janet M. Young
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Robin Cheung
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Ajai A. Dandekar
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Harmit S. Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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2
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Weikum J, van Dyck JF, Subramani S, Klebl DP, Storflor M, Muench SP, Abel S, Sobott F, Morth JP. The bacterial magnesium transporter MgtA reveals highly selective interaction with specific cardiolipin species. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119614. [PMID: 37879515 DOI: 10.1016/j.bbamcr.2023.119614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/13/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023]
Abstract
The bacterial magnesium transporter A (MgtA) is a specialized P-type ATPase important for Mg2+ import into the cytoplasm; disrupted magnesium homeostasis is linked to intrinsic ribosome instability and antibacterial resistance in Salmonella strains. Here, we show that MgtA has functional specificity for cardiolipin 18:1. Still, it reaches maximum activity only in combination with cardiolipin 16:0, equivalent to the major components of native cardiolipin found in E. coli membranes. Native mass spectrometry indicates the presence of two binding sites for cardiolipin, agreeing with the kinetic studies revealing that a cooperative relationship likely exists between the two cardiolipin variants. This is the first experimental evidence of cooperative effects between lipids of the same class, with only minor variations in their acyl chain composition, acting on a membrane protein. In summary, our results reveal that MgtA exhibits a highly complex interaction with one cardiolipin 18:1 and one cardiolipin 16:0, affecting protein activity and stability, contributing to our understanding of the particular interactions between lipid environment and membrane proteins. Further, a better understanding of Mg2+ homeostasis in bacteria, due to its role as a virulence regulator, will provide further insights into the regulation and mechanism of bacterial infections.
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Affiliation(s)
- Julia Weikum
- Membrane Transport Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, P.O. Box 1137, Blindern, 0318 Oslo, Norway; Enzyme and Protein Chemistry, Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs. Lyngby, Denmark
| | - Jeroen F van Dyck
- Department of Chemistry, University of Antwerp, Campus Groenenborger, Groenenborgerlaan 171, G.V. 418, 2020 Antwerpen, Belgium
| | - Saranya Subramani
- Membrane Transport Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, P.O. Box 1137, Blindern, 0318 Oslo, Norway
| | - David P Klebl
- School of Biomedical Sciences & The Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Merete Storflor
- Infections Biology Lab, Department of Pharmacy, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Stephen P Muench
- School of Biomedical Sciences & The Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Sören Abel
- Infections Biology Lab, Department of Pharmacy, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Frank Sobott
- Department of Chemistry, University of Antwerp, Campus Groenenborger, Groenenborgerlaan 171, G.V. 418, 2020 Antwerpen, Belgium; School of Molecular and Cellular Biology & The Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom.
| | - J Preben Morth
- Membrane Transport Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, P.O. Box 1137, Blindern, 0318 Oslo, Norway; Enzyme and Protein Chemistry, Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs. Lyngby, Denmark; Institute for Experimental Medical Research (IEMR), Oslo University Hospital, Ullevål PB 4956 Nydalen, NO-0424 Oslo, Norway.
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3
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Chiu CY, Chang KC, Chang LC, Wang CJ, Chung WH, Hsieh WP, Su SC. Phenotype-specific signatures of systems-level gut microbiome associated with childhood airway allergies. Pediatr Allergy Immunol 2023; 34:e13905. [PMID: 36705037 DOI: 10.1111/pai.13905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND Perturbation of gut symbiosis has been linked to childhood allergic diseases. However, the underlying host-microbe interaction connected with specific phenotypes is poorly understood. METHODS To address this, integrative analyses of stool metagenomic and metabolomic profiles associated with IgE reactions in 56 children with mite-sensitized airway allergies (25 with rhinitis and 31 with asthma) and 28 nonallergic healthy controls were conducted. RESULTS We noted a decrease in the number and abundance of gut microbiome-encoded carbohydrate-active enzyme (CAZyme) genes, accompanied with a reduction in species richness, in the asthmatic gut microflora but not in that from allergic rhinitis. Such loss of CAZymes was consistent with the observation that a CAZyme-linked decrease in fecal butyrate was found in asthmatics and negatively correlated with mite-specific IgE responses. Different from the CAZymes, we demonstrated an increase in α diversity at the virulome levels in asthmatic gut microbiota and identified phenotype-specific variations of gut virulome. Moreover, use of fecal metagenomic and metabolomic signatures resulted in distinct effects on differentiating rhinitis and asthma from nonallergic healthy controls. CONCLUSION Overall, our integrative analyses reveal several signatures of systems-level gut microbiome in robust associations with fecal metabolites and disease phenotypes, which may be of etiological and diagnostic implications in childhood airway allergies.
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Affiliation(s)
- Chih-Yung Chiu
- Division of Pediatric Pulmonology, Chang Gung Memorial Hospital at Linkou, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Clinical Metabolomics Core Laboratory, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Ko-Chun Chang
- Institute of Statistics, National Tsing-Hua University, Hsinchu, Taiwan
| | - Lun-Ching Chang
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, USA
| | - Chia-Jung Wang
- Division of Pediatric Pulmonology, Chang Gung Memorial Hospital at Linkou, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Clinical Metabolomics Core Laboratory, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Wen-Hung Chung
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Wen-Ping Hsieh
- Institute of Statistics, National Tsing-Hua University, Hsinchu, Taiwan
| | - Shih-Chi Su
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan
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4
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Wang Z, Zhu S, Li C, Lyu L, Yu J, Wang D, Xu Z, Ni J, Gao B, Lu J, Yao YF. Gene essentiality profiling reveals a novel determinant of stresses preventing protein aggregation in Salmonella. Emerg Microbes Infect 2022; 11:1554-1571. [PMID: 35603550 PMCID: PMC9176671 DOI: 10.1080/22221751.2022.2081618] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Adaptation to various stresses during infection is important for Salmonella Typhimurium virulence, while the fitness determinants under infection-relevant stress conditions remain unknown. Here, we simulated conditions Salmonella encountered within the host or in the environment by 15 individual stresses as well as two model cell lines (epithelium and macrophage) to decipher the genes and pathways required for fitness. By high-resolution Tn-seq analysis, a total of 1242 genes were identified as essential for fitness under at least one stress condition. The comparative analysis of fitness determinants in 17 stress conditions indicated the essentiality of genes varied in different mimicking host niches. A total of 12 genes were identified as fitness determinants in all stress conditions, including recB, recC, and xseA (encode three exonuclease subunits necessary for DNA recombination repair) and a novel essential fitness gene yheM. YheM is a putative sulfurtransferase subunit that is responsible for tRNA modification, and our results showed that Salmonella lacking yheM accumulated more aggregates of endogenous protein than wild-type. Moreover, we established a scoring scheme for sRNA essentiality analysis and found STnc2080 of unknown function was essential for resistance to LL-37. In summary, we systematically dissected Salmonella gene essentiality profiling and demonstrated the general and specific adaptive requirements in infection-relevant niches. Our data not only provide valuable insights on how Salmonella responds to environmental stresses during infections but also highlight the potential clinical application of fitness determinants in vaccine development.
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Affiliation(s)
- Zuoqiang Wang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Siqi Zhu
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, People's Republic of China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Congcong Li
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Lin Lyu
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Jingchen Yu
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Danni Wang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Zhihong Xu
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Jinjing Ni
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, People's Republic of China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, People's Republic of China
| | - Jie Lu
- Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai, People's Republic of China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.,Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, People's Republic of China
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5
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Preharvest Environmental and Management Drivers of Multidrug Resistance in Major Bacterial Zoonotic Pathogens in Pastured Poultry Flocks. Microorganisms 2022; 10:microorganisms10091703. [PMID: 36144304 PMCID: PMC9505790 DOI: 10.3390/microorganisms10091703] [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: 06/28/2022] [Revised: 07/25/2022] [Accepted: 08/18/2022] [Indexed: 12/25/2022] Open
Abstract
Due to nutritional benefits and perceived humane ways of treating the animals, the demand for antibiotic-free pastured poultry chicken has continued to be steadily rise. Despite the non-usage of antibiotics in pastured poultry broiler production, antibiotic resistance (AR) is reported in zoonotic poultry pathogens. However, factors that drive multidrug resistance (MDR) in pastured poultry are not well understood. In this study, we used machine learning and deep learning approaches to predict farm management practices and physicochemical properties of feces and soil that drive MDR in zoonotic poultry pathogens. Antibiotic use in agroecosystems is known to contribute to resistance. Evaluation of the development of resistance in environments that are free of antibiotics such as the all-natural, antibiotic-free, pastured poultry production systems described here is critical to understand the background AR in the absence of any selection pressure, i.e., basal levels of resistance. We analyzed 1635 preharvest (feces and soil) samples collected from forty-two pastured poultry flocks and eleven farms in the Southeastern United States. CDC National Antimicrobial Resistance Monitoring System guidelines were used to determine antimicrobial/multidrug resistance profiles of Salmonella, Listeria, and Campylobacter. A combination of two traditional machine learning (RandomForest and XGBoost) and three deep learning (Multi-layer Perceptron, Generative Adversarial Network, and Auto-Encoder) approaches identified critical farm management practices and environmental variables that drive multidrug resistance in poultry pathogens in broiler production systems that represents background resistance. This study enumerates management practices that contribute to AR and makes recommendations to potentially mitigate multidrug resistance and the prevalence of Salmonella and Listeria in pastured poultry.
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6
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Bhowmik BK, Kumar A, Gangaiah D. Transcriptome Analyses of Chicken Primary Macrophages Infected With Attenuated Salmonella Typhimurium Mutants. Front Microbiol 2022; 13:857378. [PMID: 35591991 PMCID: PMC9111174 DOI: 10.3389/fmicb.2022.857378] [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: 01/18/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica is one of the most common foodborne illnesses in the United States and worldwide, with nearly one-third of the cases attributed to contaminated eggs and poultry products. Vaccination has proven to be an effective strategy to reduce Salmonella load in poultry. The Salmonella Typhimurium Δcrp-cya (MeganVac1) strain is the most commonly used vaccine in the United States; however, the mechanisms of virulence attenuation and host response to this vaccine strain are poorly understood. Here, we profiled the invasion and intracellular survival phenotypes of Δcrp-cya and its derivatives (lacking key genes required for intra-macrophage survival) in HD11 macrophages and the transcriptome response in primary chicken macrophages using RNA-seq. Compared to the parent strain UK1, all the mutant strains were highly defective in metabolizing carbon sources related to the TCA cycle and had greater doubling times in macrophage-simulating conditions. Compared to UK1, the majority of the mutants were attenuated for invasion and intra-macrophage survival. Compared to Δcrp-cya, while derivatives lacking phoPQ, ompR-envZ, feoABC and sifA were highly attenuated for invasion and intracellular survival within macrophages, derivatives lacking ssrAB, SPI13, SPI2, mgtRBC, sitABCD, sopF, sseJ and sspH2 showed increased ability to invade and survive within macrophages. Transcriptome analyses of macrophages infected with UK1, Δcrp-cya and its derivatives lacking phoPQ, sifA and sopF demonstrated that, compared to uninfected macrophages, 138, 148, 153, 155 and 142 genes were differentially expressed in these strains, respectively. Similar changes in gene expression were observed in macrophages infected with these strains; the upregulated genes belonged to innate immune response and host defense and the downregulated genes belonged to various metabolic pathways. Together, these data provide novel insights on the relative phenotypes and early response of macrophages to the vaccine strain and its derivatives. The Δcrp-cya derivatives could facilitate development of next-generation vaccines with improved safety.
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Affiliation(s)
- Bijit K Bhowmik
- Discovery Bacteriology and Microbiome, Elanco Animal Health Inc., Greenfield, IN, United States
| | - Arvind Kumar
- Discovery Bacteriology and Microbiome, Elanco Animal Health Inc., Greenfield, IN, United States
| | - Dharanesh Gangaiah
- Discovery Bacteriology and Microbiome, Elanco Animal Health Inc., Greenfield, IN, United States
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7
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Stabilization but no functional influence of HIF-1α expression in the intestinal epithelium during Salmonella Typhimurium infection. Infect Immun 2022; 90:e0022221. [PMID: 34978927 DOI: 10.1128/iai.00222-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hypoxia-inducible transcription factor 1 (HIF-1) has been shown to enhance microbial killing and to ameliorate the course of bacterial infections. While the impact of HIF-1 on inflammatory diseases of the gut has been studied intensively, its function in bacterial infections of the gastrointestinal tract remains largely elusive. With the help of a publicly available gene expression data set, we could infer significant activation of HIF-1 after oral infection of mice with Salmonella Typhimurium. Immunohistochemistry and western blot analysis confirmed marked HIF-1α protein stabilization, especially in the intestinal epithelium. This prompted us to analyze conditional Hif1a-deficient mice to examine cell type-specific functions of HIF-1 in this model. Our results demonstrate enhanced non-canonical induction of HIF-1 activity upon Salmonella infection in the intestinal epithelium as well as in macrophages. Surprisingly, Hif1a deletion in intestinal epithelial cells did not impact on inflammatory gene expression, bacterial spread or disease outcome. In contrast, Hif1a deletion in myeloid cells enhanced intestinal Cxcl2 expression and reduced the cecal Salmonella load. In vitro, HIF-1α-deficient macrophages showed an overall impaired transcription of mRNA encoding pro-inflammatory factors, however, intracellular survival of Salmonella was not impacted by HIF-1α deficiency.
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8
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Yousuf S, Karlinsey JE, Neville SL, McDevitt CA, Libby SJ, Fang FC, Frawley ER. Manganese import protects Salmonella enterica serovar Typhimurium against nitrosative stress. Metallomics 2020; 12:1791-1801. [PMID: 33078811 DOI: 10.1039/d0mt00178c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Nitric oxide (NO˙) is a radical molecule produced by mammalian phagocytic cells as part of the innate immune response to bacterial pathogens. It exerts its antimicrobial activity in part by impairing the function of metalloproteins, particularly those containing iron and zinc cofactors. The pathogenic Gram-negative bacterium Salmonella enterica serovar typhimurium undergoes dynamic changes in its cellular content of the four most common metal cofactors following exposure to NO˙ stress. Zinc, iron and magnesium all decrease in response to NO˙ while cellular manganese increases significantly. Manganese acquisition is driven primarily by increased expression of the mntH and sitABCD transporters following derepression of MntR and Fur. ZupT also contributes to manganese acquisition in response to nitrosative stress. S. Typhimurium mutants lacking manganese importers are more sensitive to NO˙, indicating that manganese is important for resistance to nitrosative stress.
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Affiliation(s)
- Shehla Yousuf
- Rhodes College Biology Department, 2000 North Parkway, Memphis, TN 38112, USA.
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9
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Jain N, Mishra SK, Shankar U, Jaiswal A, Sharma TK, Kodgire P, Kumar A. G-quadruplex stabilization in the ions and maltose transporters gene inhibit Salmonella enterica growth and virulence. Genomics 2020; 112:4863-4874. [PMID: 32898642 PMCID: PMC7474834 DOI: 10.1016/j.ygeno.2020.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 07/15/2020] [Accepted: 09/03/2020] [Indexed: 12/20/2022]
Abstract
The G-quadruplex structure is a highly conserved drug target for preventing infection of several human pathogens. We tried to explore G-quadruplex forming motifs as promising drug targets in the genome of Salmonella enterica that causes enteric fever in humans. Herein, we report three highly conserved G-quadruplex motifs (SE-PGQ-1, 2, and 3) in the genome of Salmonella enterica. Bioinformatics analysis inferred the presence of SE-PGQ-1 in the regulatory region of mgtA, SE-PGQ-2 in ORF of entA, and SE-PGQ-3 in the promoter region of malE and malK genes. The G-quadruplex forming sequences were confirmed by biophysical and biomolecular techniques. Cellular studies affirm the inhibitory effect of G-quadruplex specific ligands on Salmonella enterica growth. Further, PCR inhibition, reporter based assay, and RT-qPCR assays emphasize the biological relevance of G-quadruplexes in these genes. Thus, this study confirmed the presence of G-quadruplex motifs in Salmonella enterica and characterized them as a promising drug target.
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Affiliation(s)
- Neha Jain
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Subodh Kumar Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Uma Shankar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Ankit Jaiswal
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Tarun Kumar Sharma
- Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India
| | - Prashant Kodgire
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India.
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10
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The pneumococcal two-component system SirRH is linked to enhanced intracellular survival of Streptococcus pneumoniae in influenza-infected pulmonary cells. PLoS Pathog 2020; 16:e1008761. [PMID: 32790758 PMCID: PMC7447016 DOI: 10.1371/journal.ppat.1008761] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 08/25/2020] [Accepted: 06/29/2020] [Indexed: 12/18/2022] Open
Abstract
The virus-bacterial synergism implicated in secondary bacterial infections caused by Streptococcus pneumoniae following infection with epidemic or pandemic influenza A virus (IAV) is well documented. However, the molecular mechanisms behind such synergism remain largely ill-defined. In pneumocytes infected with influenza A virus, subsequent infection with S. pneumoniae leads to enhanced pneumococcal intracellular survival. The pneumococcal two-component system SirRH appears essential for such enhanced survival. Through comparative transcriptomic analysis between the ΔsirR and wt strains, a list of 179 differentially expressed genes was defined. Among those, the clpL protein chaperone gene and the psaB Mn+2 transporter gene, which are involved in the stress response, are important in enhancing S. pneumoniae survival in influenza-infected cells. The ΔsirR, ΔclpL and ΔpsaB deletion mutants display increased susceptibility to acidic and oxidative stress and no enhancement of intracellular survival in IAV-infected pneumocyte cells. These results suggest that the SirRH two-component system senses IAV-induced stress conditions and controls adaptive responses that allow survival of S. pneumoniae in IAV-infected pneumocytes.
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11
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Small proteins regulate Salmonella survival inside macrophages by controlling degradation of a magnesium transporter. Proc Natl Acad Sci U S A 2020; 117:20235-20243. [PMID: 32753384 DOI: 10.1073/pnas.2006116117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
All cells require Mg2+ to replicate and proliferate. The macrophage protein Slc11a1 is proposed to protect mice from invading microbes by causing Mg2+ starvation in host tissues. However, the Mg2+ transporter MgtB enables the facultative intracellular pathogen Salmonella enterica serovar Typhimurium to cause disease in mice harboring a functional Slc11a1 protein. Here, we report that, unexpectedly, the Salmonella small protein MgtR promotes MgtB degradation by the protease FtsH, which raises the question: How does Salmonella preserve MgtB to promote survival inside macrophages? We establish that the Salmonella small protein MgtU prevents MgtB proteolysis, even when MgtR is absent. Like MgtB, MgtU is necessary for survival in Slc11a1 +/+ macrophages, resistance to oxidative stress, and growth under Mg2+ limitation conditions. The Salmonella Mg2+ transporter MgtA is not protected by MgtU despite sharing 50% amino acid identity with MgtB and being degraded in an MgtR- and FtsH-dependent manner. Surprisingly, the mgtB, mgtR, and mgtU genes are part of the same transcript, providing a singular example of transcript-specifying proteins that promote and hinder degradation of the same target. Our findings demonstrate that small proteins can confer pathogen survival inside macrophages by altering the abundance of related transporters, thereby furthering homeostasis.
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12
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Who's in control? Regulation of metabolism and pathogenesis in space and time. Curr Opin Microbiol 2020; 55:88-96. [PMID: 32532689 DOI: 10.1016/j.mib.2020.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/04/2020] [Accepted: 05/15/2020] [Indexed: 02/07/2023]
Abstract
Bacterial pathogens need to sense and respond to their environments during infection to align cell metabolism and virulence factor production to survive and battle host defenses. Complex regulatory networks including ligand-binding transcription factors, two-component systems, RNA-binding proteins, and small non-coding regulatory RNAs adjust gene expression programs in response to changes in metabolic fluxes, environmental cues, and nutrient availability. Recent studies underlined that these different layers of regulation occur along varying spatial and temporal scales, leading to changes in cell behavior and heterogeneity among the bacterial community. This brief review will highlight current research emphasizing that cell metabolism and pathogenesis are inextricably intertwined in both Gram-positive and Gram-negative bacteria.
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13
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Bawn M, Alikhan NF, Thilliez G, Kirkwood M, Wheeler NE, Petrovska L, Dallman TJ, Adriaenssens EM, Hall N, Kingsley RA. Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation. PLoS Genet 2020; 16:e1008850. [PMID: 32511244 PMCID: PMC7302871 DOI: 10.1371/journal.pgen.1008850] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 06/18/2020] [Accepted: 05/12/2020] [Indexed: 12/25/2022] Open
Abstract
Salmonella enterica serotype Typhimurium (S. Typhimurium) is a leading cause of gastroenteritis and bacteraemia worldwide, and a model organism for the study of host-pathogen interactions. Two S. Typhimurium strains (SL1344 and ATCC14028) are widely used to study host-pathogen interactions, yet genotypic variation results in strains with diverse host range, pathogenicity and risk to food safety. The population structure of diverse strains of S. Typhimurium revealed a major phylogroup of predominantly sequence type 19 (ST19) and a minor phylogroup of ST36. The major phylogroup had a population structure with two high order clades (α and β) and multiple subclades on extended internal branches, that exhibited distinct signatures of host adaptation and anthropogenic selection. Clade α contained a number of subclades composed of strains from well characterized epidemics in domesticated animals, while clade β contained multiple subclades associated with wild avian species. The contrasting epidemiology of strains in clade α and β was reflected by the distinct distribution of antimicrobial resistance (AMR) genes, accumulation of hypothetically disrupted coding sequences (HDCS), and signatures of functional diversification. These observations were consistent with elevated anthropogenic selection of clade α lineages from adaptation to circulation in populations of domesticated livestock, and the predisposition of clade β lineages to undergo adaptation to an invasive lifestyle by a process of convergent evolution with of host adapted Salmonella serotypes. Gene flux was predominantly driven by acquisition and recombination of prophage and associated cargo genes, with only occasional loss of these elements. The acquisition of large chromosomally-encoded genetic islands was limited, but notably, a feature of two recent pandemic clones (DT104 and monophasic S. Typhimurium ST34) of clade α (SGI-1 and SGI-4).
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Affiliation(s)
- Matt Bawn
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Gaëtan Thilliez
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Mark Kirkwood
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Nicole E. Wheeler
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Timothy J. Dallman
- Gastrointestinal Bacteria Reference Unit, National Infection Service, Public Health England, London, United Kingdom
| | | | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Robert A. Kingsley
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
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14
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Rice A, Rooney MT, Greenwood AI, Cotten ML, Wereszczynski J. Lipopolysaccharide Simulations Are Sensitive to Phosphate Charge and Ion Parameterization. J Chem Theory Comput 2020; 16:1806-1815. [PMID: 32023054 DOI: 10.1021/acs.jctc.9b00868] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The high proportion of lipopolysaccharide (LPS) molecules in the outer membrane of Gram-negative bacteria makes it a highly effective barrier to small molecules, antibiotic drugs, and other antimicrobial agents. Given this vital role in protecting bacteria from potentially hostile environments, simulations of LPS bilayers and outer membrane systems represent a critical tool for understanding the mechanisms of bacterial resistance and the development of new antibiotic compounds that circumvent these defenses. The basis of these simulations is parameterizations of LPS, which have been developed for all major molecular dynamics force fields. However, these parameterizations differ in both the protonation state of LPS and how LPS membranes behave in the presence of various ion species. To address these discrepancies and understand the effects of phosphate charge on bilayer properties, simulations were performed for multiple distinct LPS chemotypes with different ion parameterizations in both protonated or deprotonated lipid A states. These simulations show that bilayer properties, such as the area per lipid and inter-lipid hydrogen bonding, are highly influenced by the choice of phosphate group charges, cation type, and ion parameterization, with protonated LPS and monovalent cations with modified nonbonded parameters providing the best match to the experiments. Additionally, alchemical free energy simulations were performed to determine theoretical pKa values for LPS and subsequently validated by 31P solid-state nuclear magnetic resonance experiments. Results from these complementary computational and experimental studies demonstrate that the protonated state dominates at physiological pH, contrary to the deprotonated form modeled by many LPS force fields. Overall, these results highlight the sensitivity of LPS simulations to phosphate charge and ion parameters while offering recommendations for how existing models should be updated for consistency between force fields as well as to best match experiments.
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Affiliation(s)
- Amy Rice
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Mary T Rooney
- Department of Applied Science, College of William and Mary, Williamsburg, Virginia 23185, United States
| | - Alexander I Greenwood
- Department of Applied Science, College of William and Mary, Williamsburg, Virginia 23185, United States.,Department of Physics, College of William and Mary, Williamsburg, Virginia 23185, United States
| | - Myriam L Cotten
- Department of Applied Science, College of William and Mary, Williamsburg, Virginia 23185, United States
| | - Jeff Wereszczynski
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois 60616, United States
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15
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Zinc-dependent substrate-level phosphorylation powers Salmonella growth under nitrosative stress of the innate host response. PLoS Pathog 2018; 14:e1007388. [PMID: 30365536 PMCID: PMC6221366 DOI: 10.1371/journal.ppat.1007388] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 11/07/2018] [Accepted: 10/07/2018] [Indexed: 12/13/2022] Open
Abstract
The metabolic processes that enable the replication of intracellular Salmonella under nitrosative stress conditions engendered in the innate response of macrophages are poorly understood. A screen of Salmonella transposon mutants identified the ABC-type high-affinity zinc uptake system ZnuABC as a critical determinant of the adaptation of Salmonella to the nitrosative stress generated by the enzymatic activity of inducible nitric oxide (NO) synthase of mononuclear phagocytic cells. NO limits the virulence of a znuB mutant in an acute murine model of salmonellosis. The ZnuABC transporter is crucial for the glycolytic function of fructose bisphosphate aldolase, thereby fueling growth of Salmonella during nitrosative stress produced in the innate response of macrophages. Our investigations demonstrate that glycolysis mediates resistance of Salmonella to the antimicrobial activity of NO produced in an acute model of infection. The ATP synthesized by substrate-level phosphorylation at the payoff phase of glycolysis and acetate fermentation powers the replication of Salmonella experiencing high levels of nitrosative stress. In contrast, despite its high potential for ATP synthesis, oxidative phosphorylation is a major target of inhibition by NO and contributes little to the antinitrosative defenses of intracellular Salmonella. Our investigations have uncovered a previously unsuspected conjunction between zinc homeostasis, glucose metabolism and cellular energetics in the adaptation of intracellular Salmonella to the reactive nitrogen species synthesized in the innate host response. Microbial pathogens are exposed to multiple antimicrobial defenses during their associations with host cells. Nitric oxide generated in the innate response exerts widespread antimicrobial activity against a variety of pathogenic microorganisms. Nitric oxide has high affinity for metal groups of terminal cytochromes of the respiratory chain, and thus nitrosative stress exerts extreme deleterious actions against the cellular energetics that rely on oxidative phosphorylation. Intracellular Salmonella have resolved this dilemma by satisfying a significant portion of their energetic demands via substrate level phosphorylation in the payoff phase of glycolysis and acetate fermentation. A high affinity zinc uptake system promotes antinitrosative defense of intracellular Salmonella by in great part supporting the enzymatic activity of an essential enzyme in the preparatory phase of glycolysis. Our research provides novel insights into the metabolic and energetic adaptations that allow a bacterial pathogen to thrive in the midst of the innate host response of vertebrate cells.
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16
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Gogoi M, Shreenivas MM, Chakravortty D. Hoodwinking the Big-Eater to Prosper: The Salmonella-Macrophage Paradigm. J Innate Immun 2018; 11:289-299. [PMID: 30041182 DOI: 10.1159/000490953] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/10/2018] [Indexed: 12/12/2022] Open
Abstract
Salmonella is a major cause of morbidity and mortality in the developing and underdeveloped nations. Being a foodborne disease, Salmonella infection is primarily contracted through the ingestion of contaminated food or water, or due to close contact with infected/carrier individuals. It is an intracellular pathogen, which can survive and replicate in various cells including macrophages, dendritic cells, epithelial cells, and other white blood cells. Once Salmonella crosses the intestinal barrier, it disseminates to various systemic sites by circulation via immune cells. One of the major cell types which are involved in Salmonella infection are host macrophages. They are the niche for intracellular survival and proliferation of Salmonella and a mode of dissemination to distal systemic sites. These cells are very crucial as they mediate the mounting of an appropriate innate and adaptive anti-Salmonella immune response. In this review, we have tried to concise the current knowledge of complex interactions that occur between Salmonella and macrophages.
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Affiliation(s)
- Mayuri Gogoi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.,Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Meghanashree M Shreenivas
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.,Undergraduate Studies, Indian Institute of Science, Bangalore, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India, .,Division of Biological Sciences, Indian Institute of Science, Bangalore, India, .,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India,
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