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Kirdat K, Tiwarekar B, Manjula KN, Padma S, Sathe S, Sundararaj R, Yadav A. Draft genome sequence of ' Candidatus Phytoplasma asteris,' strain SW86 associated with sandal spike disease (SSD). 3 Biotech 2024; 14:109. [PMID: 38481824 PMCID: PMC10928027 DOI: 10.1007/s13205-024-03952-5] [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: 11/15/2022] [Accepted: 02/02/2024] [Indexed: 04/11/2024] Open
Abstract
The sandal spike disease (SSD), related to 'Ca. Phytoplasma asteris' (Aster Yellows group), poses a significant threat to Indian sandalwood (Santalum album L.), making it the second most expensive wood globally due to declining population density. The epidemiology of SSD and the nature of the pathogen remain poorly understood. The SW86 isolate, collected from the Marayoor Sandalwood Reserve, was chosen for genome sequencing subsequent to confirming its titer and enriching phytoplasma DNA. Genome sequencing, utilizing Illumina and Oxford Nanopore Technology platforms, enabled a targeted hybrid metagenomic assembly resulting in 20 scaffolds totaling 554,025 bp, housing 436 protein-coding genes, 27 tRNA, and 1 rRNA operon. The genome analysis highlighted specific gene distributions, emphasizing translation, ribosomal structure, and biogenesis, with 352 genes assigned to 18 functional categories. Additionally, 322 proteins received functional assignments in the KEGG database, emphasizing 'Genetic Information Processing' and 'Environmental Information Processing'. Key potential pathogenicity factors, including signal peptide proteins and virulence proteins, were identified. Noteworthy findings include homologs of effectors genes like SAP11 and SAP05 and pathogenesis-related proteins, such as hemolysin III and SodA genes, in the SW86 genome. The duplicated cation-transporting P-type ATPase in the SW86 genome suggests a role in enhancing adaptability and contributing to the severity of SSD symptoms. This genome analysis provides crucial insights into the genomic features and potential virulence factors of 'Ca. Phytoplasma asteris' strain SW86, advancing our understanding of pathogenicity mechanisms and offering avenues for future disease management strategies in Indian sandalwood. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03952-5.
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Affiliation(s)
- Kiran Kirdat
- National Centre for Microbial Resource, National Centre for Cell Science, NCCS Complex, Ganeshkhind, Pune, Maharashtra 411007 India
- Department of Microbiology, Tuljaram Chaturchand College, Baramati, Maharashtra 413102 India
| | - Bhavesh Tiwarekar
- National Centre for Microbial Resource, National Centre for Cell Science, NCCS Complex, Ganeshkhind, Pune, Maharashtra 411007 India
| | - K. N. Manjula
- Forest Protection Division, Institute of Wood Science and Technology, 18th Cross, Malleswaram, Bangalore, 560003 India
| | - S. Padma
- Forest Protection Division, Institute of Wood Science and Technology, 18th Cross, Malleswaram, Bangalore, 560003 India
| | - Shivaji Sathe
- Department of Microbiology, Tuljaram Chaturchand College, Baramati, Maharashtra 413102 India
| | - R. Sundararaj
- Forest Protection Division, Institute of Wood Science and Technology, 18th Cross, Malleswaram, Bangalore, 560003 India
| | - Amit Yadav
- National Centre for Microbial Resource, National Centre for Cell Science, NCCS Complex, Ganeshkhind, Pune, Maharashtra 411007 India
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Zeinert R, Zhou F, Franco P, Zöller J, Lessen HJ, Aravind L, Langer JD, Sodt AJ, Storz G, Matthies D. Magnesium Transporter MgtA revealed as a Dimeric P-type ATPase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582502. [PMID: 38464158 PMCID: PMC10925321 DOI: 10.1101/2024.02.28.582502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Magnesium (Mg2+) uptake systems are present in all domains of life given the vital role of this ion. Bacteria acquire Mg2+ via conserved Mg2+ channels and transporters. The transporters are required for growth when Mg2+ is limiting or during bacterial pathogenesis, but, despite their significance, there are no known structures for these transporters. Here we report the first structure of the Mg2+ transporter MgtA solved by single particle cryo-electron microscopy (cryo-EM). Using mild membrane extraction, we obtained high resolution structures of both a homodimeric form (2.9 Å), the first for a P-type ATPase, and a monomeric form (3.6 Å). Each monomer unit of MgtA displays a structural architecture that is similar to other P-type ATPases with a transmembrane domain and two soluble domains. The dimer interface consists of contacts between residues in adjacent soluble nucleotide binding and phosphotransfer regions of the haloacid dehalogenase (HAD) domain. We suggest oligomerization is a conserved structural feature of the diverse family of P-type ATPase transporters. The ATP binding site and conformational dynamics upon nucleotide binding to MgtA were characterized using a combination of cryo-EM, molecular dynamics simulations, hydrogen-deuterium exchange mass spectrometry, and mutagenesis. Our structure also revealed a Mg2+ ion in the transmembrane segments, which, when combined with sequence conservation and mutagenesis studies, allowed us to propose a model for Mg2+ transport across the lipid bilayer. Finally, our work revealed the N-terminal domain structure and cytoplasmic Mg2+ binding sites, which have implications for related P-type ATPases defective in human disease.
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Affiliation(s)
- Rilee Zeinert
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892, USA
| | - Fei Zhou
- Unit on Structural Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892, USA
| | - Pedro Franco
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Jonathan Zöller
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Henry J. Lessen
- Unit on Membrane Chemical Physics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892, USA
| | - L. Aravind
- National Center for Biotechnology Information, National Institutes of Health, Bethesda MD 20892, USA
| | - Julian D. Langer
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Alexander J. Sodt
- Unit on Membrane Chemical Physics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892, USA
| | - Doreen Matthies
- Unit on Structural Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892, USA
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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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The bacterial tyrosine kinase system CpsBCD governs the length of capsule polymers. Proc Natl Acad Sci U S A 2021; 118:2103377118. [PMID: 34732571 DOI: 10.1073/pnas.2103377118] [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] [Accepted: 09/16/2021] [Indexed: 12/17/2022] Open
Abstract
Many pathogenic bacteria are encased in a layer of capsular polysaccharide (CPS). This layer is important for virulence by masking surface antigens, preventing opsonophagocytosis, and avoiding mucus entrapment. The bacterial tyrosine kinase (BY-kinase) regulates capsule synthesis and helps bacterial pathogens to survive different host niches. BY-kinases autophosphorylate at the C-terminal tyrosine residues upon external stimuli, but the role of phosphorylation is still unclear. Here, we report that the BY-kinase CpsCD is required for growth in Streptococcus pneumoniae Cells lacking a functional cpsC or cpsD accumulated low molecular weight CPS and lysed because of the lethal sequestration of the lipid carrier undecaprenyl phosphate, resulting in inhibition of peptidoglycan (PG) synthesis. CpsC interacts with CpsD and the polymerase CpsH. CpsD phosphorylation reduces the length of CPS polymers presumably by controlling the activity of CpsC. Finally, pulse-chase experiments reveal the spatiotemporal coordination between CPS and PG synthesis. This coordination is dependent on CpsC and CpsD. Together, our study provides evidence that BY-kinases regulate capsule polymer length by fine-tuning CpsC activity through autophosphorylation.
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5
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Domenech M, García E. The N-Acetylglucosaminidase LytB of Streptococcus pneumoniae Is Involved in the Structure and Formation of Biofilms. Appl Environ Microbiol 2020; 86:e00280-20. [PMID: 32198170 PMCID: PMC7205503 DOI: 10.1128/aem.00280-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/15/2020] [Indexed: 02/07/2023] Open
Abstract
The N-acetylglucosaminidase LytB of Streptococcus pneumoniae is involved in nasopharyngeal colonization and is responsible for cell separation at the end of cell division; thus, ΔlytB mutants form long chains of cells. This paper reports the construction and properties of a defective pneumococcal mutant producing an inactive LytB protein (LytBE585A). It is shown that an enzymatically active LytB is required for in vitro biofilm formation, as lytB mutants (either ΔlytB or producing the inactive LytBE585A) are incapable of forming substantial biofilms, despite that extracellular DNA is present in the biofilm matrix. Adding small amounts (0.5 to 2.0 μg/ml) of exogenous LytB or some LytB constructs restored the biofilm-forming capacity of lytB mutants to wild-type levels. The LytBE585A mutant formed biofilm more rapidly than ΔlytB mutants in the presence of LytB. This suggests that the mutant protein acted in a structural role, likely through the formation of complexes with extracellular DNA. The chain-dispersing capacity of LytB allowed the separation of daughter cells, presumably facilitating the formation of microcolonies and, finally, of biofilms. A role for the possible involvement of LytB in the synthesis of the extracellular polysaccharide component of the biofilm matrix is also discussed.IMPORTANCE It has been previously accepted that biofilm formation in S. pneumoniae must be a multigenic trait because the mutation of a single gene has led to only to partial inhibition of biofilm production. In the present study, however, evidence that the N-acetylglucosaminidase LytB is crucial in biofilm formation is provided. Despite the presence of extracellular DNA, strains either deficient in LytB or producing a defective LytB enzyme formed only shallow biofilms.
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Affiliation(s)
- Mirian Domenech
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Ernesto García
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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6
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Martin JE, Le MT, Bhattarai N, Capdevila DA, Shen J, Winkler ME, Giedroc DP. A Mn-sensing riboswitch activates expression of a Mn2+/Ca2+ ATPase transporter in Streptococcus. Nucleic Acids Res 2020; 47:6885-6899. [PMID: 31165873 PMCID: PMC6649816 DOI: 10.1093/nar/gkz494] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/08/2019] [Accepted: 05/31/2019] [Indexed: 12/27/2022] Open
Abstract
Maintaining manganese (Mn) homeostasis is important for the virulence of numerous bacteria. In the human respiratory pathogen Streptococcus pneumoniae, the Mn-specific importer PsaBCA, exporter MntE, and transcriptional regulator PsaR establish Mn homeostasis. In other bacteria, Mn homeostasis is controlled by yybP-ykoY family riboswitches. Here, we characterize a yybP-ykoY family riboswitch upstream of the mgtA gene encoding a PII-type ATPase in S. pneumoniae, suggested previously to function in Ca2+ efflux. We show that the mgtA riboswitch aptamer domain adopts a canonical yybP-ykoY structure containing a three-way junction that is compacted in the presence of Ca2+ or Mn2+ at a physiological Mg2+ concentration. Although Ca2+ binds to the RNA aptamer with higher affinity than Mn2+, in vitro activation of transcription read-through of mgtA by Mn2+ is much greater than by Ca2+. Consistent with this result, mgtA mRNA and protein levels increase ≈5-fold during cellular Mn stress, but only in genetic backgrounds of S. pneumoniae and Bacillus subtilis that exhibit Mn2+ sensitivity, revealing that this riboswitch functions as a failsafe ‘on’ signal to prevent Mn2+ toxicity in the presence of high cellular Mn2+. In addition, our results suggest that the S. pneumoniae yybP-ykoY riboswitch functions to regulate Ca2+ efflux under these conditions.
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Affiliation(s)
- Julia E Martin
- Department of Biological Sciences, Idaho State University, Pocatello, ID 83209, USA
| | - My T Le
- Department of Cell Biology, Faculty of Biological Sciences, Vietnam National University, Hanoi, Vietnam
| | - Nabin Bhattarai
- Department of Biological Sciences, Idaho State University, Pocatello, ID 83209, USA
| | | | - Jiangchuan Shen
- Department of Cellular and Molecular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Malcolm E Winkler
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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7
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Ebrahimi A, Csonka LN, Alam MA. Analyzing Thermal Stability of Cell Membrane of Salmonella Using Time-Multiplexed Impedance Sensing. Biophys J 2019; 114:609-618. [PMID: 29414707 DOI: 10.1016/j.bpj.2017.10.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 09/12/2017] [Accepted: 10/17/2017] [Indexed: 01/16/2023] Open
Abstract
Heat treatment is one of the most widely used methods for inactivation of bacteria in food products. Heat-induced loss of bacterial viability has been variously attributed to protein denaturation, oxidative stress, or membrane leakage; indeed, it is likely to involve a combination of these processes. We examine the effect of mild heat stress (50-55°C for ≤12 min) on cell permeability by directly measuring the electrical conductance of samples of Salmonella enterica serovar Typhimurium to answer a fundamental biophysical question, namely, how bacteria die under mild heat stress. Our results show that when exposed to heat shock, the cell membrane is damaged and cells die mainly due to the leakage of small cytoplasmic species to the surrounding media without lysis (confirmed by fluorescent imaging). We measured the conductance change, ΔY, of wild-type versus genetically modified heat-resistant (HR) cells in response to pulse and ramp heating profiles with different thermal time constants. In addition, we developed a phenomenological model to correlate the membrane damage, cytoplasmic leakage, and cell viability. This model traces the differential viability and ΔY of wild-type and HR cells to the difference in the effective activation energies needed to permeabilize the cells, implying that HR cells are characterized by stronger lateral interactions between molecules, such as lipids, in their cell envelope.
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Affiliation(s)
- Aida Ebrahimi
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana; Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana
| | - Laszlo N Csonka
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Muhammad A Alam
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana; Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana.
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Hupp S, Ribes S, Seele J, Bischoff C, Förtsch C, Maier E, Benz R, Mitchell TJ, Nau R, Iliev AI. Magnesium therapy improves outcome in Streptococcus pneumoniae meningitis by altering pneumolysin pore formation. Br J Pharmacol 2017; 174:4295-4307. [PMID: 28888095 DOI: 10.1111/bph.14027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 08/26/2017] [Accepted: 08/29/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND AND PURPOSE Streptococcus pneumoniae is the most common cause of bacterial meningitis in adults and is characterized by high lethality and substantial cognitive disabilities in survivors. Here, we have studied the capacity of an established therapeutic agent, magnesium, to improve survival in pneumococcal meningitis by modulating the neurological effects of the major pneumococcal pathogenic factor, pneumolysin. EXPERIMENTAL APPROACH We used mixed primary glial and acute brain slice cultures, pneumolysin injection in infant rats, a mouse meningitis model and complementary approaches such as Western blot, a black lipid bilayer conductance assay and live imaging of primary glial cells. KEY RESULTS Treatment with therapeutic concentrations of magnesium chloride (500 mg·kg-1 in animals and 2 mM in cultures) prevented pneumolysin-induced brain swelling and tissue remodelling both in brain slices and in animal models. In contrast to other divalent ions, which diminish the membrane binding of pneumolysin in non-therapeutic concentrations, magnesium delayed toxin-driven pore formation without affecting its membrane binding or the conductance profile of its pores. Finally, magnesium prolonged the survival and improved clinical condition of mice with pneumococcal meningitis, in the absence of antibiotic treatment. CONCLUSIONS AND IMPLICATIONS Magnesium is a well-established and safe therapeutic agent that has demonstrated capacity for attenuating pneumolysin-triggered pathogenic effects on the brain. The improved animal survival and clinical condition in the meningitis model identifies magnesium as a promising candidate for adjunctive treatment of pneumococcal meningitis, together with antibiotic therapy.
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Affiliation(s)
- Sabrina Hupp
- Institute of Anatomy, University of Bern, Bern, Switzerland.,DFG Membrane/Cytoskeleton Interaction Group, Institute of Pharmacology and Toxicology & Rudolf Virchow Center for Experimental Medicine, University of Würzburg, Würzburg, Germany
| | - Sandra Ribes
- Department of Neuropathology, University Medical Center Göttingen, Göttingen, Germany.,Department of Geriatrics, Evangelisches Krankenhaus Göttingen-Weende, Göttingen, Germany
| | - Jana Seele
- Department of Neuropathology, University Medical Center Göttingen, Göttingen, Germany.,Department of Geriatrics, Evangelisches Krankenhaus Göttingen-Weende, Göttingen, Germany
| | - Carolin Bischoff
- DFG Membrane/Cytoskeleton Interaction Group, Institute of Pharmacology and Toxicology & Rudolf Virchow Center for Experimental Medicine, University of Würzburg, Würzburg, Germany
| | - Christina Förtsch
- DFG Membrane/Cytoskeleton Interaction Group, Institute of Pharmacology and Toxicology & Rudolf Virchow Center for Experimental Medicine, University of Würzburg, Würzburg, Germany
| | - Elke Maier
- Rudolf Virchow Center for Experimental Medicine, University of Würzburg, Würzburg, Germany
| | - Roland Benz
- Rudolf Virchow Center for Experimental Medicine, University of Würzburg, Würzburg, Germany
| | - Timothy J Mitchell
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Roland Nau
- Department of Neuropathology, University Medical Center Göttingen, Göttingen, Germany.,Department of Geriatrics, Evangelisches Krankenhaus Göttingen-Weende, Göttingen, Germany
| | - Asparouh I Iliev
- Institute of Anatomy, University of Bern, Bern, Switzerland.,DFG Membrane/Cytoskeleton Interaction Group, Institute of Pharmacology and Toxicology & Rudolf Virchow Center for Experimental Medicine, University of Würzburg, Würzburg, Germany
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9
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Subramani S, Perdreau-Dahl H, Morth JP. The magnesium transporter A is activated by cardiolipin and is highly sensitive to free magnesium in vitro. eLife 2016; 5. [PMID: 26780187 PMCID: PMC4758953 DOI: 10.7554/elife.11407] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 01/16/2016] [Indexed: 01/19/2023] Open
Abstract
The magnesium transporter A (MgtA) is a specialized P-type ATPase, believed to import Mg2+ into the cytoplasm. In Salmonella typhimurium and Escherichia coli, the virulence determining two-component system PhoQ/PhoP regulates the transcription of mgtA gene by sensing Mg2+ concentrations in the periplasm. However, the factors that affect MgtA function are not known. This study demonstrates, for the first time, that MgtA is highly dependent on anionic phospholipids and in particular, cardiolipin. Colocalization studies confirm that MgtA is found in the cardiolipin lipid domains in the membrane. The head group of cardiolipin plays major role in activation of MgtA suggesting that cardiolipin may act as a Mg2+ chaperone for MgtA. We further show that MgtA is highly sensitive to free Mg2+ (Mg2+free) levels in the solution. MgtA is activated when the Mg2+free concentration is reduced below 10 μM and is strongly inhibited above 1 mM, indicating that Mg2+free acts as product inhibitor. Combined, our findings conclude that MgtA may act as a sensor as well as a transporter of Mg2+. DOI:http://dx.doi.org/10.7554/eLife.11407.001 Magnesium is an essential element for living cells, meaning that organisms from bacteria to humans need magnesium to survive. All cells are surrounded by a membrane made of fatty molecules called lipids, which is also embedded with proteins. Magnesium, like other metal ions, is transported inside cells across the cell’s membrane by specific membrane proteins. A species of gut bacteria called E. coli has two separate magnesium transport systems: one that works at high concentrations of magnesium and one at lower concentrations. The latter system involves a membrane protein called magnesium transporter A (or MgtA for short), which works like a molecular pump. However, it was not known exactly how this transporter was affected by magnesium nor how sensitive it was to this divalent metal ion. It was also unclear whether MgtA worked alone in the bacterial membrane or if it worked in conjunction with other molecules. Now Subramani et al. have managed to show that MgtA can sense magnesium ions down to micromolar concentrations, which is the equivalent to a pinch (1 gram) of magnesium salt in 10,000 liters of water. The experiments also showed that this detection system depended on a specific lipid molecule in the membrane called cardiolipin. MgtA and cardiolipin were found together in the membrane of living E. coli suggesting that the two do indeed work together. The discovery that a membrane transporter that pumps ions needs cardiolipin to work suggests that cells could indirectly control the movement of ions by changing the levels of specific lipids in their membranes. Subramani et al. now hope to use techniques, such as X-ray crystallography, to visualize how magnesium and cardiolipin bind to MtgA and explore how the three molecules work together as a complete system. Information about these interactions could in the future help researchers understand how these bacteria try to protect themself in the hostile environment in the human gut or cells of the immune systems. Further studies of this system could be used to develop biological sensors for magnesium or to design antibiotics that interfere with the magnesium transporter to treat bacterial infections. DOI:http://dx.doi.org/10.7554/eLife.11407.002
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Affiliation(s)
- Saranya Subramani
- Norwegian Centre of Molecular Medicine, Nordic EMBL Partnership University of Oslo, Oslo, Norway
| | - Harmonie Perdreau-Dahl
- Norwegian Centre of Molecular Medicine, Nordic EMBL Partnership University of Oslo, Oslo, Norway.,Institute for Experimental Medical Research, Oslo University Hospital, Oslo, Norway
| | - Jens Preben Morth
- Norwegian Centre of Molecular Medicine, Nordic EMBL Partnership University of Oslo, Oslo, Norway.,Institute for Experimental Medical Research, Oslo University Hospital, Oslo, Norway
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10
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Domenech M, Ruiz S, Moscoso M, García E. In vitro biofilm development of Streptococcus pneumoniae and formation of choline-binding protein-DNA complexes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:715-727. [PMID: 25950767 DOI: 10.1111/1758-2229.12295] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/08/2015] [Indexed: 06/04/2023]
Abstract
Extracellular deoxyribonucleic acid (eDNA) is an essential component of bacterial biofilm matrices, and is required in their formation and maintenance. Extracellular DNA binds to exopolysaccharides or extracellular proteins, affording biofilms greater structural integrity. Recently, we reported evidence of intercellular eDNA-LytC complexes in pneumococcal biofilms. The LytC lysozyme is a member of the choline-binding family of proteins (CBPs) located on the pneumococcal surface. The present work shows that other CBPs, i.e. LytA, LytB, Pce, PspC and CbpF, which have a pI between 5 and 6, can bind DNA in vitro. This process requires the presence of divalent cations other than Mg(2+). This DNA binding capacity of CBPs appears to be independent of their enzymatic activity and, at least in the case of LytA, does not require the choline-binding domain characteristic of CBPs. Positively charged, surface-exposed, 25 amino acid-long peptides derived from the catalytic domain of LytB, were also found capable of DNA binding through electrostatic interactions. Confocal laser scanning microcopy revealed the existence of cell-associated LytB-eDNA complexes in Streptococcus pneumoniae biofilms. These and other findings suggest that these surface-located proteins of S. pneumoniae could play roles of varying importance in the colonization and/or invasion of human host where different environmental conditions exist.
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Affiliation(s)
- Mirian Domenech
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, 28040, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Susana Ruiz
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Miriam Moscoso
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, 28040, Spain
| | - Ernesto García
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, 28040, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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Physiology, Genomics, and Pathway Engineering of an Ethanol-Tolerant Strain of Clostridium phytofermentans. Appl Environ Microbiol 2015; 81:5440-8. [PMID: 26048945 DOI: 10.1128/aem.00619-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/27/2015] [Indexed: 01/21/2023] Open
Abstract
Novel processing strategies for hydrolysis and fermentation of lignocellulosic biomass in a single reactor offer large potential cost savings for production of biocommodities and biofuels. One critical challenge is retaining high enzyme production in the presence of elevated product titers. Toward this goal, the cellulolytic, ethanol-producing bacterium Clostridium phytofermentans was adapted to increased ethanol concentrations. The resulting ethanol-tolerant (ET) strain has nearly doubled ethanol tolerance relative to the wild-type level but also reduced ethanol yield and growth at low ethanol concentrations. The genome of the ET strain has coding changes in proteins involved in membrane biosynthesis, the Rnf complex, cation homeostasis, gene regulation, and ethanol production. In particular, purification of the mutant bifunctional acetaldehyde coenzyme A (CoA)/alcohol dehydrogenase showed that a G609D variant abolished its activities, including ethanol formation. Heterologous expression of Zymomonas mobilis pyruvate decarboxylase and alcohol dehydrogenase in the ET strain increased cellulose consumption and restored ethanol production, demonstrating how metabolic engineering can be used to overcome disadvantageous mutations incurred during adaptation to ethanol. We discuss how genetic changes in the ET strain reveal novel potential strategies for improving microbial solvent tolerance.
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Abstract
Polyamines are small cationic molecules that have far-reaching roles in biology. In the case of pathogenic bacteria, these functions include those central to their pathogenesis. Streptococcus pneumoniae is a major bacterial pathogen, causing a diverse range of diseases that account for significant morbidity and mortality worldwide. In this work, we characterize the polyamine biosynthetic pathway of S. pneumoniae, demonstrating that this organism produces spermidine from arginine. The synthesis of spermidine was found to be nonessential for growth in a polyamine-free chemically defined medium. However, mutant strains lacking the ability to synthesize or transport spermidine displayed a significant delay in the onset of autolysis. We provide evidence for a model in which spermidine modulates the activity of the major autolysin LytA in the pneumococcal cell wall compartment via interactions with negatively charged molecules, such as teichoic acids.
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Novoa-Aponte L, Soto Ospina CY. Mycobacterium tuberculosis P-type ATPases: possible targets for drug or vaccine development. BIOMED RESEARCH INTERNATIONAL 2014; 2014:296986. [PMID: 25110669 PMCID: PMC4119724 DOI: 10.1155/2014/296986] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 06/23/2014] [Indexed: 12/31/2022]
Abstract
Tuberculosis (TB) has been the biggest killer in the human history; currently, Mycobacterium tuberculosis (Mtb) kills nearly 2 million people each year worldwide. The high prevalence of TB obligates the identification of new therapeutic targets and the development of anti-TB vaccines that can control multidrug resistance and latent TB infections. Membrane proteins have recently been suggested as key targets for bacterial viability. Current studies have shown that mycobacteria P-type ATPases may play critical roles in ion homeostasis and in the response of mycobacteria to toxic substances in the intraphagosomal environment. In this review, we bring together the genomic, transcriptomic, and structural aspects of the P-type ATPases that are relevant during active and latent Mtb infections, which can be useful in determining the potential of these ATPases as drug targets and in uncovering their possible roles in the development of new anti-TB attenuated vaccines.
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Affiliation(s)
- Lorena Novoa-Aponte
- Chemistry Department, Faculty of Sciences, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Bogotá, Cundinamarca 111321, Colombia
| | - Carlos Yesid Soto Ospina
- Chemistry Department, Faculty of Sciences, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Bogotá, Cundinamarca 111321, Colombia
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Rosch JW, Iverson AR, Humann J, Mann B, Gao G, Vogel P, Mina M, Murrah KA, Perez AC, Edward Swords W, Tuomanen EI, McCullers JA. A live-attenuated pneumococcal vaccine elicits CD4+ T-cell dependent class switching and provides serotype independent protection against acute otitis media. EMBO Mol Med 2014; 6:141-54. [PMID: 24408968 PMCID: PMC3936495 DOI: 10.1002/emmm.201202150] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 09/06/2013] [Accepted: 09/23/2013] [Indexed: 01/19/2023] Open
Abstract
Acute otitis media (AOM) caused by Streptococcus pneumoniae remains one of the most common infectious diseases worldwide despite widespread vaccination. A major limitation of the currently licensed pneumococcal vaccines is the lack of efficacy against mucosal disease manifestations such as AOM, acute bacterial sinusitis and pneumonia. We sought to generate a novel class of live vaccines that (1) retain all major antigenic virulence proteins yet are fully attenuated and (2) protect against otitis media. A live vaccine candidate based on deletion of the signal recognition pathway component ftsY induced potent, serotype-independent protection against otitis media, sinusitis, pneumonia and invasive pneumococcal disease. Protection was maintained in animals coinfected with influenza virus, but was lost if mice were depleted of CD4(+) T cells at the time of vaccination. The live vaccine induced a strong serum IgG2a and IgG2b response that correlated with CD4(+) T-cell mediated class switching. Deletion of genes required for microbial adaptation to the host environment is a novel live attenuated vaccine strategy yielding the first experimental vaccine effective against pneumococcal otitis media.
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Affiliation(s)
- Jason W Rosch
- Department of Infectious Diseases, St. Jude Children's Research HospitalMemphis, TN, USA
| | - Amy R Iverson
- Department of Infectious Diseases, St. Jude Children's Research HospitalMemphis, TN, USA
| | - Jessica Humann
- Department of Infectious Diseases, St. Jude Children's Research HospitalMemphis, TN, USA
| | - Beth Mann
- Department of Infectious Diseases, St. Jude Children's Research HospitalMemphis, TN, USA
| | - Geli Gao
- Department of Infectious Diseases, St. Jude Children's Research HospitalMemphis, TN, USA
| | - Peter Vogel
- Department of Pathology, St. Jude Children's Research HospitalMemphis, TN, USA
| | - Michael Mina
- Emory University School of MedicineAtlanta, GA, USA
| | - Kyle A Murrah
- Department of Microbiology and Immunology, Wake Forest School of MedicineWinston-Salem, NC, USA
| | - Antonia C Perez
- Department of Microbiology and Immunology, Wake Forest School of MedicineWinston-Salem, NC, USA
| | - W Edward Swords
- Department of Microbiology and Immunology, Wake Forest School of MedicineWinston-Salem, NC, USA
| | - Elaine I Tuomanen
- Department of Infectious Diseases, St. Jude Children's Research HospitalMemphis, TN, USA
| | - Jonathan A McCullers
- Department of Infectious Diseases, St. Jude Children's Research HospitalMemphis, TN, USA
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15
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Carvalho SM, Farshchi Andisi V, Gradstedt H, Neef J, Kuipers OP, Neves AR, Bijlsma JJE. Pyruvate oxidase influences the sugar utilization pattern and capsule production in Streptococcus pneumoniae. PLoS One 2013; 8:e68277. [PMID: 23844180 PMCID: PMC3701046 DOI: 10.1371/journal.pone.0068277] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 06/02/2013] [Indexed: 11/18/2022] Open
Abstract
Pyruvate oxidase is a key function in the metabolism and lifestyle of many lactic acid bacteria and its activity depends on the presence of environmental oxygen. In Streptococcus pneumoniae the protein has been suggested to play a major role in metabolism and has been implicated in virulence, oxidative stress survival and death in stationary phase. Under semi-aerobic conditions, transcriptomic and metabolite profiling analysis of a spxB mutant grown on glucose showed minor changes compared to the wild type, apart from the significant induction of two operons involved in carbohydrate uptake and processing. This induction leads to a change in the sugar utilization capabilities of the bacterium, as indicated by the analysis of the growth profiles of the D39 parent and spxB mutant on alternative carbohydrates. Metabolic analysis and growth experiments showed that inactivation of SpxB has no effect on the glucose fermentation pattern, except under aerobic conditions. More importantly, we show that mutation of spxB results in the production of increased amounts of capsule, the major virulence factor of S. pneumoniae. Part of this increase can be attributed to induction of capsule operon (cps) transcription. Therefore, we propose that S. pneumoniae utilizes pyruvate oxidase as an indirect sensor of the oxygenation of the environment, resulting in the adaption of its nutritional capability and the amount of capsule to survive in the host.
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Affiliation(s)
- Sandra M. Carvalho
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Vahid Farshchi Andisi
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Henrik Gradstedt
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jolanda Neef
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Ana R. Neves
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jetta J. E. Bijlsma
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- * E-mail:
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Clementi EA, Marks LR, Duffey ME, Hakansson AP. A novel initiation mechanism of death in Streptococcus pneumoniae induced by the human milk protein-lipid complex HAMLET and activated during physiological death. J Biol Chem 2012; 287:27168-82. [PMID: 22700972 DOI: 10.1074/jbc.m112.371070] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
To cause colonization or infection, most bacteria grow in biofilms where differentiation and death of subpopulations is critical for optimal survival of the whole population. However, little is known about initiation of bacterial death under physiological conditions. Membrane depolarization has been suggested, but never shown to be involved, due to the difficulty of performing such studies in bacteria and the paucity of information that exists regarding ion transport mechanisms in prokaryotes. In this study, we performed the first extensive investigation of ion transport and membrane depolarization in a bacterial system. We found that HAMLET, a human milk protein-lipid complex, kills Streptococcus pneumoniae (the pneumococcus) in a manner that shares features with activation of physiological death from starvation. Addition of HAMLET to pneumococci dissipated membrane polarity, but depolarization per se was not enough to trigger death. Rather, both HAMLET- and starvation-induced death of pneumococci specifically required a sodium-dependent calcium influx, as shown using calcium and sodium transport inhibitors. This mechanism was verified under low sodium conditions, and in the presence of ionomycin or monensin, which enhanced pneumococcal sensitivity to HAMLET- and starvation-induced death. Pneumococcal death was also inhibited by kinase inhibitors, and indicated the involvement of Ser/Thr kinases in these processes. The importance of this activation mechanism was made evident, as dysregulation and manipulation of physiological death was detrimental to biofilm formation, a hallmark of bacterial colonization. Overall, our findings provide novel information on the role of ion transport during bacterial death, with the potential to uncover future antimicrobial targets.
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Affiliation(s)
- Emily A Clementi
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, New York 14214, USA
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Soldati T, Neyrolles O. Mycobacteria and the intraphagosomal environment: take it with a pinch of salt(s)! Traffic 2012; 13:1042-52. [PMID: 22462580 DOI: 10.1111/j.1600-0854.2012.01358.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/27/2012] [Accepted: 03/30/2012] [Indexed: 01/13/2023]
Abstract
Ancient protozoan phagocytes and modern professional phagocytes of metazoans, such as macrophages, employ evolutionarily conserved mechanisms to kill microbes. These mechanisms rely on microbial ingestion, followed by maturation of the phagocytic vacuole, or so-called phagosome. Phagosome maturation includes a series of fusion and fission events with the host cell endosomes and lysosomes, leading to a rapid increase of the degradative properties of the vacuole and to the destruction of the ingested microbe within a very hostile intracellular compartment, the phagolysosome. Historically, the mechanisms and weapons used by phagocytes to kill microbes have been separated into different classes. Phagosomal acidification, together with the production of reactive oxygen and nitrogen species, the selective manipulation of various ions in the phagosomal lumen, and finally the engagement of a battery of acidic hydrolases, are well-recognized players in this process. However, it is relatively recently that interconnections among these mechanisms have become apparent. In this review, we will focus on some emerging concepts about these interconnected aspects of the warfare at the host-pathogen interface, using mostly Mycobacterium tuberculosis as an example of intracellular pathogen. In particular, recent discoveries on the role of phagosomal ions and other chemicals in the control of pathogens, as well as mechanisms evolved by intracellular pathogens to circumvent or even exploit the weapons of the host cell will be discussed.
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Affiliation(s)
- Thierry Soldati
- Départment de Biochimie, Faculté des Sciences, Université de Genève, Sciences II, 30 quai Ernest Ansermet, CH-1211, Genève-4, Switzerland.
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Pneumococcal gene complex involved in resistance to extracellular oxidative stress. Infect Immun 2012; 80:1037-49. [PMID: 22215735 DOI: 10.1128/iai.05563-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Streptococcus pneumoniae is a gram-positive bacterium which is a member of the normal human nasopharyngeal flora but can also cause serious disease such as pneumonia, bacteremia, and meningitis. Throughout its life cycle, S. pneumoniae is exposed to significant oxidative stress derived from endogenously produced hydrogen peroxide (H(2)O(2)) and from the host through the oxidative burst. How S. pneumoniae, an aerotolerant anaerobic bacterium that lacks catalase, protects itself against hydrogen peroxide stress is still unclear. Bioinformatic analysis of its genome identified a hypothetical open reading frame belonging to the thiol-specific antioxidant (TlpA/TSA) family, located in an operon consisting of three open reading frames. For all four strains tested, deletion of the gene resulted in an approximately 10-fold reduction in survival when strains were exposed to external peroxide stress. However, no role for this gene in survival of internal superoxide stress was observed. Mutagenesis and complementation analysis demonstrated that all three genes are necessary and sufficient for protection against oxidative stress. Interestingly, in a competitive index mouse pneumonia model, deletion of the operon had no impact shortly after infection but was detrimental during the later stages of disease. Thus, we have identified a gene complex involved in the protection of S. pneumoniae against external oxidative stress, which plays an important role during invasive disease.
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