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Sachla AJ, Soni V, Piñeros M, Luo Y, Im JJ, Rhee KY, Helmann JD. The Bacillus subtilis yqgC-sodA operon protects magnesium-dependent enzymes by supporting manganese efflux. J Bacteriol 2024:e0005224. [PMID: 38819154 DOI: 10.1128/jb.00052-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 05/08/2024] [Indexed: 06/01/2024] Open
Abstract
Microbes encounter a myriad of stresses during their life cycle. Dysregulation of metal ion homeostasis is increasingly recognized as a key factor in host-microbe interactions. Bacterial metal ion homeostasis is tightly regulated by dedicated metalloregulators that control uptake, sequestration, trafficking, and efflux. Here, we demonstrate that deletion of the Bacillus subtilis yqgC-sodA (YS) complex operon, but not deletion of the individual genes, causes hypersensitivity to manganese (Mn). YqgC is an integral membrane protein of unknown function, and SodA is a Mn-dependent superoxide dismutase (MnSOD). The YS strain has reduced expression of two Mn efflux proteins, MneP and MneS, consistent with the observed Mn sensitivity. The YS strain accumulated high levels of Mn, had increased reactive radical species (RRS), and had broad metabolic alterations that can be partially explained by the inhibition of Mg-dependent enzymes. Although the YS operon deletion strain and an efflux-deficient mneP mneS double mutant both accumulate Mn and have similar metabolic perturbations, they also display phenotypic differences. Several mutations that suppressed Mn intoxication of the mneP mneS efflux mutant did not benefit the YS mutant. Further, Mn intoxication in the YS mutant, but not the mneP mneS strain, was alleviated by expression of Mg-dependent, chorismate-utilizing enzymes of the menaquinone, siderophore, and tryptophan (MST) family. Therefore, despite their phenotypic similarities, the Mn sensitivity in the mneP mneS and the YS deletion mutants results from distinct enzymatic vulnerabilities.IMPORTANCEBacteria require multiple trace metal ions for survival. Metal homeostasis relies on the tightly regulated expression of metal uptake, storage, and efflux proteins. Metal intoxication occurs when metal homeostasis is perturbed and often results from enzyme mis-metalation. In Bacillus subtilis, Mn-dependent superoxide dismutase (MnSOD) is the most abundant Mn-containing protein and is important for oxidative stress resistance. Here, we report novel roles for MnSOD and a co-regulated membrane protein, YqgC, in Mn homeostasis. Loss of both MnSOD and YqgC (but not the individual proteins) prevents the efficient expression of Mn efflux proteins and leads to a large-scale perturbation of the metabolome due to inhibition of Mg-dependent enzymes, including key chorismate-utilizing MST (menaquinone, siderophore, and tryptophan) family enzymes.
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Affiliation(s)
- Ankita J Sachla
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Vijay Soni
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Miguel Piñeros
- School of Integrative Plant Sciences, Plant Biology Section, Cornell University, Ithaca, New York, USA
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Ithaca, New York, USA
| | - Yuanchan Luo
- Department of Microbiology, Cornell University, Ithaca, New York, USA
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Janice J Im
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Kyu Y Rhee
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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2
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Thapa S, Rathnaiah G, Zinniel DK, Barletta RG, Bannantine JP, Huebner M, Sreevatsan S. The Fur-like regulatory protein MAP3773c modulates key metabolic pathways in Mycobacterium avium subsp. paratuberculosis under in-vitro iron starvation. Sci Rep 2024; 14:8941. [PMID: 38637716 PMCID: PMC11026511 DOI: 10.1038/s41598-024-59691-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024] Open
Abstract
Johne's disease (JD) is a chronic enteric infection of dairy cattle worldwide. Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of JD, is fastidious often requiring eight to sixteen weeks to produce colonies in culture-a major hurdle in the diagnosis and therefore in implementation of optimal JD control measures. A significant gap in knowledge is the comprehensive understanding of the metabolic networks deployed by MAP to regulate iron both in-vitro and in-vivo. The genome of MAP carries MAP3773c, a putative metal regulator, which is absent in all other mycobacteria. The role of MAP3773c in intracellular iron regulation is poorly understood. In the current study, a field isolate (K-10) and an in-frame MAP3773c deletion mutant (ΔMAP3773c) derived from K-10, were exposed to iron starvation for 5, 30, 60, and 90 min and RNA-Seq was performed. A comparison of transcriptional profiles between K-10 and ΔMAP3773c showed 425 differentially expressed genes (DEGs) at 30 min time post-iron restriction. Functional analysis of DEGs in ΔMAP3773c revealed that pantothenate (Pan) biosynthesis, polysaccharide biosynthesis and sugar metabolism genes were downregulated at 30 min post-iron starvation whereas ATP-binding cassette (ABC) type metal transporters, putative siderophore biosynthesis, PPE and PE family genes were upregulated. Pathway analysis revealed that the MAP3773c knockout has an impairment in Pan and Coenzyme A (CoA) biosynthesis pathways suggesting that the absence of those pathways likely affect overall metabolic processes and cellular functions, which have consequences on MAP survival and pathogenesis.
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Affiliation(s)
- Sajani Thapa
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, 784 Wilson Road, STEG300, East Lansing, MI, 48824, USA
| | - Govardhan Rathnaiah
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, USA
- University Of Nebraska, Eppley Institute for Cancer Research, Lincoln, USA
| | - Denise K Zinniel
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, USA
| | - Raul G Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, USA
| | | | - Marianne Huebner
- Department of Statistics and Probability, Michigan State University, East Lansing, MI, USA
| | - Srinand Sreevatsan
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, 784 Wilson Road, STEG300, East Lansing, MI, 48824, USA.
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Kim M, Le MT, Fan L, Campbell C, Sen S, Capdevila DA, Stemmler TL, Giedroc DP. Characterization of the Zinc Uptake Repressor (Zur) from Acinetobacter baumannii. Biochemistry 2024; 63:660-670. [PMID: 38385972 PMCID: PMC11019503 DOI: 10.1021/acs.biochem.3c00679] [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] [Indexed: 02/23/2024]
Abstract
Bacterial cells tightly regulate the intracellular concentrations of essential transition metal ions by deploying a panel of metal-regulated transcriptional repressors and activators that bind to operator-promoter regions upstream of regulated genes. Like other zinc uptake regulator (Zur) proteins, Acinetobacter baumannii Zur represses transcription of its regulon when ZnII is replete and binds more weakly to DNA when ZnII is limiting. Previous studies established that Zur proteins are homodimeric and harbor at least two metal sites per protomer or four per dimer. CdII X-ray absorption spectroscopy (XAS) of the Cd2Zn2 AbZur metalloderivative with CdII bound to the allosteric sites reveals a S(N/O)3 first coordination shell. Site-directed mutagenesis suggests that H89 and C100 from the N-terminal DNA binding domain and H107 and E122 from the C-terminal dimerization domain comprise the regulatory metal site. KZn for this allosteric site is 6.0 (±2.2) × 1012 M-1 with a functional "division of labor" among the four metal ligands. N-terminal domain ligands H89 and C100 contribute far more to KZn than H107 and E122, while C100S AbZur uniquely fails to bind to DNA tightly as measured by an in vitro transcription assay. The heterotropic allosteric coupling free energy, ΔGc, is negative, consistent with a higher KZn for the AbZur-DNA complex and defining a bioavailable ZnII set-point of ≈6 × 10-14 M. Small-angle X-ray scattering (SAXS) experiments reveal that only the wild-type Zn homodimer undergoes allosteric switching, while the C100S AbZur fails to switch. These data collectively suggest that switching to a high affinity DNA-binding conformation involves a rotation/translation of one protomer relative to the other in a way that is dependent on the integrity of C100. We place these findings in the context of other Zur proteins and Fur family repressors more broadly.
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Affiliation(s)
- Minyong Kim
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - My Tra Le
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core Facility of the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Courtney Campbell
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201-2417, United States
| | - Sambuddha Sen
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Daiana A Capdevila
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405 BWE Buenos Aires, Argentina
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201-2417, United States
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
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4
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Fontenot CR, Ding H. The C-terminal domain of the ferric uptake regulator (Fur) binds a [2Fe-2S] cluster to sense the intracellular free iron content in Escherichia coli. Biometals 2023; 36:1285-1294. [PMID: 37344741 DOI: 10.1007/s10534-023-00517-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 06/14/2023] [Indexed: 06/23/2023]
Abstract
Escherichia coli ferric uptake regulator (Fur) binds a [2Fe-2S] cluster, not a mononuclear iron, when the intracellular free iron content is elevated in E. coli cells. Here we report that the C-terminal domain (residues 83-148) of E. coli Fur (Fur-CTD) is sufficient to bind the [2Fe-2S] cluster in response to elevation of the intracellular free iron content in E. coli cells. Deletion of gene fur in E. coli cells increases the intracellular free iron content and promotes the [2Fe-2S] cluster binding in the Fur-CTD in the cells grown in LB medium under aerobic growth conditions. When the Fur-CTD is expressed in wild type E. coli cells grown in M9 medium supplemented with increasing concentrations of iron, the Fur-CTD also progressively binds a [2Fe-2S] cluster with a maximum occupancy of about 36%. Like the E. coli Fur-CTD, the CTD of the Haemophilus influenzae Fur can also bind a [2Fe-2S] cluster in wild type E. coli cells grown in M9 medium supplemented with increasing concentrations of iron, indicating that binding of the [2Fe-2S] cluster in the C-terminal domain is highly conserved among Fur proteins. The results suggest that the Fur-CTD can be used as a physiological probe to assess the intracellular free iron content in bacteria.
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Affiliation(s)
- Chelsey R Fontenot
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Huangen Ding
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
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Steingard CH, Helmann JD. Meddling with Metal Sensors: Fur-Family Proteins as Signaling Hubs. J Bacteriol 2023; 205:e0002223. [PMID: 37010421 PMCID: PMC10127796 DOI: 10.1128/jb.00022-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
The ferric uptake regulator (Fur) protein is the founding member of the FUR superfamily of metalloregulatory proteins that control metal homeostasis in bacteria. FUR proteins regulate metal homeostasis in response to the binding of iron (Fur), zinc (Zur), manganese (Mur), or nickel (Nur). FUR family proteins are generally dimers in solution, but the DNA-bound complex can involve a single dimer, a dimer-of-dimers, or an extended array of bound protein. Elevated FUR levels due to changes in cell physiology increase DNA occupancy and may also kinetically facilitate protein dissociation. Interactions between FUR proteins and other regulators are commonplace, often including cooperative and competitive DNA-binding interactions within the regulatory region. Further, there are many emerging examples of allosteric regulators that interact directly with FUR family proteins. Here, we focus on newly uncovered examples of allosteric regulation by diverse Fur antagonists (Escherichia coli YdiV/SlyD, Salmonella enterica EIIANtr, Vibrio parahaemolyticus FcrX, Acinetobacter baumannii BlsA, Bacillus subtilis YlaN, and Pseudomonas aeruginosa PacT) as well as one Zur antagonist (Mycobacterium bovis CmtR). Small molecules and metal complexes may also serve as regulatory ligands, with examples including heme binding to Bradyrhizobium japonicum Irr and 2-oxoglutarate binding to Anabaena FurA. How these protein-protein and protein-ligand interactions act in conjunction with regulatory metal ions to facilitate signal integration is an active area of investigation.
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Affiliation(s)
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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6
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Park J, Cleary MB, Li D, Mattocks JA, Xu J, Wang H, Mukhopadhyay S, Gale EM, Cotruvo JA. A genetically encoded fluorescent sensor for manganese(II), engineered from lanmodulin. Proc Natl Acad Sci U S A 2022; 119:e2212723119. [PMID: 36508659 PMCID: PMC9907080 DOI: 10.1073/pnas.2212723119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/10/2022] [Indexed: 12/15/2022] Open
Abstract
The design of selective metal-binding sites is a challenge in both small-molecule and macromolecular chemistry. Selective recognition of manganese (II)-the first-row transition metal ion that tends to bind with the lowest affinity to ligands, as described by the Irving-Williams series-is particularly difficult. As a result, there is a dearth of chemical biology tools with which to study manganese physiology in live cells, which would advance understanding of photosynthesis, host-pathogen interactions, and neurobiology. Here we report the rational re-engineering of the lanthanide-binding protein, lanmodulin, into genetically encoded fluorescent sensors for MnII, MnLaMP1 and MnLaMP2. These sensors with effective Kd(MnII) of 29 and 7 µM, respectively, defy the Irving-Williams series to selectively detect MnII in vitro and in vivo. We apply both sensors to visualize kinetics of bacterial labile manganese pools. Biophysical studies indicate the importance of coordinated solvent and hydrophobic interactions in the sensors' selectivity. Our results establish lanmodulin as a versatile scaffold for design of selective protein-based biosensors and chelators for metals beyond the f-block.
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Affiliation(s)
- Jennifer Park
- Department of Chemistry, The Pennsylvania State University, University Park, PA16802
| | - Michael B. Cleary
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital / Harvard Medical School, Charlestown, MA02129
| | - Danyang Li
- Division of Pharmacology and Toxicology, College of Pharmacy, Institute for Cellular and Molecular Biology, and Institute for Neuroscience, The University of Texas at Austin, Austin, TX78712
| | - Joseph A. Mattocks
- Department of Chemistry, The Pennsylvania State University, University Park, PA16802
| | - Jiansong Xu
- Department of Chemistry, The Pennsylvania State University, University Park, PA16802
| | - Huan Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital / Harvard Medical School, Charlestown, MA02129
| | - Somshuvra Mukhopadhyay
- Division of Pharmacology and Toxicology, College of Pharmacy, Institute for Cellular and Molecular Biology, and Institute for Neuroscience, The University of Texas at Austin, Austin, TX78712
| | - Eric M. Gale
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital / Harvard Medical School, Charlestown, MA02129
| | - Joseph A. Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, PA16802
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7
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Luo Y, Chen L, Lu Z, Zhang W, Liu W, Chen Y, Wang X, Du W, Luo J, Wu H. Genome sequencing of biocontrol strain Bacillus amyloliquefaciens Bam1 and further analysis of its heavy metal resistance mechanism. BIORESOUR BIOPROCESS 2022; 9:74. [PMID: 38647608 PMCID: PMC10991351 DOI: 10.1186/s40643-022-00563-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) or Biocontrol strains inevitably encounter heavy metal excess stress during the product's processing and application. Bacillus amyloliquefaciens Bam1 was a potential biocontrol strain with strong heavy metal resistant ability. To understand its heavy metal resistance mechanism, the complete genome of Bam1 had been sequenced, and the comparative genomic analysis of Bam1 and FZB42, an industrialized PGPR and biocontrol strain with relatively lower heavy metal tolerance, was conducted. The comparative genomic analysis of Bam1 and the other nine B. amyloliquefaciens strains as well as one Bacillus velezensis (genetically and physiologically very close to B. amyloliquefaciens) was also performed. Our results showed that the complete genome size of Bam1 was 3.95 Mb, 4219 coding sequences were predicted, and it possessed the highest number of unique genes among the eleven analyzed strains. Nine genes related to heavy metal resistance were detected within the twelve DNA islands of Bam1, while only two of them were detected within the seventeen DNA islands of FZB42. When compared with B. amyloliquefaciens type strain DSM7, Bam1 lacked contig L, whereas FZB42 lacked contig D and I, as well as just possessed contig B with a very small size. Our results could also deduce that Bam1 promoted its essential heavy metal resistance mainly by decreasing the import and increasing the export of heavy metals with the corresponding homeostasis systems, which are regulated by different metalloregulators. While Bam1 promoted its non-essential heavy metal resistance mainly by the activation of some specific or non-specific exporters responding to different heavy metals. The variation of the genes related to heavy metal resistance and the other differences of the genomes, including the different number and arrangement of contigs, as well as the number of the heavy metal resistant genes in Prophages and Genomic islands, led to the significant different resistance of Bam1 and FZB42 to heavy metals.
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Affiliation(s)
- Yuanchan Luo
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Lei Chen
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai, 201103, China
| | - Zhibo Lu
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Weijian Zhang
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Wentong Liu
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yuwei Chen
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xinran Wang
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Wei Du
- Agricultural Technology Extension Station of Ningxia, 2, West Shanghai Road, Yinchuan, 750001, China
| | - Jinyan Luo
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai, 201103, China.
| | - Hui Wu
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai, 200237, China.
- Key Laboratory of Bio-Based Material Engineering of China National Light Industry Council, 130 Meilong Road, Shanghai, 200237, China.
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8
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Sachla AJ, Luo Y, Helmann JD. Manganese impairs the QoxABCD terminal oxidase leading to respiration-associated toxicity. Mol Microbiol 2021; 116:729-742. [PMID: 34097790 DOI: 10.1111/mmi.14767] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/29/2022]
Abstract
Cell physiology relies on metalloenzymes and can be easily disrupted by imbalances in metal ion pools. Bacillus subtilis requires manganese for growth and has highly regulated mechanisms for import and efflux that help maintain homeostasis. Cells defective for manganese (Mn) efflux are highly sensitive to intoxication, but the processes impaired by Mn excess are often unknown. Here, we employed a forward genetics approach to identify pathways affected by manganese intoxication. Our results highlight a central role for the membrane-localized electron transport chain in metal intoxication during aerobic growth. In the presence of elevated manganese, there is an increased generation of reactive radical species associated with dysfunction of the major terminal oxidase, the cytochrome aa3 heme-copper menaquinol oxidase (QoxABCD). Intoxication is suppressed by diversion of menaquinol to alternative oxidases or by a mutation affecting heme A synthesis that is known to convert QoxABCD from an aa3 to a bo3 -type oxidase. Manganese sensitivity is also reduced by derepression of the MhqR regulon, which protects cells against reactive quinones. These results suggest that dysfunction of the cytochrome aa3 -type quinol oxidase contributes to metal-induced intoxication.
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Affiliation(s)
- Ankita J Sachla
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Yuanchan Luo
- Department of Microbiology, Cornell University, Ithaca, NY, USA.,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY, USA
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Rasha F, Mims BM, Castro-Piedras I, Barnes BJ, Grisham MB, Rahman RL, Pruitt K. The Versatility of Sirtuin-1 in Endocrinology and Immunology. Front Cell Dev Biol 2020; 8:589016. [PMID: 33330467 PMCID: PMC7717970 DOI: 10.3389/fcell.2020.589016] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/27/2020] [Indexed: 12/13/2022] Open
Abstract
Sirtuins belong to the class III family of NAD-dependent histone deacetylases (HDAC) and are involved in diverse physiological processes that range from regulation of metabolism and endocrine function to coordination of immunity and cellular responses to stress. Sirtuin-1 (SIRT1) is the most well-studied family member and has been shown to be critically involved in epigenetics, immunology, and endocrinology. The versatile roles of SIRT1 include regulation of energy sensing metabolic homeostasis, deacetylation of histone and non-histone proteins in numerous tissues, neuro-endocrine regulation via stimulation of hypothalamus-pituitary axes, synthesis and maintenance of reproductive hormones via steroidogenesis, maintenance of innate and adaptive immune system via regulation of T- and B-cell maturation, chronic inflammation and autoimmune diseases. Moreover, SIRT1 is an appealing target in various disease contexts due to the promise of pharmacological and/or natural modulators of SIRT1 activity within the context of endocrine and immune-related disease models. In this review we aim to provide a broad overview on the role of SIRT1 particularly within the context of endocrinology and immunology.
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Affiliation(s)
- Fahmida Rasha
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Brianyell McDaniel Mims
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Isabel Castro-Piedras
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Betsy J. Barnes
- Laboratory of Autoimmune and Cancer Research, Center for Autoimmune Musculoskeletal and Hematopoietic Disease, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
- Department of Molecular Medicine and Department of Pediatrics, Zucker School of Medicine at Hofstra-Northwell, Hempstead, NY, United States
| | - Matthew B. Grisham
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | | | - Kevin Pruitt
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
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10
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RETRACTED ARTICLE: Discovery of iron-sensing bacterial riboswitches. Nat Chem Biol 2020; 17:924. [PMID: 33020663 DOI: 10.1038/s41589-020-00665-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 07/29/2020] [Accepted: 08/26/2020] [Indexed: 01/17/2023]
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11
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Genetic Regulation of Metal Ion Homeostasis in Staphylococcus aureus. Trends Microbiol 2020; 28:821-831. [PMID: 32381454 DOI: 10.1016/j.tim.2020.04.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/16/2022]
Abstract
The acquisition of metal ions and the proper maturation of holo-metalloproteins are essential processes for all organisms. However, metal ion homeostasis is a double-edged sword. A cytosolic accumulation of metal ions can lead to mismetallation of proteins and cell death. Therefore, maintenance of proper concentrations of intracellular metals is essential for cell fitness and pathogenesis. Staphylococcus aureus, like all bacterial pathogens, uses transcriptional metalloregulatory proteins to aid in the detection and the genetic response to changes in metal ion concentrations. Herein, we review the mechanisms by which S. aureus senses and responds to alterations in the levels of cellular zinc, iron, heme, and copper. The interplay between metal ion sensing and metal-dependent expression of virulence factors is also discussed.
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Bacillus subtilis Fur Is a Transcriptional Activator for the PerR-Repressed pfeT Gene, Encoding an Iron Efflux Pump. J Bacteriol 2020; 202:JB.00697-19. [PMID: 31988078 DOI: 10.1128/jb.00697-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/23/2020] [Indexed: 12/30/2022] Open
Abstract
The physiological relevance of bacterial iron efflux has only recently been appreciated. The Bacillus subtilis P1B4-type ATPase PfeT (peroxide-induced ferrous efflux transporter) was one of the first iron efflux pumps to be characterized, and cells lacking pfeT accumulate high levels of intracellular iron. The pfeT promoter region has binding sites for both PerR, a peroxide-sensing Fur-family metalloregulator, and the ferric uptake repressor Fur. Both Fur and PerR bind DNA with Fe(II) as a cofactor. While reaction of PerR-Fe(II) with peroxide can account for the induction of pfeT under oxidative stress, binding of Fur-Fe(II) would be expected to lead to repression, which is inconsistent with the known role of PfeT as an iron efflux protein. Here, we show that expression of pfeT is repressed by PerR, as anticipated, and induced by Fur in response to Fe(II). Activation by Fur is mediated both by antagonism of the PerR repressor and by direct transcriptional activation, as confirmed using in vitro transcription assays. A similar mechanism of regulation can explain the iron induction of the Listeria monocytogenes PfeT ortholog and virulence factor, FrvA. Mutational studies support a model in which Fur activation involves regions both upstream and downstream of the pfeT promoter, and Fur and PerR have overlapping recognition of a shared regulatory element in this complex promoter region. This work demonstrates that B. subtilis Fur can function as an iron-dependent activator of transcription.IMPORTANCE Iron homeostasis plays a key role at the host-pathogen interface during the process of infection. Bacterial growth restriction resulting from host-imposed iron starvation (nutritional immunity) highlights the importance of iron import during pathogenesis. Conversely, bacterial iron efflux pumps function as virulence factors in several systems. The requirement for iron efflux in pathogens such as Listeria monocytogenes, Streptococcus pyogenes, and Mycobacterium tuberculosis suggests that both import and efflux are needed for cells to successfully navigate rapidly changing levels of iron availability in the host. Here, we provide insight into how iron efflux genes are controlled, an aspect of bacterial iron homeostasis relevant to infectious disease processes.
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Harbison-Price N, Ferguson SA, Heikal A, Taiaroa G, Hards K, Nakatani Y, Rennison D, Brimble MA, El-Deeb IM, Bohlmann L, McDevitt CA, von Itzstein M, Walker MJ, Cook GM. Multiple Bactericidal Mechanisms of the Zinc Ionophore PBT2. mSphere 2020; 5:e00157-20. [PMID: 32188750 PMCID: PMC7082140 DOI: 10.1128/msphere.00157-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 02/29/2020] [Indexed: 12/21/2022] Open
Abstract
Globally, more antimicrobials are used in food-producing animals than in humans, and the extensive use of medically important human antimicrobials poses a significant public health threat in the face of rising antimicrobial resistance (AMR). The development of novel ionophores, a class of antimicrobials used exclusively in animals, holds promise as a strategy to replace or reduce essential human antimicrobials in veterinary practice. PBT2 is a zinc ionophore with recently demonstrated antibacterial activity against several Gram-positive pathogens, although the underlying mechanism of action is unknown. Here, we investigated the bactericidal mechanism of PBT2 in the bovine mastitis-causing pathogen, Streptococcus uberis In this work, we show that PBT2 functions as a Zn2+/H+ ionophore, exchanging extracellular zinc for intracellular protons in an electroneutral process that leads to cellular zinc accumulation. Zinc accumulation occurs concomitantly with manganese depletion and the production of reactive oxygen species (ROS). PBT2 inhibits the activity of the manganese-dependent superoxide dismutase, SodA, thereby impairing oxidative stress protection. We propose that PBT2-mediated intracellular zinc toxicity in S. uberis leads to lethality through multiple bactericidal mechanisms: the production of toxic ROS and the impairment of manganese-dependent antioxidant functions. Collectively, these data show that PBT2 represents a new class of antibacterial ionophores capable of targeting bacterial metal ion homeostasis and cellular redox balance. We propose that this novel and multitarget mechanism of PBT2 makes the development of cross-resistance to medically important antimicrobials unlikely.IMPORTANCE More antimicrobials are used in food-producing animals than in humans, and the extensive use of medically important human antimicrobials poses a significant public health threat in the face of rising antimicrobial resistance. Therefore, the elimination of antimicrobial crossover between human and veterinary medicine is of great interest. Unfortunately, the development of new antimicrobials is an expensive high-risk process fraught with difficulties. The repurposing of chemical agents provides a solution to this problem, and while many have not been originally developed as antimicrobials, they have been proven safe in clinical trials. PBT2, a zinc ionophore, is an experimental therapeutic that met safety criteria but failed efficacy checkpoints against both Alzheimer's and Huntington's diseases. It was recently found that PBT2 possessed potent antimicrobial activity, although the mechanism of bacterial cell death is unresolved. In this body of work, we show that PBT2 has multiple mechanisms of antimicrobial action, making the development of PBT2 resistance unlikely.
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Affiliation(s)
| | - Scott A Ferguson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Adam Heikal
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - George Taiaroa
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Kiel Hards
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Yoshio Nakatani
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - David Rennison
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | | | - Lisa Bohlmann
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, Queensland, Australia
| | - Christopher A McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Mark J Walker
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, Queensland, Australia
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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Dysregulation of Magnesium Transport Protects Bacillus subtilis against Manganese and Cobalt Intoxication. J Bacteriol 2020; 202:JB.00711-19. [PMID: 31964700 DOI: 10.1128/jb.00711-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/16/2020] [Indexed: 12/11/2022] Open
Abstract
Transition metals are essential for life but are toxic when in excess. Metal ion intoxication may result from the mismetallation of essential metal-dependent enzymes with a noncognate metal. To begin to identify enzymes and processes that are susceptible to mismetallation, we have selected for strains with increased resistance to Mn(II) and Co(II). In Bacillus subtilis, cells lacking the MntR metalloregulator are exquisitely sensitive to Mn(II) but can easily become resistant by acquiring mutations affecting the MntH Mn(II) importer. Using transposon mutagenesis, and starting with an mntR mntH strain, we recovered mariner insertions that inactivated the mpfA gene encoding a putative Mg(II) efflux system. Loss of MpfA leads to elevated intracellular Mg(II), increased sensitivity to high Mg(II), and reduced Mn(II) sensitivity. Consistently, we also recovered an insertion disrupting the mgtE riboswitch, which normally restricts expression of the major Mg(II) importer. These results suggest that Mn(II) intoxication results from disruption of a Mg(II)-dependent enzyme or process. Mutations that inactivate MpfA were also recovered in a selection for Co(II) resistance beginning with sensitized strains lacking the major Co(II) efflux pump, CzcD. Since both Mn(II) and Co(II) may mismetallate iron-dependent enzymes, we repeated the selections under conditions of iron depletion imposed by expression of the Listeria monocytogenes FrvA iron exporter. Under conditions of iron depletion, a wider variety of suppressor mutations were recovered, but they still point to a central role for Mg(II) in maintaining metal ion homeostasis.IMPORTANCE Cellular metal ion homeostasis is tightly regulated. When metal ion levels are imbalanced, or when one metal is at toxic levels, enzymes may bind to the wrong metal cofactor. Enzyme mismetallation can impair metabolism, lead to new and deleterious reactions, and cause cell death. Beginning with Bacillus subtilis strains genetically sensitized to metal intoxication through loss of efflux or by lowering intracellular iron, we identified mutations that suppress the deleterious effects of excess Mn(II) or Co(II). For both metals, mutations in mpfA, encoding a Mg(II) efflux pump, suppressed toxicity. These mutant strains have elevated intracellular Mg(II), suggesting that Mg(II)-dependent processes are very sensitive to disruption by transition metals.
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Jordan MR, Wang J, Capdevila DA, Giedroc DP. Multi-metal nutrient restriction and crosstalk in metallostasis systems in microbial pathogens. Curr Opin Microbiol 2020; 55:17-25. [PMID: 32062305 DOI: 10.1016/j.mib.2020.01.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/03/2020] [Accepted: 01/09/2020] [Indexed: 12/26/2022]
Abstract
Transition metals from manganese to zinc function as catalytic and structural cofactors for an amazing diversity of proteins and enzymes, and thus are essential for all forms of life. During infection, inflammatory host proteins limit the accessibility of multiple transition metals to invading pathogens in a process termed nutritional immunity. In order to respond to host-mediated metal starvation, bacteria employ both protein and RNA-based mechanisms to sense prevailing transition metal concentrations that collectively regulate systems-level strategies to maintain cellular metallostasis. In this review, we discuss a number of recent advances in our understanding of how bacteria orchestrate the adaptive response to host-mediated multi-metal restriction, highlighting crosstalk among these regulatory systems.
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Affiliation(s)
- Matthew R Jordan
- Departments of Chemistry and of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, United States
| | - Jiefei Wang
- Departments of Chemistry and of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, United States
| | - Daiana A Capdevila
- Fundación Instituto Leloir, Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina
| | - David P Giedroc
- Departments of Chemistry and of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, United States.
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Frindert J, Kahloon MA, Zhang Y, Ahmed YL, Sinning I, Jäschke A. YvcI from Bacillus subtilis has in vitro RNA pyrophosphohydrolase activity. J Biol Chem 2019; 294:19967-19977. [PMID: 31740579 DOI: 10.1074/jbc.ra119.011485] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/15/2019] [Indexed: 12/23/2022] Open
Abstract
RNA degradation is one of several ways for organisms to regulate gene expression. In bacteria, the removal of two terminal phosphate moieties as orthophosphate (Bacillus subtilis) or pyrophosphate (Escherichia coli) triggers ribonucleolytic decay of primary transcripts by 5'-monophosphate-dependent ribonucleases. In the soil-dwelling firmicute species B. subtilis, the RNA pyrophosphohydrolase BsRppH, a member of the Nudix family, triggers RNA turnover by converting primary transcripts to 5'-monophospate RNA. In addition to BsRppH, a source of redundant activity in B. subtilis has been proposed. Here, using recombinant protein expression and in vitro enzyme assays, we provide evidence for several additional RNA pyrophosphohydrolases, among them MutT, NudF, YmaB, and YvcI in B. subtilis We found that in vitro, YvcI converts RNA 5'-di- and triphosphates into monophosphates in the presence of manganese at neutral to slightly acidic pH. It preferred G-initiating RNAs and required at least one unpaired nucleotide at the 5'-end of its substrates, with the 5'-terminal nucleotide determining whether primarily ortho- or pyrophosphate is released. Exchanges of catalytically important glutamate residues in the Nudix motif impaired or abolished the enzymatic activity of YvcI. In summary, the results of our extensive in vitro biochemical characterization raise the possibility that YvcI is an additional RNA pyrophosphohydrolase in B. subtilis.
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Affiliation(s)
- Jens Frindert
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, D-69120 Heidelberg, Germany
| | - Masroor Ahmad Kahloon
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, D-69120 Heidelberg, Germany
| | - Yaqing Zhang
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, D-69120 Heidelberg, Germany
| | - Yasar Luqman Ahmed
- Heidelberg University Biochemistry Center, Heidelberg University, D-69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, Heidelberg University, D-69120 Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, D-69120 Heidelberg, Germany
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Śmiga M, Bielecki M, Olczak M, Olczak T. Porphyromonas gingivalis PgFur Is a Member of a Novel Fur Subfamily With Non-canonical Function. Front Cell Infect Microbiol 2019; 9:233. [PMID: 31312617 PMCID: PMC6613475 DOI: 10.3389/fcimb.2019.00233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/14/2019] [Indexed: 12/11/2022] Open
Abstract
Porphyromonas gingivalis, a keystone pathogen of chronic periodontitis, uses ferric uptake regulator homolog (PgFur) to regulate production of virulence factors. This study aimed to characterize PgFur protein in regard to its structure-function relationship. We experimentally identified the 5′ mRNA sequence encoding the 171-amino-acid-long PgFur protein in the A7436 strain and examined this PgFur version as a full-length protein. PgFur protein did not bind to the canonical Escherichia coli Fur box, but the wild-type phenotype of the mutant Δpgfur strain was restored partially when expression of the ecfur gene was induced from the native pgfur promoter. The full-length PgFur protein contained one zinc atom per protein monomer, but did not bind iron, manganese, or heme. Single cysteine substitutions of CXXC motifs resulted in phenotypes similar to the mutant Δpgfur strain. The modified proteins were produced in E. coli at significantly lower levels, were highly unstable, and did not bind zinc. The pgfur gene was expressed at the highest levels in bacteria cultured for 24 h in the absence of iron and heme or at higher levels in bacteria cultured for 10 h in the presence of protoporphyrin IX source. No influence of high availability of Fe2+, Zn2+, or Mn2+ on pgfur gene expression was observed. Two chromosomal mutant strains producing protein lacking 4 (pgfurΔ4aa) or 13 (pgfurΔ13aa) C-terminal amino acid residues were examined in regard to importance of the C-terminal lysine-rich region. The pgfurΔ13aa strain showed a phenotype typical for the mutant Δpgfur strain, but both the wild-type PgFur protein and its truncated version bound zinc with similar ability. The Δpgfur mutant strain produced higher amounts of HmuY protein compared with the wild-type strain, suggesting compromised regulation of its expression. Potential PgFur ligands, Fe2+, Mn2+, Zn2+, PPIX, or serum components, did not influence HmuY production in the Δpgfur mutant strain. The mutant pgfurΔ4aa and pgfurΔ13aa strains exhibited affected HmuY protein production. PgFur, regardless of the presence of the C-terminal lysine-rich region, bound to the hmu operon promoter. Our data suggest that cooperation of PgFur with partners/cofactors and/or protein/DNA modifications would be required to accomplish its role played in an in vivo multilayer regulatory network.
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Affiliation(s)
- Michał Śmiga
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Marcin Bielecki
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Mariusz Olczak
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Teresa Olczak
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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Manganese Detoxification by MntE Is Critical for Resistance to Oxidative Stress and Virulence of Staphylococcus aureus. mBio 2019; 10:mBio.02915-18. [PMID: 30808698 PMCID: PMC6391924 DOI: 10.1128/mbio.02915-18] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Manganese (Mn) is generally viewed as a critical nutrient that is beneficial to pathogenic bacteria due to its function as an enzymatic cofactor and its capability of acting as an antioxidant; yet paradoxically, high concentrations of this transition metal can be toxic. In this work, we demonstrate Staphylococcus aureus utilizes the cation diffusion facilitator (CDF) family protein MntE to alleviate Mn toxicity through efflux of excess Mn. Inactivation of mntE leads to a significant reduction in S. aureus resistance to oxidative stress and S. aureus-mediated mortality within a mouse model of systemic infection. These results highlight the importance of MntE-mediated Mn detoxification in intracellular Mn homeostasis, resistance to oxidative stress, and S. aureus virulence. Therefore, this establishes MntE as a potential target for development of anti-S. aureus therapeutics. Manganese (Mn) is an essential micronutrient critical for the pathogenesis of Staphylococcus aureus, a significant cause of human morbidity and mortality. Paradoxically, excess Mn is toxic; therefore, maintenance of intracellular Mn homeostasis is required for survival. Here we describe a Mn exporter in S. aureus, MntE, which is a member of the cation diffusion facilitator (CDF) protein family and conserved among Gram-positive pathogens. Upregulation of mntE transcription in response to excess Mn is dependent on the presence of MntR, a transcriptional repressor of the mntABC Mn uptake system. Inactivation of mntE or mntR leads to reduced growth in media supplemented with Mn, demonstrating MntE is required for detoxification of excess Mn. Inactivation of mntE results in elevated levels of intracellular Mn, but reduced intracellular iron (Fe) levels, supporting the hypothesis that MntE functions as a Mn efflux pump and Mn efflux influences Fe homeostasis. Strains inactivated for mntE are more sensitive to the oxidants NaOCl and paraquat, indicating Mn homeostasis is critical for resisting oxidative stress. Furthermore, mntE and mntR are required for full virulence of S. aureus during infection, suggesting S. aureus experiences Mn toxicity in vivo. Combined, these data support a model in which MntR controls Mn homeostasis by balancing transcriptional repression of mntABC and induction of mntE, both of which are critical for S. aureus pathogenesis. Thus, Mn efflux contributes to bacterial survival and virulence during infection, establishing MntE as a potential antimicrobial target and expanding our understanding of Mn homeostasis.
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Abstract
SIGNIFICANCE Iron is required for growth and is often redox active under cytosolic conditions. As a result of its facile redox chemistry, iron homeostasis is intricately involved with oxidative stress. Bacterial adaptation to iron limitation and oxidative stress often involves ferric uptake regulator (Fur) proteins: a diverse set of divalent cation-dependent, DNA-binding proteins that vary widely in both metal selectivity and sensitivity to metal-catalyzed oxidation. Recent Advances: Bacteria contain two Fur family metalloregulators that use ferrous iron (Fe2+) as their cofactor, Fur and PerR. Fur functions to regulate iron homeostasis in response to changes in intracellular levels of Fe2+. PerR also binds Fe2+, which enables metal-catalyzed protein oxidation as a mechanism for sensing hydrogen peroxide (H2O2). CRITICAL ISSUES To effectively regulate iron homeostasis, Fur has an Fe2+ affinity tuned to monitor the labile iron pool of the cell and may be under selective pressure to minimize iron oxidation, which would otherwise lead to an inappropriate increase in iron uptake under oxidative stress conditions. Conversely, Fe2+ is bound more tightly to PerR but exhibits high H2O2 reactivity, which enables a rapid induction of peroxide stress genes. FUTURE DIRECTIONS The features that determine the disparate reactivity of these proteins with oxidants are still poorly understood. A controlled, comparative analysis of the affinities of Fur/PerR proteins for their metal cofactors and their rate of reactivity with H2O2, combined with structure/function analyses, will be needed to define the molecular mechanisms that have facilitated this divergence of function between these two paralogous regulators.
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Affiliation(s)
| | - John D Helmann
- Department of Microbiology, Cornell University , Ithaca, New York
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20
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Wofford JD, Bolaji N, Dziuba N, Outten FW, Lindahl PA. Evidence that a respiratory shield in Escherichia coli protects a low-molecular-mass Fe II pool from O 2-dependent oxidation. J Biol Chem 2018; 294:50-62. [PMID: 30337367 DOI: 10.1074/jbc.ra118.005233] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/16/2018] [Indexed: 11/06/2022] Open
Abstract
Iron is critical for virtually all organisms, yet major questions remain regarding the systems-level understanding of iron in whole cells. Here, we obtained Mössbauer and EPR spectra of Escherichia coli cells prepared under different nutrient iron concentrations, carbon sources, growth phases, and O2 concentrations to better understand their global iron content. We investigated WT cells and those lacking Fur, FtnA, Bfr, and Dps proteins. The coarse-grain iron content of exponentially growing cells consisted of iron-sulfur clusters, variable amounts of nonheme high-spin FeII species, and an unassigned residual quadrupole doublet. The iron in stationary-phase cells was dominated by magnetically ordered FeIII ions due to oxyhydroxide nanoparticles. Analysis of cytosolic extracts by size-exclusion chromatography detected by an online inductively coupled plasma mass spectrometer revealed a low-molecular-mass (LMM) FeII pool consisting of two iron complexes with masses of ∼500 (major) and ∼1300 (minor) Da. They appeared to be high-spin FeII species with mostly oxygen donor ligands, perhaps a few nitrogen donors, and probably no sulfur donors. Surprisingly, the iron content of E. coli and its reactivity with O2 were remarkably similar to those of mitochondria. In both cases, a "respiratory shield" composed of membrane-bound iron-rich respiratory complexes may protect the LMM FeII pool from reacting with O2 When exponentially growing cells transition to stationary phase, the shield deactivates as metabolic activity declines. Given the universality of oxidative phosphorylation in aerobic biology, the iron content and respiratory shield in other aerobic prokaryotes might be similar to those of E. coli and mitochondria.
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Affiliation(s)
- Joshua D Wofford
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Naimah Bolaji
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Nathaniel Dziuba
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - F Wayne Outten
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Paul A Lindahl
- Department of Chemistry, Texas A&M University, College Station, Texas 77843; Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843.
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Chen KM, Tan J, Way GP, Doing G, Hogan DA, Greene CS. PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia. BioData Min 2018; 11:14. [PMID: 29988723 PMCID: PMC6029133 DOI: 10.1186/s13040-018-0175-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/18/2018] [Indexed: 12/29/2022] Open
Abstract
Background Investigators often interpret genome-wide data by analyzing the expression levels of genes within pathways. While this within-pathway analysis is routine, the products of any one pathway can affect the activity of other pathways. Past efforts to identify relationships between biological processes have evaluated overlap in knowledge bases or evaluated changes that occur after specific treatments. Individual experiments can highlight condition-specific pathway-pathway relationships; however, constructing a complete network of such relationships across many conditions requires analyzing results from many studies. Results We developed PathCORE-T framework by implementing existing methods to identify pathway-pathway transcriptional relationships evident across a broad data compendium. PathCORE-T is applied to the output of feature construction algorithms; it identifies pairs of pathways observed in features more than expected by chance as functionally co-occurring. We demonstrate PathCORE-T by analyzing an existing eADAGE model of a microbial compendium and building and analyzing NMF features from the TCGA dataset of 33 cancer types. The PathCORE-T framework includes a demonstration web interface, with source code, that users can launch to (1) visualize the network and (2) review the expression levels of associated genes in the original data. PathCORE-T creates and displays the network of globally co-occurring pathways based on features observed in a machine learning analysis of gene expression data. Conclusions The PathCORE-T framework identifies transcriptionally co-occurring pathways from the results of unsupervised analysis of gene expression data and visualizes the relationships between pathways as a network. PathCORE-T recapitulated previously described pathway-pathway relationships and suggested experimentally testable additional hypotheses that remain to be explored. Electronic supplementary material The online version of this article (10.1186/s13040-018-0175-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kathleen M Chen
- 1Department of Systems Pharmacology and Translational Therapeutics. Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104 USA
| | - Jie Tan
- 2Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | - Gregory P Way
- 1Department of Systems Pharmacology and Translational Therapeutics. Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104 USA
| | - Georgia Doing
- 3Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | - Deborah A Hogan
- 3Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | - Casey S Greene
- 1Department of Systems Pharmacology and Translational Therapeutics. Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104 USA
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The roles of two O-donor ligands in the Fe 2+-binding and H 2O 2-sensing by the Fe 2+-dependent H 2O 2 sensor PerR. Biochem Biophys Res Commun 2018; 501:458-464. [PMID: 29738773 DOI: 10.1016/j.bbrc.2018.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/02/2018] [Indexed: 01/18/2023]
Abstract
PerR is a metal-dependent peroxide sensing transcription factor which controls the expression of genes involved in peroxide resistance. The function of Bacillus subtilis PerR is mainly dictated by the regulatory metal ion (Fe2+ or Mn2+) coordinated by three N-donor ligands (His37, His91, and His93) and two O-donor ligands (Asp85 and Asp104). While H2O2 sensing by PerR is mediated by Fe2+-dependent oxidation of N-donor ligand (either His37 or His91), one of the O-donor ligands (Asp104), but not Asp85, has been proposed as the key residue that regulates the sensitivity of PerR to H2O2. Here we systematically investigated the relative roles of two O-donor ligands of PerR in metal-binding affinity and H2O2 sensitivity in vivo and in vitro. Consistent with the previous report, in vitro the D104E-PerR could not sense low levels of H2O2 in the presence of excess Fe2+ sufficient for the formation of the Fe2+-bound D104E-PerR. However, the expression of PerR-regulated reporter fusion was not repressed by D104E-PerR in the presence of Fe2+, suggesting that Fe2+ is not an effective corepressor for this mutant protein in vivo. Furthermore, in vitro metal titration assays indicate that D104E-PerR has a significantly reduced affinity for Fe2+, but not for Mn2+, when compared to wild type PerR. These data indicate that the type of O-donor ligand (Asp vs. Glu) at position 104 is an important determinant in providing high Fe2+-binding affinity required for the sensing of the physiologically relevant Fe2+-levels, in addition to its role in rendering PerR highly sensitive to physiological levels of H2O2. In comparison, the D85E-PerR did not show a perturbed change in Fe2+-binding affinity, however, it displayed a slightly decreased sensitivity to H2O2 both in vivo and in vitro, suggesting that the type of O-donor ligand (Asp vs. Glu) at position 85 may be important for the fine-tuning of H2O2 sensitivity.
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Sarvan S, Charih F, Askoura M, Butcher J, Brunzelle JS, Stintzi A, Couture JF. Functional insights into the interplay between DNA interaction and metal coordination in ferric uptake regulators. Sci Rep 2018; 8:7140. [PMID: 29739988 PMCID: PMC5940780 DOI: 10.1038/s41598-018-25157-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/11/2018] [Indexed: 12/19/2022] Open
Abstract
Ferric uptake regulators (Fur) are a family of transcription factors coupling gene regulatory events to metal concentration. Recent evidence has expanded the mechanistic repertoires employed by Fur to activate or repress gene expression in the presence or absence of regulatory metals. However, the mechanistic basis underlying this extended repertoire has remained largely unexplored. In this study, we used an extensive set of mutations to demonstrate that Campylobacter jejuni Fur (CjFur) employs the same surface to positively and negatively control gene expression regardless of the presence or absence of metals. Moreover, the crystal structure determination of a CjFur devoid of any regulatory metals shows that subtle reorientation of the transcription factor DNA binding domain negatively impacts DNA binding, gene expression and gut colonization in chickens. Overall, these results highlight the versatility of the CjFur DNA binding domain in mediating all gene regulatory events controlled by the metalloregulator and that the full metalation of CjFur is critical to the Campylobacter jejuni life cycle in vivo.
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Affiliation(s)
- Sabina Sarvan
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - François Charih
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Momen Askoura
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - James Butcher
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Joseph S Brunzelle
- Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois, 60611, USA
| | - Alain Stintzi
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.
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24
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Abstract
SIGNIFICANCE Since the discovery and structural characterization of bacillithiol (BSH), the biochemical functions of BSH-biosynthesis enzymes (BshA/B/C) and BSH-dependent detoxification enzymes (FosB, Bst, GlxA/B) have been explored in Bacillus and Staphylococcus species. It was shown that BSH plays an important role in detoxification of reactive oxygen and electrophilic species, alkylating agents, toxins, and antibiotics. Recent Advances: More recently, new functions of BSH were discovered in metal homeostasis (Zn buffering, Fe-sulfur cluster, and copper homeostasis) and virulence control in Staphylococcus aureus. Unexpectedly, strains of the S. aureus NCTC8325 lineage were identified as natural BSH-deficient mutants. Modern mass spectrometry-based approaches have revealed the global reach of protein S-bacillithiolation in Firmicutes as an important regulatory redox modification under hypochlorite stress. S-bacillithiolation of OhrR, MetE, and glyceraldehyde-3-phosphate dehydrogenase (Gap) functions, analogous to S-glutathionylation, as both a redox-regulatory device and in thiol protection under oxidative stress. CRITICAL ISSUES Although the functions of the bacilliredoxin (Brx) pathways in the reversal of S-bacillithiolations have been recently addressed, significantly more work is needed to establish the complete Brx reduction pathway, including the major enzyme(s), for reduction of oxidized BSH (BSSB) and the targets of Brx action in vivo. FUTURE DIRECTIONS Despite the large number of identified S-bacillithiolated proteins, the physiological relevance of this redox modification was shown for only selected targets and should be a subject of future studies. In addition, many more BSH-dependent detoxification enzymes are evident from previous studies, although their roles and biochemical mechanisms require further study. This review of BSH research also pin-points these missing gaps for future research. Antioxid. Redox Signal. 28, 445-462.
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Affiliation(s)
- Pete Chandrangsu
- 1 Department of Microbiology, Cornell University , Ithaca, New York
| | - Vu Van Loi
- 2 Institute for Biology-Microbiology , Freie Universität Berlin, Berlin, Germany
| | - Haike Antelmann
- 2 Institute for Biology-Microbiology , Freie Universität Berlin, Berlin, Germany
| | - John D Helmann
- 1 Department of Microbiology, Cornell University , Ithaca, New York
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25
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Osman D, Foster AW, Chen J, Svedaite K, Steed JW, Lurie-Luke E, Huggins TG, Robinson NJ. Fine control of metal concentrations is necessary for cells to discern zinc from cobalt. Nat Commun 2017; 8:1884. [PMID: 29192165 PMCID: PMC5709419 DOI: 10.1038/s41467-017-02085-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022] Open
Abstract
Bacteria possess transcription factors whose DNA-binding activity is altered upon binding to specific metals, but metal binding is not specific in vitro. Here we show that tight regulation of buffered intracellular metal concentrations is a prerequisite for metal specificity of Zur, ZntR, RcnR and FrmR in Salmonella Typhimurium. In cells, at non-inhibitory elevated concentrations, Zur and ZntR, only respond to Zn(II), RcnR to cobalt and FrmR to formaldehyde. However, in vitro all these sensors bind non-cognate metals, which alters DNA binding. We model the responses of these sensors to intracellular-buffered concentrations of Co(II) and Zn(II) based upon determined abundances, metal affinities and DNA affinities of each apo- and metalated sensor. The cognate sensors are modelled to respond at the lowest concentrations of their cognate metal, explaining specificity. However, other sensors are modelled to respond at concentrations only slightly higher, and cobalt or Zn(II) shock triggers mal-responses that match these predictions. Thus, perfect metal specificity is fine-tuned to a narrow range of buffered intracellular metal concentrations.
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Affiliation(s)
- Deenah Osman
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK.,Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Andrew W Foster
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK.,Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - Junjun Chen
- Procter and Gamble, Mason Business Center, Cincinnati, OH, 45040, USA
| | - Kotryna Svedaite
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK.,Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | | | - Elena Lurie-Luke
- Procter and Gamble, Singapore Innovation Center, Singapore, 138589, Singapore
| | - Thomas G Huggins
- Procter and Gamble, Mason Business Center, Cincinnati, OH, 45040, USA
| | - Nigel J Robinson
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK. .,Department of Chemistry, Durham University, Durham, DH1 3LE, UK.
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26
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Wedekind JE, Dutta D, Belashov IA, Jenkins JL. Metalloriboswitches: RNA-based inorganic ion sensors that regulate genes. J Biol Chem 2017; 292:9441-9450. [PMID: 28455443 DOI: 10.1074/jbc.r117.787713] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Divalent ions fulfill essential cellular roles and are required for virulence by certain bacteria. Free intracellular Mg2+ can approach 5 mm, but at this level Mn2+, Ni2+, or Co2+ can be growth-inhibitory, and magnesium fluoride is toxic. To maintain ion homeostasis, many bacteria have evolved ion sensors embedded in the 5'-leader sequences of mRNAs encoding ion uptake or efflux channels. Here, we review current insights into these "metalloriboswitches," emphasizing ion-specific binding by structured RNA aptamers and associated conformational changes in downstream signal sequences. This riboswitch-effector interplay produces a layer of gene regulatory feedback that has elicited interest as an antibacterial target.
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Affiliation(s)
- Joseph E Wedekind
- From the Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Debapratim Dutta
- From the Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Ivan A Belashov
- From the Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Jermaine L Jenkins
- From the Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
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27
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Chandrangsu P, Rensing C, Helmann JD. Metal homeostasis and resistance in bacteria. Nat Rev Microbiol 2017; 15:338-350. [PMID: 28344348 DOI: 10.1038/nrmicro.2017.15] [Citation(s) in RCA: 384] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metal ions are essential for many reactions, but excess metals can be toxic. In bacteria, metal limitation activates pathways that are involved in the import and mobilization of metals, whereas excess metals induce efflux and storage. In this Review, we highlight recent insights into metal homeostasis, including protein-based and RNA-based sensors that interact directly with metals or metal-containing cofactors. The resulting transcriptional response to metal stress takes place in a stepwise manner and is reinforced by post-transcriptional regulatory systems. Metal limitation and intoxication by the host are evolutionarily ancient strategies for limiting bacterial growth. The details of the resulting growth restriction are beginning to be understood and seem to be organism-specific.
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Affiliation(s)
- Pete Chandrangsu
- Department of Microbiology, Cornell University, Wing Hall, 123 Wing Drive, Ithaca, New York 14853, USA
| | - Christopher Rensing
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.,Department of Agricultural Resource and Environment, College of Resources and the Environment, Fujian Agriculture &Forestry University, Boxbue Building, 15 Shangxiadian Road, Cangshan District, Fuzhou, Fujian 350002, China.,J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Wing Hall, 123 Wing Drive, Ithaca, New York 14853, USA
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28
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Chandrangsu P, Helmann JD. Intracellular Zn(II) Intoxication Leads to Dysregulation of the PerR Regulon Resulting in Heme Toxicity in Bacillus subtilis. PLoS Genet 2016; 12:e1006515. [PMID: 27935957 PMCID: PMC5189952 DOI: 10.1371/journal.pgen.1006515] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/27/2016] [Accepted: 11/30/2016] [Indexed: 12/20/2022] Open
Abstract
Transition metal ions (Zn(II), Cu(II)/(I), Fe(III)/(II), Mn(II)) are essential for life and participate in a wide range of biological functions. Cellular Zn(II) levels must be high enough to ensure that it can perform its essential roles. Yet, since Zn(II) binds to ligands with high avidity, excess Zn(II) can lead to protein mismetallation. The major targets of mismetallation, and the underlying causes of Zn(II) intoxication, are not well understood. Here, we use a forward genetic selection to identify targets of Zn(II) toxicity. In wild-type cells, in which Zn(II) efflux prevents intoxication of the cytoplasm, extracellular Zn(II) inhibits the electron transport chain due to the inactivation of the major aerobic cytochrome oxidase. This toxicity can be ameliorated by depression of an alternate oxidase or by mutations that restrict access of Zn(II) to the cell surface. Conversely, efflux deficient cells are sensitive to low levels of Zn(II) that do not inhibit the respiratory chain. Under these conditions, intracellular Zn(II) accumulates and leads to heme toxicity. Heme accumulation results from dysregulation of the regulon controlled by PerR, a metal-dependent repressor of peroxide stress genes. When metallated with Fe(II) or Mn(II), PerR represses both heme biosynthesis (hemAXCDBL operon) and the abundant heme protein catalase (katA). Metallation of PerR with Zn(II) disrupts this coordination, resulting in depression of heme biosynthesis but continued repression of catalase. Our results support a model in which excess heme partitions to the membrane and undergoes redox cycling catalyzed by reduced menaquinone thereby resulting in oxidative stress.
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Affiliation(s)
- Pete Chandrangsu
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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29
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Shin JH, Helmann JD. Molecular logic of the Zur-regulated zinc deprivation response in Bacillus subtilis. Nat Commun 2016; 7:12612. [PMID: 27561249 PMCID: PMC5007448 DOI: 10.1038/ncomms12612] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/15/2016] [Indexed: 11/17/2022] Open
Abstract
Bacteria respond dynamically to the changes in zinc availability. Repression by the Bacillus subtilis transcription factor Zur requires Zn(II), which binds with negative cooperativity to two regulatory sites per dimer to form, sequentially, Zur2:Zn3 and Zur2:Zn4 forms of the repressor. Here we show that, as cells transition from zinc sufficiency to deficiency, operons regulated by Zur are derepressed in three distinct waves. The first includes the alternative RpmEB(L31*) and RpmGC(L33*) ribosomal proteins, which mobilize zinc from the ribosome, whereas the second includes the ZnuACB uptake system and the YciC metallochaperone. Finally, as zinc levels decrease further, the Zur2:Zn3 form loses Zn(II) leading to derepression of RpsNB(S14*) and FolE2, which allow continued ribosome assembly and folate synthesis, respectively. We infer that zinc mobilization from intracellular zinc stores takes priority over energy-dependent import, and our results link the biochemistry of zinc sensing by Zur to the molecular logic of the zinc deprivation response. The transcription factor Zur controls the zinc deprivation response in Bacillus subtilis. Here, Shin and Helmann show that Zur-regulated genes are derepressed in three waves in response to zinc deprivation, and this is linked to the biochemistry of zinc sensing by Zur.
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Affiliation(s)
- Jung-Ho Shin
- Department of Microbiology, Cornell University, Wing Hall, Ithaca, New York 14853-8101, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Wing Hall, Ithaca, New York 14853-8101, USA
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30
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Fang FC, Frawley ER, Tapscott T, Vázquez-Torres A. Discrimination and Integration of Stress Signals by Pathogenic Bacteria. Cell Host Microbe 2016; 20:144-153. [PMID: 27512902 PMCID: PMC5111874 DOI: 10.1016/j.chom.2016.07.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/23/2016] [Accepted: 07/26/2016] [Indexed: 02/08/2023]
Abstract
For pathogenic bacteria, the ability to sense and respond to environmental stresses encountered within the host is critically important, allowing them to adapt to changing conditions and express virulence genes appropriately. This review considers the diverse molecular mechanisms by which stress conditions are sensed by bacteria, how related signals are discriminated, and how stress responses are integrated, highlighting recent studies in selected bacterial pathogens of clinical relevance.
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Affiliation(s)
- Ferric C Fang
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Department Laboratory Medicine, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Elaine R Frawley
- Department Laboratory Medicine, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Timothy Tapscott
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Andrés Vázquez-Torres
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
- Veterans Affairs Eastern Colorado Health Care System, 1055 Clermont Street, Denver, CO 80220, USA
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31
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Abstract
Pathogenic bacteria must withstand diverse host environments during infection. Environmental signals, such as pH, temperature, nutrient limitation, etc., not only trigger adaptive responses within bacteria to these specific stress conditions but also direct the expression of virulence genes at an appropriate time and place. An appreciation of stress responses and their regulation is therefore essential for an understanding of bacterial pathogenesis. This review considers specific stresses in the host environment and their relevance to pathogenesis, with a particular focus on the enteric pathogen Salmonella.
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Affiliation(s)
- Ferric C Fang
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195-7735, USA; Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, WA 98195-7735, USA.
| | - Elaine R Frawley
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, WA 98195-7735, USA
| | - Timothy Tapscott
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Andrés Vázquez-Torres
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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32
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Capdevila DA, Wang J, Giedroc DP. Bacterial Strategies to Maintain Zinc Metallostasis at the Host-Pathogen Interface. J Biol Chem 2016; 291:20858-20868. [PMID: 27462080 DOI: 10.1074/jbc.r116.742023] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Among the biologically required first row, late d-block metals from MnII to ZnII, the catalytic and structural reach of ZnII ensures that this essential micronutrient touches nearly every major metabolic process or pathway in the cell. Zn is also toxic in excess, primarily because it is a highly competitive divalent metal and will displace more weakly bound transition metals in the active sites of metalloenzymes if left unregulated. The vertebrate innate immune system uses several strategies to exploit this "Achilles heel" of microbial physiology, but bacterial evolution has responded in kind. This review highlights recent insights into transcriptional, transport, and trafficking mechanisms that pathogens use to "win the fight" over zinc and thrive in an otherwise hostile environment.
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Affiliation(s)
- Daiana A Capdevila
- From the Departments of Chemistry and the Departamento de Quimica Inorganica, Analitica y Quimica Fisica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
| | - Jiefei Wang
- From the Departments of Chemistry and Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405-7102 and
| | - David P Giedroc
- From the Departments of Chemistry and Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405-7102 and
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33
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Kim JH, Ji CJ, Ju SY, Yang YM, Ryu SH, Kwon Y, Won YB, Lee YE, Youn H, Lee JW. Bacillus licheniformis Contains Two More PerR-Like Proteins in Addition to PerR, Fur, and Zur Orthologues. PLoS One 2016; 11:e0155539. [PMID: 27176811 PMCID: PMC4866751 DOI: 10.1371/journal.pone.0155539] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/29/2016] [Indexed: 11/18/2022] Open
Abstract
The ferric uptake regulator (Fur) family proteins include sensors of Fe (Fur), Zn (Zur), and peroxide (PerR). Among Fur family proteins, Fur and Zur are ubiquitous in most prokaryotic organisms, whereas PerR exists mainly in Gram positive bacteria as a functional homologue of OxyR. Gram positive bacteria such as Bacillus subtilis, Listeria monocytogenes and Staphylococcus aureus encode three Fur family proteins: Fur, Zur, and PerR. In this study, we identified five Fur family proteins from B. licheniformis: two novel PerR-like proteins (BL00690 and BL00950) in addition to Fur (BL05249), Zur (BL03703), and PerR (BL00075) homologues. Our data indicate that all of the five B. licheniformis Fur homologues contain a structural Zn2+ site composed of four cysteine residues like many other Fur family proteins. Furthermore, we provide evidence that the PerR-like proteins (BL00690 and BL00950) as well as PerRBL (BL00075), but not FurBL (BL05249) and ZurBL (BL03703), can sense H2O2 by histidine oxidation with different sensitivity. We also show that PerR2 (BL00690) has a PerR-like repressor activity for PerR-regulated genes in vivo. Taken together, our results suggest that B. licheniformis contains three PerR subfamily proteins which can sense H2O2 by histidine oxidation not by cysteine oxidation, in addition to Fur and Zur.
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Affiliation(s)
- Jung-Hoon Kim
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Chang-Jun Ji
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Shin-Yeong Ju
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Yoon-Mo Yang
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Su-Hyun Ryu
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Yumi Kwon
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Young-Bin Won
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Yeh-Eun Lee
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Hwan Youn
- Department of Biology, California State University Fresno, Fresno, California, 93740–8034, United States of America
| | - Jin-Won Lee
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
- * E-mail:
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34
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Mn(2+)-sensing mechanisms of yybP-ykoY orphan riboswitches. Mol Cell 2016; 57:1110-1123. [PMID: 25794619 DOI: 10.1016/j.molcel.2015.02.016] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/30/2015] [Accepted: 02/09/2015] [Indexed: 02/05/2023]
Abstract
Gene regulation in cis by riboswitches is prevalent in bacteria. The yybP-ykoY riboswitch family is quite widespread, yet its ligand and function remained unknown. Here, we characterize the Lactococcus lactis yybP-ykoY orphan riboswitch as a Mn(2+)-dependent transcription-ON riboswitch, with a ∼30-40 μM affinity for Mn(2+). We further determined its crystal structure at 2.7 Å to elucidate the metal sensing mechanism. The riboswitch resembles a hairpin, with two coaxially stacked helices tethered by a four-way junction and a tertiary docking interface. The Mn(2+)-sensing region, strategically located at the highly conserved docking interface, has two metal binding sites. Whereas one site tolerates the binding of either Mg(2+) or Mn(2+), the other site strongly prefers Mn(2+) due to a direct contact from the N7 of an invariable adenosine. Mutagenesis and a Mn(2+)-free E. coli yybP-ykoY structure further reveal that Mn(2+) binding is coupled with stabilization of the Mn(2+)-sensing region and the aptamer domain.
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35
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Pi H, Patel SJ, Argüello JM, Helmann JD. The Listeria monocytogenes Fur-regulated virulence protein FrvA is an Fe(II) efflux P1B4 -type ATPase. Mol Microbiol 2016; 100:1066-79. [PMID: 26946370 DOI: 10.1111/mmi.13368] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2016] [Indexed: 01/07/2023]
Abstract
Listeria monocytogenes FrvA (Lmo0641) is critical for virulence in the mouse model and is an ortholog of the Bacillus subtilis Fur- and PerR-regulated Fe(II) efflux P1B4 -type ATPase PfeT. Previously, FrvA was suggested to protect against heme toxicity. Here, we demonstrate that an frvA mutant is sensitive to iron intoxication, but not to other metals. Expression of frvA is induced by high iron and this induction requires Fur. FrvA functions in vitro as a divalent cation specific ATPase most strongly activated by ferrous iron. When expressed in B. subtilis, FrvA increases resistance to iron both in wild-type and in a pfeT null strain. FrvA is a high affinity Fe(II) exporter and its induction imposes severe iron limitation in B. subtilis resulting in derepression of both Fur- and PerR-regulated genes. FrvA also recognizes Co(II) and Zn(II) as substrates and can complement B. subtilis strains defective in the endogenous export systems for these cations. Building on these results, we conclude that FrvA functions in the efflux of Fe(II), and not heme during listerial infection.
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Affiliation(s)
- Hualiang Pi
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Sarju J Patel
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - José M Argüello
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
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36
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Guan G, Pinochet-Barros A, Gaballa A, Patel SJ, Argüello JM, Helmann JD. PfeT, a P1B4 -type ATPase, effluxes ferrous iron and protects Bacillus subtilis against iron intoxication. Mol Microbiol 2015; 98:787-803. [PMID: 26261021 DOI: 10.1111/mmi.13158] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2015] [Indexed: 11/30/2022]
Abstract
Iron is an essential element for nearly all cells and limited iron availability often restricts growth. However, excess iron can also be deleterious, particularly when cells expressing high affinity iron uptake systems transition to iron rich environments. Bacillus subtilis expresses numerous iron importers, but iron efflux has not been reported. Here, we describe the B. subtilis PfeT protein (formerly YkvW/ZosA) as a P1B4 -type ATPase in the PerR regulon that serves as an Fe(II) efflux pump and protects cells against iron intoxication. Iron and manganese homeostasis in B. subtilis are closely intertwined: a pfeT mutant is iron sensitive, and this sensitivity can be suppressed by low levels of Mn(II). Conversely, a pfeT mutant is more resistant to Mn(II) overload. In vitro, the PfeT ATPase is activated by both Fe(II) and Co(II), although only Fe(II) efflux is physiologically relevant in wild-type cells, and null mutants accumulate elevated levels of intracellular iron. Genetic studies indicate that PfeT together with the ferric uptake repressor (Fur) cooperate to prevent iron intoxication, with iron sequestration by the MrgA mini-ferritin playing a secondary role. Protection against iron toxicity may also be a key role for related P1B4 -type ATPases previously implicated in bacterial pathogenesis.
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Affiliation(s)
- Guohua Guan
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA.,State Key Laboratories for Agro-biotechnology and College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | | | - Ahmed Gaballa
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Sarju J Patel
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - José M Argüello
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
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Osman D, Piergentili C, Chen J, Chakrabarti B, Foster AW, Lurie-Luke E, Huggins TG, Robinson NJ. Generating a Metal-responsive Transcriptional Regulator to Test What Confers Metal Sensing in Cells. J Biol Chem 2015; 290:19806-22. [PMID: 26109070 PMCID: PMC4528141 DOI: 10.1074/jbc.m115.663427] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Indexed: 11/06/2022] Open
Abstract
FrmR from Salmonella enterica serovar typhimurium (a CsoR/RcnR-like transcriptional de-repressor) is shown to repress the frmRA operator-promoter, and repression is alleviated by formaldehyde but not manganese, iron, cobalt, nickel, copper, or Zn(II) within cells. In contrast, repression by a mutant FrmRE64H (which gains an RcnR metal ligand) is alleviated by cobalt and Zn(II). Unexpectedly, FrmR was found to already bind Co(II), Zn(II), and Cu(I), and moreover metals, as well as formaldehyde, trigger an allosteric response that weakens DNA affinity. However, the sensory metal sites of the cells' endogenous metal sensors (RcnR, ZntR, Zur, and CueR) are all tighter than FrmR for their cognate metals. Furthermore, the endogenous metal sensors are shown to out-compete FrmR. The metal-sensing FrmRE64H mutant has tighter metal affinities than FrmR by approximately 1 order of magnitude. Gain of cobalt sensing by FrmRE64H remains enigmatic because the cobalt affinity of FrmRE64H is substantially weaker than that of the endogenous cobalt sensor. Cobalt sensing requires glutathione, which may assist cobalt access, conferring a kinetic advantage. For Zn(II), the metal affinity of FrmRE64H approaches the metal affinities of cognate Zn(II) sensors. Counter-intuitively, the allosteric coupling free energy for Zn(II) is smaller in metal-sensing FrmRE64H compared with nonsensing FrmR. By determining the copies of FrmR and FrmRE64H tetramers per cell, then estimating promoter occupancy as a function of intracellular Zn(II) concentration, we show how a modest tightening of Zn(II) affinity, plus weakened DNA affinity of the apoprotein, conspires to make the relative properties of FrmRE64H (compared with ZntR and Zur) sufficient to sense Zn(II) inside cells.
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Affiliation(s)
- Deenah Osman
- From the School of Biological and Biomedical Sciences and Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Cecilia Piergentili
- From the School of Biological and Biomedical Sciences and Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Junjun Chen
- Procter and Gamble, Mason Business Centre, Cincinnati, Ohio 45040, and
| | - Buddhapriya Chakrabarti
- From the School of Biological and Biomedical Sciences and Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Andrew W Foster
- From the School of Biological and Biomedical Sciences and Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Elena Lurie-Luke
- Life Sciences Open Innovation, London Innovation Centre, Procter and Gamble Technical Centres, Ltd., Egham TW20 9NW, United Kingdom
| | - Thomas G Huggins
- Procter and Gamble, Mason Business Centre, Cincinnati, Ohio 45040, and
| | - Nigel J Robinson
- From the School of Biological and Biomedical Sciences and Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom,
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Butler CA, Dashper SG, Khan HS, Zhang L, Reynolds EC. The interplay between iron, haem and manganese in Porphyromonas gingivalis. J Oral Biosci 2015. [DOI: 10.1016/j.job.2014.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Furnholm TR, Tisa LS. The ins and outs of metal homeostasis by the root nodule actinobacterium Frankia. BMC Genomics 2014; 15:1092. [PMID: 25495525 PMCID: PMC4531530 DOI: 10.1186/1471-2164-15-1092] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Frankia are actinobacteria that form a symbiotic nitrogen-fixing association with actinorhizal plants, and play a significant role in actinorhizal plant colonization of metal contaminated areas. Many Frankia strains are known to be resistant to several toxic metals and metalloids including Pb(2+), Al(+3), SeO2, Cu(2+), AsO4, and Zn(2+). With the availability of eight Frankia genome databases, comparative genomics approaches employing phylogeny, amino acid composition analysis, and synteny were used to identify metal homeostasis mechanisms in eight Frankia strains. Characterized genes from the literature and a meta-analysis of 18 heavy metal gene microarray studies were used for comparison. RESULTS Unlike most bacteria, Frankia utilize all of the essential trace elements (Ni, Co, Cu, Se, Mo, B, Zn, Fe, and Mn) and have a comparatively high percentage of metalloproteins, particularly in the more metal resistant strains. Cation diffusion facilitators, being one of the few known metal resistance mechanisms found in the Frankia genomes, were strong candidates for general divalent metal resistance in all of the Frankia strains. Gene duplication and amino acid substitutions that enhanced the metal affinity of CopA and CopCD proteins may be responsible for the copper resistance found in some Frankia strains. CopA and a new potential metal transporter, DUF347, may be involved in the particularly high lead tolerance in Frankia. Selenite resistance involved an alternate sulfur importer (CysPUWA) that prevents sulfur starvation, and reductases to produce elemental selenium. The pattern of arsenate, but not arsenite, resistance was achieved by Frankia using the novel arsenite exporter (AqpS) previously identified in the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Based on the presence of multiple tellurite resistance factors, a new metal resistance (tellurite) was identified and confirmed in Frankia. CONCLUSIONS Each strain had a unique combination of metal import, binding, modification, and export genes that explain differences in patterns of metal resistance between strains. Frankia has achieved similar levels of metal and metalloid resistance as bacteria from highly metal-contaminated sites. From a bioremediation standpoint, it is important to understand mechanisms that allow the endosymbiont to survive and infect actinorhizal plants in metal contaminated soils.
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Affiliation(s)
- Teal R Furnholm
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
| | - Louis S Tisa
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
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Abstract
The metal binding preferences of most metalloproteins do not match their metal requirements. Thus, metallation of an estimated 30% of metalloenzymes is aided by metal delivery systems, with ∼ 25% acquiring preassembled metal cofactors. The remaining ∼ 70% are presumed to compete for metals from buffered metal pools. Metallation is further aided by maintaining the relative concentrations of these pools as an inverse function of the stabilities of the respective metal complexes. For example, magnesium enzymes always prefer to bind zinc, and these metals dominate the metalloenzymes without metal delivery systems. Therefore, the buffered concentration of zinc is held at least a million-fold below magnesium inside most cells.
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Affiliation(s)
- Andrew W Foster
- From the Department of Chemistry and School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Deenah Osman
- From the Department of Chemistry and School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Nigel J Robinson
- From the Department of Chemistry and School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
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Mazzon RR, Braz VS, da Silva Neto JF, do Valle Marques M. Analysis of the Caulobacter crescentus Zur regulon reveals novel insights in zinc acquisition by TonB-dependent outer membrane proteins. BMC Genomics 2014; 15:734. [PMID: 25168179 PMCID: PMC4176598 DOI: 10.1186/1471-2164-15-734] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 08/21/2014] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Intracellular zinc concentration needs to be maintained within strict limits due to its toxicity at high levels, and this is achieved by a finely regulated balance between uptake and efflux. Many bacteria use the Zinc Uptake Regulator Zur to orchestrate zinc homeostasis, but little is known regarding the transport of this metal across the bacterial outer membrane. RESULTS In this work we determined the Caulobacter crescentus Zur regulon by global transcriptional and in silico analyses. Among the genes directly repressed by Zur in response to zinc availability are those encoding a putative high affinity ABC uptake system (znuGHI), three TonB-dependent receptors (znuK, znuL and znuM) and one new putative transporter of a family not yet characterized (zrpW). Zur is also directly involved in the activation of a RND and a P-type ATPase efflux systems, as revealed by β-galactosidase and site-directed mutagenesis assays. Several genes belonging to the Fur regulon were also downregulated in the zur mutant, suggesting a putative cross-talk between Zur and Fur regulatory networks. Interestingly, a phenotypic analysis of the znuK and znuL mutants has shown that these genes are essential for growth under zinc starvation, suggesting that C. crescentus uses these TonB-dependent outer membrane transporters as key zinc scavenging systems. CONCLUSIONS The characterization of the C. crescentus Zur regulon showed that this regulator coordinates not only uptake, but also the extrusion of zinc. The uptake of zinc by C. crescentus in conditions of scarcity of this metal is highly dependent on TonB-dependent receptors, and the extrusion is mediated by an RND and P-type ATPase transport systems. The absence of Zur causes a disturbance in the dynamic equilibrium of zinc intracellular concentration, which in turn can interfere with other regulatory networks as seen for the Fur regulon.
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Affiliation(s)
| | | | | | - Marilis do Valle Marques
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av, Prof, Lineu Prestes 1374, 05508-900 São Paulo, Brazil.
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42
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Helmann JD. Specificity of metal sensing: iron and manganese homeostasis in Bacillus subtilis. J Biol Chem 2014; 289:28112-20. [PMID: 25160631 DOI: 10.1074/jbc.r114.587071] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Metalloregulatory proteins allow cells to sense metal ions and appropriately adjust the expression of metal uptake, storage, and efflux pathways. Bacillus subtilis provides a model for the coordinate regulation of iron and manganese homeostasis that involves three key regulators: Fur senses iron sufficiency, MntR senses manganese sufficiency, and PerR senses the intracellular Fe/Mn ratio. Here, I review the structural and physiological bases of selective metal perception, the effects of non-cognate metals, and mechanisms that may serve to coordinate iron and manganese homeostasis.
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Affiliation(s)
- John D Helmann
- From the Department of Microbiology, Cornell University, Ithaca, New York 14853-8101
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Abstract
Mononuclear iron enzymes can tightly bind non-activating metals. How do cells avoid mismetallation? The model bacterium Escherichia coli may control its metal pools so that thermodynamics favor the correct metallation of each enzyme. This system is disrupted, however, by superoxide and hydrogen peroxide. These species oxidize ferrous iron and thereby displace it from many iron-dependent mononuclear enzymes. Ultimately, zinc binds in its place, confers little activity, and imposes metabolic bottlenecks. Data suggest that E. coli compensates by using thiols to extract the zinc and by importing manganese to replace the catalytic iron atom. Manganese resists oxidants and provides substantial activity.
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Affiliation(s)
- James A Imlay
- From the Department of Microbiology, University of Illinois, Urbana, Illinois 61801
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Bobrov AG, Kirillina O, Fetherston JD, Miller MC, Burlison JA, Perry RD. The Yersinia pestis siderophore, yersiniabactin, and the ZnuABC system both contribute to zinc acquisition and the development of lethal septicaemic plague in mice. Mol Microbiol 2014; 93:759-75. [PMID: 24979062 DOI: 10.1111/mmi.12693] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2014] [Indexed: 01/06/2023]
Abstract
Bacterial pathogens must overcome host sequestration of zinc (Zn(2+) ), an essential micronutrient, during the infectious disease process. While the mechanisms to acquire chelated Zn(2+) by bacteria are largely undefined, many pathogens rely upon the ZnuABC family of ABC transporters. Here we show that in Yersinia pestis, irp2, a gene encoding the synthetase (HMWP2) for the siderophore yersiniabactin (Ybt) is required for growth under Zn(2+) -deficient conditions in a strain lacking ZnuABC. Moreover, growth stimulation with exogenous, purified apo-Ybt provides evidence that Ybt may serve as a zincophore for Zn(2+) acquisition. Studies with the Zn(2+) -dependent transcriptional reporter znuA::lacZ indicate that the ability to synthesize Ybt affects the levels of intracellular Zn(2+) . However, the outer membrane receptor Psn and TonB as well as the inner membrane (IM) ABC transporter YbtPQ, which are required for Fe(3+) acquisition by Ybt, are not needed for Ybt-dependent Zn(2+) uptake. In contrast, the predicted IM protein YbtX, a member of the Major Facilitator Superfamily, was essential for Ybt-dependent Zn(2+) uptake. Finally, we show that the ZnuABC system and the Ybt synthetase HMWP2, presumably by Ybt synthesis, both contribute to the development of a lethal infection in a septicaemic plague mouse model.
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Affiliation(s)
- Alexander G Bobrov
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY, USA
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45
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Foster AW, Pernil R, Patterson CJ, Robinson NJ. Metal specificity of cyanobacterial nickel-responsive repressor InrS: cells maintain zinc and copper below the detection threshold for InrS. Mol Microbiol 2014; 92:797-812. [PMID: 24666373 PMCID: PMC4235346 DOI: 10.1111/mmi.12594] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2014] [Indexed: 12/25/2022]
Abstract
InrS is a Ni(II)-responsive, CsoR/RcnR-like, DNA-binding transcriptional repressor of the nrsD gene, but the Ni(II) co-ordination sphere of InrS is unlike Ni(II)-RcnR. We show that copper and Zn(II) also bind tightly to InrS and in vitro these ions also impair InrS binding to the nrsD operator-promoter. InrS does not respond to Zn(II) (or copper) in vivo after 48 h, when Zn(II) sensor ZiaR responds, but InrS transiently responds (1 h) to both metals. InrS conserves only one (of two) second co-ordination shell residues of CsoR (Glu98 in InrS). The allosteric mechanism of InrS is distinct from Cu(I)-CsoR and conservation of deduced second shell residues better predicts metal specificity than do the metal ligands. The allosteric mechanism of InrS permits greater promiscuity in vitro than CsoR. The factors dictating metal-selectivity in vivo are that KNi(II) and ΔGCNi(II)-InrS·DNA are sufficiently high, relative to other metal sensors, for InrS to detect Ni(II), while the equivalent parameters for copper may be insufficient for copper-sensing in S ynechocystis (at 48 h). InrS KZn(II) (5.6 × 10−13 M) is comparable to the sensory sites of ZiaR (and Zur), but ΔGCZn(II)-InrS·DNA is less than ΔGCZn(II)-ZiaR·DNA implying that relative to other sensors, ΔGCZn(II)-Sensor·DNA rather than KZn(II) determines the final detection threshold for Zn(II).
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Affiliation(s)
- Andrew W Foster
- Department of Chemistry, School of Biological and Biomedical Sciences, Durham University, Durham, DH1 3LE, UK
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46
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Lisher JP, Giedroc DP. Manganese acquisition and homeostasis at the host-pathogen interface. Front Cell Infect Microbiol 2013; 3:91. [PMID: 24367765 PMCID: PMC3851752 DOI: 10.3389/fcimb.2013.00091] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 11/18/2013] [Indexed: 11/21/2022] Open
Abstract
Pathogenic bacteria acquire transition metals for cell viability and persistence of infection in competition with host nutritional defenses. The human host employs a variety of mechanisms to stress the invading pathogen with both cytotoxic metal ions and oxidative and nitrosative insults while withholding essential transition metals from the bacterium. For example, the S100 family protein calprotectin (CP) found in neutrophils is a calcium-activated chelator of extracellular Mn and Zn and is found in tissue abscesses at sites of infection by Staphylococcus aureus. In an adaptive response, bacteria have evolved systems to acquire the metals in the face of this competition while effluxing excess or toxic metals to maintain a bioavailability of transition metals that is consistent with a particular inorganic "fingerprint" under the prevailing conditions. This review highlights recent biological, chemical and structural studies focused on manganese (Mn) acquisition and homeostasis and connects this process to oxidative stress resistance and iron (Fe) availability that operates at the human host-pathogen interface.
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Affiliation(s)
- John P. Lisher
- Graduate Program in Biochemistry, Indiana UniversityBloomington, IN, USA
| | - David P. Giedroc
- Graduate Program in Biochemistry, Indiana UniversityBloomington, IN, USA
- Department of Chemistry, Indiana UniversityBloomington, IN, USA
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47
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Experimental phasing using zinc and sulfur anomalous signals measured at the zinc absorption peak. J Microbiol 2013; 51:639-43. [PMID: 24173644 DOI: 10.1007/s12275-013-3412-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 08/27/2013] [Indexed: 10/26/2022]
Abstract
Iron is an essential transition metal required for bacterial growth and survival. Excess free iron can lead to the generation of reactive oxygen species that can cause severe damage to cellular functions. Cells have developed iron-sensing regulators to maintain iron homeostasis at the transcription level. The ferric uptake regulator (Fur) is an iron-responsive regulator that controls the expression of genes involved in iron homeostasis, bacterial virulence, stress resistance, and redox metabolism. Here, we report the expression, purification, crystallization, and phasing of the apo-form of Bacillus subtilis Fur (BsFur) in the absence of regulatory metal ions. Crystals were obtained by microbatch crystallization method at 295 K and diffraction data at a resolution of 2.6 Å was collected at the zinc peak wavelength (λ=1.2823 Å). Experimental phasing identified the positions of one zinc atom and four sulfur atoms of cysteine residues coordinating the zinc atom, indicating that the data contained a meaningful anomalous scattering originating from the ordered zinc-coordinating sulfur atoms, in spite of the small anomalous signals of sulfur atoms at the examined wavelength.
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48
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Lisher JP, Higgins KA, Maroney MJ, Giedroc DP. Physical characterization of the manganese-sensing pneumococcal surface antigen repressor from Streptococcus pneumoniae. Biochemistry 2013; 52:7689-701. [PMID: 24067066 DOI: 10.1021/bi401132w] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Transition metals, including manganese, are required for the proper virulence and persistence of many pathogenic bacteria. In Streptococcus pneumoniae (Spn), manganese homeostasis is controlled by a high-affinity Mn(II) uptake complex, PsaBCA, and a constitutively expressed efflux transporter, MntE. psaBCA expression is transcriptionally regulated by the DtxR/MntR family metalloregulatory protein pneumococcal surface antigen repressor (PsaR) in Spn. Here, we present a comprehensive analysis of the metal and DNA binding properties of PsaR. PsaR is a homodimer in the absence and presence of metals and binds two manganese or zinc atoms per protomer (four per dimer) in two pairs of structurally distinct sites, termed site 1 and site 2. Site 1 is likely filled with Zn(II) in vivo (K(Zn1) ≥ 10¹³ M⁻¹; K(Mn1) ≈ 10⁸ M⁻¹). The Zn(II)-site 1 complex adopts a pentacoordinate geometry as determined by X-ray absorption spectroscopy containing a single cysteine and appears to be analogous to the Cd(II) site observed in Streptococcus gordonii ScaR. Site 1 is necessary but not sufficient for full positive allosteric activation of DNA operator binding by metals as measured by ΔGc, the allosteric coupling free energy, because site 1 mutants show an intermediate ΔGc. Site 2 is the primary regulatory site and governs specificity for Mn(II) over Zn(II) in PsaR, where ΔGc(Zn,Mn) >> ΔGc(Zn,Zn) despite the fact that Zn(II) binds site 2 with an affinity 40-fold higher than that of Mn(II); i.e., K(Zn2) > K(Mn2). Mutational studies reveal that Asp7 in site 2 is a critical ligand for Mn(II)-dependent allosteric activation of DNA binding. These findings are discussed in the context of other well-studied DtxR/MntR Mn(II)/Fe(II) metallorepressors.
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Affiliation(s)
- John P Lisher
- Department of Chemistry and ‡Interdisciplinary Graduate Program in Biochemistry, Indiana University , Bloomington, Indiana 47405-7102, United States
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49
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Gilbreath JJ, Pich OQ, Benoit SL, Besold AN, Cha JH, Maier RJ, Michel SLJ, Maynard EL, Merrell DS. Random and site-specific mutagenesis of the Helicobacter pylori ferric uptake regulator provides insight into Fur structure-function relationships. Mol Microbiol 2013; 89:304-23. [PMID: 23710935 DOI: 10.1111/mmi.12278] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2013] [Indexed: 12/29/2022]
Abstract
The ferric uptake regulator (Fur) of Helicobacter pylori is a global regulator that is important for colonization and survival within the gastric mucosa. H. pylori Fur is unique in its ability to activate and repress gene expression in both the iron-bound (Fe-Fur) and apo forms (apo-Fur). In the current study we combined random and site-specific mutagenesis to identify amino acid residues important for both Fe-Fur and apo-Fur function. We identified 25 mutations that affected Fe-Fur repression and 23 mutations that affected apo-Fur repression, as determined by transcriptional analyses of the Fe-Fur target gene amiE, and the apo-Fur target gene, pfr. In addition, eight of these mutations also significantly affected levels of Fur in the cell. Based on regulatory phenotypes, we selected several representative mutations to characterize further. Of those selected, we purified the wild-type (HpFurWT) and three mutant Fur proteins (HpFurE5A, HpFurA92T and HpFurH134Y), which represent mutations in the N-terminal extension, the regulatory metal binding site (S2) and the structural metal binding site (S3) respectively. Purified proteins were evaluated for secondary structure by circular dichroism spectroscopy, iron-binding by atomic absorption spectrophotometry, oligomerization in manganese-substituted and apo conditions by in vitro cross-linking assays, and DNA binding to Fe-Fur and apo-Fur target sequences by fluorescence anisotropy. The results showed that the N-terminal, S2 and S3 regions play distinct roles in terms of Fur structure-function relationships. Overall, these studies provide novel information regarding the role of these residues in Fur function, and provide mechanistic insight into how H. pylori Fur regulates gene expression in both the iron-bound and apo forms of the protein.
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Affiliation(s)
- Jeremy J Gilbreath
- Department of Microbiology and Immunology, Uniformed Services University of Health Sciences, Bethesda, MD, USA
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50
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McGuire AM, Cuthbert BJ, Ma Z, Grauer-Gray KD, Brunjes Brophy M, Spear KA, Soonsanga S, Kliegman JI, Griner SL, Helmann JD, Glasfeld A. Roles of the A and C sites in the manganese-specific activation of MntR. Biochemistry 2013; 52:701-13. [PMID: 23298157 DOI: 10.1021/bi301550t] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The manganese transport regulator (MntR) represses the expression of genes involved in manganese uptake in Bacillus subtilis. It selectively responds to Mn(2+) and Cd(2+) over other divalent metal cations, including Fe(2+), Co(2+), and Zn(2+). Previous work has shown that MntR forms binuclear complexes with Mn(2+) or Cd(2+) at two binding sites, labeled A and C, that are separated by 4.4 Å. Zinc activates MntR poorly and binds only to the A site, forming a mononuclear complex. The difference in metal binding stoichiometry suggested a mechanism for selectivity in MntR. Larger metal cations are strongly activating because they can form the binuclear complex, while smaller metal ions cannot bind with the geometry needed to fully occupy both metal binding sites. To investigate this hypothesis, structures of MntR in complex with two other noncognate metal ions, Fe(2+) and Co(2+), have been determined. Each metal forms a mononuclear complex with MntR with the metal ion bound in the A site, supporting the conclusions drawn from the Zn(2+) complex. Additionally, we investigated two site-specific mutants of MntR, E11K and H77A, that contain substitutions of metal binding residues in the A site. While metal binding in each mutant is significantly altered relative to that of wild-type MntR, both mutants retain activity and selectivity for Mn(2+) in vitro and in vivo. That observation, coupled with previous studies, suggests that the A and C sites both contribute to the selectivity of MntR.
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