1
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Williams LJ, Tristram SG, Zosky GR. Geogenic particles induce bronchial susceptibility to non-typeable Haemophilus influenzae. ENVIRONMENTAL RESEARCH 2023; 236:116868. [PMID: 37567381 DOI: 10.1016/j.envres.2023.116868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Exposure to geogenic (earth-derived) particulate matter (PM) is linked to an increased prevalence of bronchiectasis and other respiratory infections in Australian Indigenous communities. Experimental studies have shown that the concentration of iron in geogenic PM is associated with the magnitude of respiratory health effects, however, the mechanism is unclear. We investigated the effect of geogenic PM and iron oxide on the invasiveness of non-typeable Haemophilus influenzae (NTHi). Peripheral blood mononuclear cell-derived macrophages or epithelial cell lines (A549 & BEAS-2B) were exposed to whole geogenic PM, their primary constituents (haematite, magnetite or silica) or diesel exhaust particles (DEP). The uptake of bacteria was quantified by flow cytometry and whole genome sequencing (WGS) was performed on NTHi strains. Geogenic PM increased the invasiveness of NTHi in bronchial epithelial cells. Of the primary constituents, haematite also increased NTHi invasion with magnetite and silica having significantly less impact. Furthermore, we observed varying levels of invasiveness amongst NTHi isolates. WGS analysis suggested isolates with more genes associated with heme acquisition were more virulent in BEAS-2B cells. The present study suggests that geogenic particles can increase the susceptibility of bronchial epithelial cells to select bacterial pathogens in vitro, a response primarily driven by haematite content in the dust. This demonstrates a potential mechanism linking exposure to iron-laden geogenic PM and high rates of chronic respiratory infections in remote communities in arid environments.
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Affiliation(s)
- Lewis J Williams
- Tasmanian School of Medicine, University of Tasmania, Hobart, 7000, Australia
| | - Stephen G Tristram
- School of Health Sciences, University of Tasmania, Launceston, 7250, Australia
| | - Graeme R Zosky
- Tasmanian School of Medicine, University of Tasmania, Hobart, 7000, Australia; Menzies Institute for Medical Research, University of Tasmania, Hobart, 7000, Australia.
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2
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Sankari S, Babu VM, Bian K, Alhhazmi A, Andorfer MC, Avalos DM, Smith TA, Yoon K, Drennan CL, Yaffe MB, Lourido S, Walker GC. A haem-sequestering plant peptide promotes iron uptake in symbiotic bacteria. Nat Microbiol 2022; 7:1453-1465. [PMID: 35953657 PMCID: PMC9420810 DOI: 10.1038/s41564-022-01192-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/29/2022] [Indexed: 11/09/2022]
Abstract
Symbiotic partnerships with rhizobial bacteria enable legumes to grow without nitrogen fertilizer because rhizobia convert atmospheric nitrogen gas into ammonia via nitrogenase. After Sinorhizobium meliloti penetrate the root nodules that they have elicited in Medicago truncatula, the plant produces a family of about 700 nodule cysteine-rich (NCR) peptides that guide the differentiation of endocytosed bacteria into nitrogen-fixing bacteroids. The sequences of the NCR peptides are related to the defensin class of antimicrobial peptides, but have been adapted to play symbiotic roles. Using a variety of spectroscopic, biophysical and biochemical techniques, we show here that the most extensively characterized NCR peptide, 24 amino acid NCR247, binds haem with nanomolar affinity. Bound haem molecules and their iron are initially made biologically inaccessible through the formation of hexamers (6 haem/6 NCR247) and then higher-order complexes. We present evidence that NCR247 is crucial for effective nitrogen-fixing symbiosis. We propose that by sequestering haem and its bound iron, NCR247 creates a physiological state of haem deprivation. This in turn induces an iron-starvation response in rhizobia that results in iron import, which itself is required for nitrogenase activity. Using the same methods as for L-NCR247, we show that the D-enantiomer of NCR247 can bind and sequester haem in an equivalent manner. The special abilities of NCR247 and its D-enantiomer to sequester haem suggest a broad range of potential applications related to human health.
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Affiliation(s)
- Siva Sankari
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Vignesh M.P. Babu
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Ke Bian
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Areej Alhhazmi
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Mary C. Andorfer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Dante M. Avalos
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
| | - Tyler A. Smith
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Kwan Yoon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Catherine L. Drennan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Michael B. Yaffe
- Departments of Biology and Biological Engineering, and Center for Precision Cancer Medicine, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute for Technology, Cambridge, MA 02139, USA.,Divisions of Acute Care Surgery, Trauma, and Surgical Critical Care, and Surgical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215 USA
| | - Sebastian Lourido
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Graham C. Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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3
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A High-Throughput Method for Identifying Novel Genes That Influence Metabolic Pathways Reveals New Iron and Heme Regulation in Pseudomonas aeruginosa. mSystems 2021; 6:6/1/e00933-20. [PMID: 33531406 PMCID: PMC7857532 DOI: 10.1128/msystems.00933-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The ability to simultaneously and more directly correlate genes with metabolite levels on a global level would provide novel information for many biological platforms yet has thus far been challenging. Here, we describe a method to help address this problem, which we dub “Met-Seq” (metabolite-coupled Tn sequencing). Heme is an essential metabolite for most life on earth. Bacterial pathogens almost universally require iron to infect a host, often acquiring this nutrient in the form of heme. The Gram-negative pathogen Pseudomonas aeruginosa is no exception, where heme acquisition and metabolism are known to be crucial for both chronic and acute infections. To unveil unknown genes and pathways that could play a role with heme metabolic flux in this pathogen, we devised an omic-based approach we dubbed “Met-Seq,” for metabolite-coupled transposon sequencing. Met-Seq couples a biosensor with fluorescence-activated cell sorting (FACS) and massively parallel sequencing, allowing for direct identification of genes associated with metabolic changes. In this work, we first construct and validate a heme biosensor for use with P. aeruginosa and exploit Met-Seq to identify 188 genes that potentially influence intracellular heme levels. Identified genes largely consisted of metabolic pathways not previously associated with heme, including many secreted virulence effectors, as well as 11 predicted small RNAs (sRNAs) and riboswitches whose functions are not currently understood. We verify that five Met-Seq hits affect intracellular heme levels; a predicted extracytoplasmic function (ECF) factor, a phospholipid acquisition system, heme biosynthesis regulator Dnr, and two predicted antibiotic monooxygenase (ABM) domains of unknown function (PA0709 and PA3390). Finally, we demonstrate that PA0709 and PA3390 are novel heme-binding proteins. Our data suggest that Met-Seq could be extrapolated to other biological systems and metabolites for which there is an available biosensor, and provides a new template for further exploration of iron/heme regulation and metabolism in P. aeruginosa and other pathogens. IMPORTANCE The ability to simultaneously and more directly correlate genes with metabolite levels on a global level would provide novel information for many biological platforms yet has thus far been challenging. Here, we describe a method to help address this problem, which we dub “Met-Seq” (metabolite-coupled Tn sequencing). Met-Seq uses the powerful combination of fluorescent biosensors, fluorescence-activated cell sorting (FACS), and next-generation sequencing (NGS) to rapidly identify genes that influence the levels of specific intracellular metabolites. For proof of concept, we create and test a heme biosensor and then exploit Met-Seq to identify novel genes involved in the regulation of heme in the pathogen Pseudomonas aeruginosa. Met-Seq-generated data were largely comprised of genes which have not previously been reported to influence heme levels in this pathogen, two of which we verify as novel heme-binding proteins. As heme is a required metabolite for host infection in P. aeruginosa and most other pathogens, our studies provide a new list of targets for potential antimicrobial therapies and shed additional light on the balance between infection, heme uptake, and heme biosynthesis.
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4
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Ganley JG, D'Ambrosio HK, Shieh M, Derbyshire ER. Coculturing of Mosquito-Microbiome Bacteria Promotes Heme Degradation in Elizabethkingia anophelis. Chembiochem 2020; 21:1279-1284. [PMID: 31845464 DOI: 10.1002/cbic.201900675] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Indexed: 12/31/2022]
Abstract
Anopheles mosquito microbiomes are intriguing ecological niches. Within the gut, microbes adapt to oxidative stress due to heme and iron after blood meals. Although metagenomic sequencing has illuminated spatial and temporal fluxes of microbiome populations, limited data exist on microbial growth dynamics. Here, we analyze growth interactions between a dominant microbiome species, Elizabethkingia anophelis, and other Anopheles-associated bacteria. We find E. anophelis inhibits a Pseudomonas sp. via an antimicrobial-independent mechanism and observe biliverdins, heme degradation products, upregulated in cocultures. Purification and characterization of E. anophelis HemS demonstrates heme degradation, and we observe hemS expression is upregulated when cocultured with Pseudomonas sp. This study reveals a competitive microbial interaction between mosquito-associated bacteria and characterizes the stimulation of heme degradation in E. anophelis when grown with Pseudomonas sp.
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Affiliation(s)
- Jack G Ganley
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC, 27708, USA
| | - Hannah K D'Ambrosio
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC, 27708, USA
| | - Meg Shieh
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC, 27708, USA
| | - Emily R Derbyshire
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC, 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC, 27710, USA
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5
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Rodríguez-Arce I, Al-Jubair T, Euba B, Fernández-Calvet A, Gil-Campillo C, Martí S, Törnroth-Horsefield S, Riesbeck K, Garmendia J. Moonlighting of Haemophilus influenzae heme acquisition systems contributes to the host airway-pathogen interplay in a coordinated manner. Virulence 2019; 10:315-333. [PMID: 30973092 PMCID: PMC6550540 DOI: 10.1080/21505594.2019.1596506] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/18/2019] [Accepted: 03/12/2019] [Indexed: 01/30/2023] Open
Abstract
Nutrient iron sequestration is the most significant form of nutritional immunity and causes bacterial pathogens to evolve strategies of host iron scavenging. Cigarette smoking contains iron particulates altering lung and systemic iron homeostasis, which may enhance colonization in the lungs of patients suffering chronic obstructive pulmonary disease (COPD) by opportunistic pathogens such as nontypeable. NTHi is a heme auxotroph, and the NTHi genome contains multiple heme acquisition systems whose role in pulmonary infection requires a global understanding. In this study, we determined the relative contribution to NTHi airway infection of the four heme-acquisition systems HxuCBA, PE, SapABCDFZ, and HbpA-DppBCDF that are located at the bacterial outer membrane or the periplasm. Our computational studies provided plausible 3D models for HbpA, SapA, PE, and HxuA interactions with heme. Generation and characterization of single mutants in the hxuCBA, hpe, sapA, and hbpA genes provided evidence for participation in heme binding-storage and inter-bacterial donation. The hxuA, sapA, hbpA, and hpe genes showed differential expression and responded to heme. Moreover, HxuCBA, PE, SapABCDFZ, and HbpA-DppBCDF presented moonlighting properties related to resistance to antimicrobial peptides or glutathione import, together likely contributing to the NTHi-host airway interplay, as observed upon cultured airway epithelia and in vivo lung infection. The observed multi-functionality was shown to be system-specific, thus limiting redundancy. Together, we provide evidence for heme uptake systems as bacterial factors that act in a coordinated and multi-functional manner to subvert nutritional- and other sources of host innate immunity during NTHi airway infection.
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Affiliation(s)
| | - Tamim Al-Jubair
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Begoña Euba
- Instituto de Agrobiotecnología, CSIC-Gobierno, Navarra, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | | | | | - Sara Martí
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Departamento Microbiología, Hospital Universitari Bellvitge, University of Barcelona, IDIBELL, Barcelona, Spain
| | - Susanna Törnroth-Horsefield
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Lund, Sweden
| | - Kristian Riesbeck
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Junkal Garmendia
- Instituto de Agrobiotecnología, CSIC-Gobierno, Navarra, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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6
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Bacterial ABC transporters of iron containing compounds. Res Microbiol 2019; 170:345-357. [DOI: 10.1016/j.resmic.2019.10.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/15/2019] [Accepted: 10/15/2019] [Indexed: 11/20/2022]
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7
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Mitra A, Ko YH, Cingolani G, Niederweis M. Heme and hemoglobin utilization by Mycobacterium tuberculosis. Nat Commun 2019; 10:4260. [PMID: 31534126 PMCID: PMC6751184 DOI: 10.1038/s41467-019-12109-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 08/21/2019] [Indexed: 12/31/2022] Open
Abstract
Iron is essential for growth of Mycobacterium tuberculosis (Mtb), but most iron in the human body is stored in heme within hemoglobin. Here, we demonstrate that the substrate-binding protein DppA of the inner membrane Dpp transporter is required for heme and hemoglobin utilization by Mtb. The 1.27 Å crystal structure of DppA shows a tetrapeptide bound in the protein core and a large solvent-exposed crevice for heme binding. Mutation of arginine 179 in this cleft eliminates heme binding to DppA and prevents heme utilization by Mtb. The outer membrane proteins PPE36 and PPE62 are also required for heme and hemoglobin utilization, indicating that these pathways converge at the cell surface of Mtb. Albumin, the most abundant blood protein, binds heme specifically and bypasses the requirements for PPE36, PPE62 and Dpp. Thus, our study reveals albumin-dependent and -independent heme uptake pathways, highlighting the importance of iron acquisition from heme for Mtb.
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Affiliation(s)
- Avishek Mitra
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Ying-Hui Ko
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233S. 10th Street, Philadelphia, PA, 19107, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233S. 10th Street, Philadelphia, PA, 19107, USA. .,Institute of Biomembranes and Bioenergetics, National Research Council, Via Amendola 165/A, 70126, Bari, Italy.
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA.
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8
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Tanaka KJ, Pinkett HW. Oligopeptide-binding protein from nontypeable Haemophilus influenzae has ligand-specific sites to accommodate peptides and heme in the binding pocket. J Biol Chem 2018; 294:1070-1082. [PMID: 30455346 DOI: 10.1074/jbc.ra118.004479] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/14/2018] [Indexed: 11/06/2022] Open
Abstract
In nontypeable Haemophilus influenzae (NTHi), the oligopeptide-binding protein (OppA) serves as the substrate-binding protein (SBP) of the oligopeptide transport system responsible for the import of peptides. We solved the crystal structure of nthiOppA in complex with hydrophobic peptides of various sizes. Our novel hexapeptide complex demonstrates the flexibility of the nthiOppA-binding cavity to expand and accommodate the longer peptide while maintaining similar protein-peptide interactions of smaller peptide complexes. In addition to acquiring peptides from the host environment, as a heme auxotroph NTHi utilizes host hemoproteins as a source of essential iron. OppA is a member of the Cluster C SBP family, and unlike other SBP families, some members recognize two distinctly different substrates. DppA (dipeptide), MppA (murein tripeptide), and SapA (antimicrobial peptides) are Cluster C proteins known to also transport heme. We observed nthiOppA shares this heme-binding characteristic and established heme specificity and affinity by surface plasmon resonance (SPR) of the four Cluster C proteins in NTHi. Ligand-docking studies predicted a distinct heme-specific cleft in the binding pocket, and using SPR competition assays, we observed that heme does not directly compete with peptide in the substrate-binding pocket. Additionally, we identified that the individual nthiOppA domains differentially contribute to substrate binding, with one domain playing a dominant role in heme binding and the other in peptide binding. Our results demonstrate the multisubstrate specificity of nthiOppA and the role of NTHi Cluster C proteins in the heme-uptake pathway for this pathogen.
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Affiliation(s)
- Kari J Tanaka
- From the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Heather W Pinkett
- From the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
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9
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Choby JE, Skaar EP. Heme Synthesis and Acquisition in Bacterial Pathogens. J Mol Biol 2016; 428:3408-28. [PMID: 27019298 PMCID: PMC5125930 DOI: 10.1016/j.jmb.2016.03.018] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 02/06/2023]
Abstract
Bacterial pathogens require the iron-containing cofactor heme to cause disease. Heme is essential to the function of hemoproteins, which are involved in energy generation by the electron transport chain, detoxification of host immune effectors, and other processes. During infection, bacterial pathogens must synthesize heme or acquire heme from the host; however, host heme is sequestered in high-affinity hemoproteins. Pathogens have evolved elaborate strategies to acquire heme from host sources, particularly hemoglobin, and both heme acquisition and synthesis are important for pathogenesis. Paradoxically, excess heme is toxic to bacteria and pathogens must rely on heme detoxification strategies. Heme is a key nutrient in the struggle for survival between host and pathogen, and its study has offered significant insight into the molecular mechanisms of bacterial pathogenesis.
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Affiliation(s)
- Jacob E Choby
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA; Tennessee Valley Healthcare System, U.S. Department of Veterans Affairs, Nashville, TN, USA.
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10
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Wilks A, Ikeda-Saito M. Heme utilization by pathogenic bacteria: not all pathways lead to biliverdin. Acc Chem Res 2014; 47:2291-8. [PMID: 24873177 PMCID: PMC4139177 DOI: 10.1021/ar500028n] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The eukaryotic heme oxygenases (HOs) (E.C. 1.14.99.3) convert heme
to biliverdin, iron, and carbon monoxide (CO) in three successive
oxygenation steps. Pathogenic bacteria require iron for survival and
infection. Extracellular heme uptake from the host plays a critical
role in iron acquisition and virulence. In the past decade, several
HOs required for the release of iron from extracellular heme have
been identified in pathogenic bacteria, including Corynebacterium
diphtheriae, Neisseriae meningitides, and Pseudomonas aeruginosa. The
bacterial enzymes were shown to be structurally and mechanistically
similar to those of the canonical eukaryotic HO enzymes. However,
the recent discovery of the structurally and mechanistically distinct
noncanonical heme oxygenases of Staphylococcus aureus and Mycobacterium tuberculosis has
expanded the reaction manifold of heme degradation. The distinct ferredoxin-like
structural fold and extreme heme ruffling are proposed to give rise
to the alternate heme degradation products in the S.
aureus and M. tuberculosis enzymes. In addition, several “heme-degrading factors”
with no structural homology to either class of HOs have recently been
reported. The identification of these “heme-degrading proteins”
has largely been determined on the basis of in vitro heme degradation
assays. Many of these proteins were reported to produce biliverdin,
although no extensive characterization of the products was performed.
Prior to the characterization of the canonical HO enzymes, the nonenzymatic
degradation of heme and heme proteins in the presence of a reductant
such as ascorbate or hydrazine, a reaction termed “coupled
oxidation”, served as a model for biological heme degradation.
However, it was recognized that there were important mechanistic differences
between the so-called coupled oxidation of heme proteins and enzymatic
heme oxygenation. In the coupled oxidation reaction, the final product,
verdoheme, can readily be converted to biliverdin under hydrolytic
conditions. The differences between heme oxygenation by the canonical
and noncanonical HOs and coupled oxidation will be discussed in the
context of the stabilization of the reactive FeIII–OOH
intermediate and regioselective heme hydroxylation. Thus, in the determination
of heme oxygenase activity in vitro, it is important to ensure that
the reaction proceeds through successive oxygenation steps. We further
suggest that when bacterial heme degradation is being characterized,
a systems biology approach combining genetics, mechanistic enzymology,
and metabolite profiling should be undertaken.
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Affiliation(s)
- Angela Wilks
- Department
of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201-1140, United States
| | - Masao Ikeda-Saito
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University Katahira, Aoba, Sendai 980-8577, Japan
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11
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Su YC, Resman F, Hörhold F, Riesbeck K. Comparative genomic analysis reveals distinct genotypic features of the emerging pathogen Haemophilus influenzae type f. BMC Genomics 2014; 15:38. [PMID: 24438474 PMCID: PMC3928620 DOI: 10.1186/1471-2164-15-38] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 01/09/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The incidence of invasive disease caused by encapsulated Haemophilus influenzae type f (Hif) has increased in the post-H. influenzae type b (Hib) vaccine era. We previously annotated the first complete Hif genome from a clinical isolate (KR494) that caused septic shock and necrotizing myositis. Here, the full genome of Hif KR494 was compared to sequenced reference strains Hib 10810, capsule type d (Hid) Rd Kw20, and finally nontypeable H. influenzae 3655. The goal was to identify possible genomic characteristics that may shed light upon the pathogenesis of Hif. RESULTS The Hif KR494 genome exhibited large regions of synteny with other H. influenzae, but also distinct genome rearrangements. A predicted Hif core genome of 1390 genes was shared with the reference strains, and 6 unique genomic regions comprising half of the 191 unique coding sequences were revealed. The majority of these regions were inserted genetic fragments, most likely derived from the closely-related Haemophilus spp. including H. aegyptius, H. haemolyticus and H. parainfluenzae. Importantly, the KR494 genome possessed several putative virulence genes that were distinct from non-type f strains. These included the sap2 operon, aef3 fimbriae, and genes for kanamycin nucleotidyltranserase, iron-utilization proteins, and putative YadA-like trimeric autotransporters that may increase the bacterial virulence. Furthermore, Hif KR494 lacked a hisABCDEFGH operon for de novo histidine biosynthesis, hmg locus for lipooligosaccharide biosynthesis and biofilm formation, the Haemophilus antibiotic resistance island and a Haemophilus secondary molybdate transport system. We confirmed the histidine auxotrophy and kanamycin resistance in Hif by functional experiments. Moreover, the pattern of unique or missing genes of Hif KR494 was similar in 20 Hif clinical isolates obtained from different years and geographical areas. A cross-species comparison revealed that the Hif genome shared more characteristics with H. aegyptius than Hid and NTHi. CONCLUSIONS The genomic comparative analyses facilitated identification of genotypic characteristics that may be related to the specific virulence of Hif. In relation to non-type f H. influenzae strains, the Hif genome contains differences in components involved in metabolism and survival that may contribute to its invasiveness.
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Affiliation(s)
| | | | | | - Kristian Riesbeck
- Medical Microbiology, Department of Laboratory Medicine Malmö, Lund University, Jan Waldenströms gata 59, SE-205 02 Malmö, Sweden.
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12
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Caza M, Kronstad JW. Shared and distinct mechanisms of iron acquisition by bacterial and fungal pathogens of humans. Front Cell Infect Microbiol 2013; 3:80. [PMID: 24312900 PMCID: PMC3832793 DOI: 10.3389/fcimb.2013.00080] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 10/30/2013] [Indexed: 12/12/2022] Open
Abstract
Iron is the most abundant transition metal in the human body and its bioavailability is stringently controlled. In particular, iron is tightly bound to host proteins such as transferrin to maintain homeostasis, to limit potential damage caused by iron toxicity under physiological conditions and to restrict access by pathogens. Therefore, iron acquisition during infection of a human host is a challenge that must be surmounted by every successful pathogenic microorganism. Iron is essential for bacterial and fungal physiological processes such as DNA replication, transcription, metabolism, and energy generation via respiration. Hence, pathogenic bacteria and fungi have developed sophisticated strategies to gain access to iron from host sources. Indeed, siderophore production and transport, iron acquisition from heme and host iron-containing proteins such as hemoglobin and transferrin, and reduction of ferric to ferrous iron with subsequent transport are all strategies found in bacterial and fungal pathogens of humans. This review focuses on a comparison of these strategies between bacterial and fungal pathogens in the context of virulence and the iron limitation that occurs in the human body as a mechanism of innate nutritional defense.
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Affiliation(s)
| | - James W. Kronstad
- The Michael Smith Laboratories, Department of Microbiology and Immunology, University of British ColumbiaVancouver, BC, Canada
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13
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Runyen-Janecky LJ. Role and regulation of heme iron acquisition in gram-negative pathogens. Front Cell Infect Microbiol 2013; 3:55. [PMID: 24116354 PMCID: PMC3792355 DOI: 10.3389/fcimb.2013.00055] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 09/10/2013] [Indexed: 12/14/2022] Open
Abstract
Bacteria that reside in animal tissues and/or cells must acquire iron from their host. However, almost all of the host iron is sequestered in iron-containing compounds and proteins, the majority of which is found within heme molecules. Thus, likely iron sources for bacterial pathogens (and non-pathogenic symbionts) are free heme and heme-containing proteins. Furthermore, the cellular location of the bacterial within the host (intra or extracellular) influences the amount and nature of the iron containing compounds available for transport. The low level of free iron in the host, coupled with the presence of numerous different heme sources, has resulted in a wide range of high-affinity iron acquisition strategies within bacteria. However, since excess iron and heme are toxic to bacteria, expression of these acquisition systems is highly regulated. Precise expression in the correct host environment at the appropriate times enables heme iron acquisitions systems to contribute to the growth of bacterial pathogens within the host. This mini-review will highlight some of the recent findings in these areas for gram-negative pathogens.
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Gruss A, Borezée-Durant E, Lechardeur D. Environmental heme utilization by heme-auxotrophic bacteria. Adv Microb Physiol 2013; 61:69-124. [PMID: 23046952 DOI: 10.1016/b978-0-12-394423-8.00003-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Heme, an iron-containing porphyrin, is the prosthetic group for numerous key cellular enzymatic and regulatory processes. Many bacteria encode the biosynthetic enzymes needed for autonomous heme production. Remarkably, however, numerous other bacteria lack a complete heme biosynthesis pathway, yet encode heme-requiring functions. For such heme-auxotrophic bacteria (HAB), heme or porphyrins must be captured from the environment. Functional studies, aided by genomic analyses, provide insight into the HAB lifestyle, how they acquire and manage heme, and the uses of heme that make it worthwhile, and sometimes necessary, to capture this bioactive molecule.
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Affiliation(s)
- Alexandra Gruss
- INRA, UMR1319 Micalis and AgroParisTech, UMR Micalis, Jouy-en-Josas, France
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15
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Haemophilus influenzae OxyR: characterization of its regulation, regulon and role in fitness. PLoS One 2012; 7:e50588. [PMID: 23226321 PMCID: PMC3511568 DOI: 10.1371/journal.pone.0050588] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 10/23/2012] [Indexed: 12/27/2022] Open
Abstract
To prevent damage by reactive oxygen species, many bacteria have evolved rapid detection and response systems, including the OxyR regulon. The OxyR system detects reactive oxygen and coordinates the expression of numerous defensive antioxidants. In many bacterial species the coordinated OxyR-regulated response is crucial for in vivo survival. Regulation of the OxyR regulon of Haemophilus influenzae was examined in vitro, and significant variation in the regulated genes of the OxyR regulon among strains of H. influenzae was observed. Quantitative PCR studies demonstrated a role for the OxyR-regulated peroxiredoxin/glutaredoxin as a mediator of the OxyR response, and also indicated OxyR self-regulation through a negative feedback loop. Analysis of transcript levels in H. influenzae samples derived from an animal model of otitis media demonstrated that the members of the OxyR regulon were actively upregulated within the chinchilla middle ear. H. influenzae mutants lacking the oxyR gene exhibited increased sensitivity to challenge with various peroxides. The impact of mutations in oxyR was assessed in various animal models of H. influenzae disease. In paired comparisons with the corresponding wild-type strains, the oxyR mutants were unaffected in both the chinchilla model of otitis media and an infant model of bacteremia. However, in weanling rats the oxyR mutant was significantly impaired compared to the wild-type strain. In contrast, in all three animal models when infected with a mixture of equal numbers of both wild-type and mutant strains the mutant strain was significantly out competed by the wild-type strain. These findings clearly establish a crucial role for OxyR in bacterial fitness.
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Lau SK, Fan RY, Ho TC, Wong GK, Tsang AK, Teng JL, Chen W, Watt RM, Curreem SO, Tse H, Yuen KY, Woo PC. Environmental adaptability and stress tolerance of Laribacter hongkongensis: a genome-wide analysis. Cell Biosci 2011; 1:22. [PMID: 21711489 PMCID: PMC3135505 DOI: 10.1186/2045-3701-1-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 06/14/2011] [Indexed: 12/31/2022] Open
Abstract
Background Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler's diarrhea and it can reside in human, fish, frogs and water. In this study, we performed an in-depth annotation of the genes in its genome related to adaptation to the various environmental niches. Results L. hongkongensis possessed genes for DNA repair and recombination, basal transcription, alternative σ-factors and 109 putative transcription factors, allowing DNA repair and global changes in gene expression in response to different environmental stresses. For acid stress, it possessed a urease gene cassette and two arc gene clusters. For alkaline stress, it possessed six CDSs for transporters of the monovalent cation/proton antiporter-2 and NhaC Na+:H+ antiporter families. For heavy metals acquisition and tolerance, it possessed CDSs for iron and nickel transport and efflux pumps for other metals. For temperature stress, it possessed genes related to chaperones and chaperonins, heat shock proteins and cold shock proteins. For osmotic stress, 25 CDSs were observed, mostly related to regulators for potassium ion, proline and glutamate transport. For oxidative and UV light stress, genes for oxidant-resistant dehydratase, superoxide scavenging, hydrogen peroxide scavenging, exclusion and export of redox-cycling antibiotics, redox balancing, DNA repair, reduction of disulfide bonds, limitation of iron availability and reduction of iron-sulfur clusters are present. For starvation, it possessed phosphorus and, despite being asaccharolytic, carbon starvation-related CDSs. Conclusions The L. hongkongensis genome possessed a high variety of genes for adaptation to acid, alkaline, temperature, osmotic, oxidative, UV light and starvation stresses and acquisition of and tolerance to heavy metals.
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Affiliation(s)
- Susanna Kp Lau
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong.,Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Rachel Yy Fan
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Tom Cc Ho
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Gilman Km Wong
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Alan Kl Tsang
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Jade Ll Teng
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Wenyang Chen
- Faculty of Dentistry, The University of Hong Kong, Hong Kong
| | - Rory M Watt
- Faculty of Dentistry, The University of Hong Kong, Hong Kong
| | | | - Herman Tse
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong.,Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong.,Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Patrick Cy Woo
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,Carol Yu Centre of Infection, The University of Hong Kong, Hong Kong.,Department of Microbiology, The University of Hong Kong, Hong Kong
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Heme utilization by nontypeable Haemophilus influenzae is essential and dependent on Sap transporter function. J Bacteriol 2011; 193:2527-35. [PMID: 21441512 DOI: 10.1128/jb.01313-10] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial strategies of innate immune evasion and essential metabolic functions are critical for commensal-host homeostasis. Previously, we showed that Sap translocator function is necessary for nontypeable Haemophilus influenzae (NTHI) behaviors that mediate diseases of the human airway. Antimicrobial peptide (AP) lethality is limited by binding mediated by the Sap complex. SapA shares homology with the dipeptide-binding protein (DppA) and the heme-binding lipoprotein (HbpA), both of which have previously been shown to bind the iron-containing compound heme, whose acquisition is essential for Haemophilus survival. Computational modeling revealed conserved SapA residues, similarly modeled to mediate heme binding in HbpA. Here, we directly demonstrate that SapA bound heme and was essential for heme utilization by iron-starved NTHI. Further, the Sap translocator permease mediated heme transport into the bacterial cytoplasm, thus defining a heretofore unknown mechanism of intracytoplasmic membrane heme transport in Haemophilus. Since we demonstrate multiple ligand specificity for the SapA-binding protein, we tested whether APs would compete with heme for SapA binding. We showed that human β-defensins 2 and 3, human cathelicidin LL-37, human neutrophil protein 1, and melittin displaced heme bound to SapA, thus supporting a hierarchy wherein immune evasion supercedes even the needed iron acquisition functions of the Sap system.
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Identification and characterization of a heme periplasmic-binding protein in Haemophilus ducreyi. Biometals 2011; 24:709-22. [PMID: 21347851 DOI: 10.1007/s10534-011-9427-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 02/03/2011] [Indexed: 10/18/2022]
Abstract
Haemophilus ducreyi, a gram-negative and heme-dependent bacterium, is the causative agent of chancroid, a genital ulcer sexually transmitted infection. Heme acquisition in H. ducreyi proceeds via a receptor mediated process in which the initial event involves binding of hemoglobin and heme to their cognate outer membrane proteins, HgbA and TdhA, respectively. Following this specific interaction, the fate of the periplasmic deposited heme is unclear. Using protein expression profiling of the H. ducreyi periplasmic proteome, a periplasmic-binding protein, termed hHbp, was identified whose expression was enhanced under heme-limited conditions. The gene encoding this protein was situated in a locus displaying genetic characteristics of an ABC transporter. The purified protein bound heme in a dose-dependent and saturable manner and this binding was specifically competitively inhibited by heme. The hhbp gene functionally complemented an Escherichia coli heme uptake mutant. Expression of the heme periplasmic-binding protein was detected in a limited survey of H. ducreyi and H. influenzae clinical strains. These results indicate that the passage of heme into the cytoplasm of H. ducreyi involves a heme dedicated ABC transporter.
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