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Transcriptomics Reveal the Survival Strategies of Enterococcus mundtii in the Gut of Spodoptera littoralis. J Chem Ecol 2021; 47:227-241. [PMID: 33459999 DOI: 10.1007/s10886-021-01246-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/22/2020] [Accepted: 01/04/2021] [Indexed: 12/25/2022]
Abstract
The complex interaction between a higher organism and its resident gut flora is a subject of immense interest in the field of symbiosis. Many insects harbor a complex community of microorganisms in their gut. Larvae of Spodoptera littoralis, a lepidopteran pest, house a bacterial community that varies both spatially (along the length of the gut) and temporally (during the insect's life cycle). To monitor the rapid adaptation of microbes to conditions in the gut, a GFP-tagged reporter strain of E. mundtii, a major player in the gut community, was constructed. After early-instar S. littoralis larvae were fed with the tagged microbes, these were recovered from the larval fore- and hindgut by flow cytometry. The fluorescent reporter confirmed the persistence of E. mundtii in the gut. RNA-sequencing of the sorted bacteria highlighted various strategies of the symbiont's survival, including upregulated pathways for tolerating alkaline stress, forming biofilms and two-component signaling systems for quorum sensing, and resisting oxidative stress. Although these symbionts depend on the host for amino acid and fatty acids, differential regulation among various metabolic pathways points to an enriched lysine synthesis pathway of E. mundtii in the hindgut of the larvae.
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Gáll T, Pethő D, Nagy A, Balla G, Balla J. Therapeutic Potential of Carbon Monoxide (CO) and Hydrogen Sulfide (H 2S) in Hemolytic and Hemorrhagic Vascular Disorders-Interaction between the Heme Oxygenase and H 2S-Producing Systems. Int J Mol Sci 2020; 22:ijms22010047. [PMID: 33374506 PMCID: PMC7793096 DOI: 10.3390/ijms22010047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 02/07/2023] Open
Abstract
Over the past decades, substantial work has established that hemoglobin oxidation and heme release play a pivotal role in hemolytic/hemorrhagic disorders. Recent reports have shown that oxidized hemoglobins, globin-derived peptides, and heme trigger diverse biological responses, such as toll-like receptor 4 activation with inflammatory response, reprogramming of cellular metabolism, differentiation, stress, and even death. Here, we discuss these cellular responses with particular focus on their mechanisms that are linked to the pathological consequences of hemorrhage and hemolysis. In recent years, endogenous gasotransmitters, such as carbon monoxide (CO) and hydrogen sulfide (H2S), have gained a lot of interest in connection with various human pathologies. Thus, many CO and H2S-releasing molecules have been developed and applied in various human disorders, including hemolytic and hemorrhagic diseases. Here, we discuss our current understanding of oxidized hemoglobin and heme-induced cell and tissue damage with particular focus on inflammation, cellular metabolism and differentiation, and endoplasmic reticulum stress in hemolytic/hemorrhagic human diseases, and the potential beneficial role of CO and H2S in these pathologies. More detailed mechanistic insights into the complex pathology of hemolytic/hemorrhagic diseases through heme oxygenase-1/CO as well as H2S pathways would reveal new therapeutic approaches that can be exploited for clinical benefit.
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Affiliation(s)
- Tamás Gáll
- Division of Nephrology, Department of Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (T.G.); (D.P.); (A.N.)
- HAS-UD Vascular Biology and Myocardial Pathophysiology Research Group, Hungarian Academy of Sciences, University of Debrecen, 4032 Debrecen, Hungary;
| | - Dávid Pethő
- Division of Nephrology, Department of Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (T.G.); (D.P.); (A.N.)
- Faculty of Medicine, University of Debrecen, Kálmán Laki Doctoral School, 4032 Debrecen, Hungary
| | - Annamária Nagy
- Division of Nephrology, Department of Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (T.G.); (D.P.); (A.N.)
- Faculty of Medicine, University of Debrecen, Kálmán Laki Doctoral School, 4032 Debrecen, Hungary
| | - György Balla
- HAS-UD Vascular Biology and Myocardial Pathophysiology Research Group, Hungarian Academy of Sciences, University of Debrecen, 4032 Debrecen, Hungary;
- Department of Pediatrics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - József Balla
- Division of Nephrology, Department of Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (T.G.); (D.P.); (A.N.)
- Correspondence: ; Tel.: +36-52-255-500/55004
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Bridges CM, Gage DJ. Development and application of aerobic, chemically defined media for Dysgonomonas. Anaerobe 2020; 67:102302. [PMID: 33271360 DOI: 10.1016/j.anaerobe.2020.102302] [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: 08/12/2020] [Revised: 10/29/2020] [Accepted: 11/22/2020] [Indexed: 12/25/2022]
Abstract
Members of Dysgonomonas are Gram-stain-negative, non-motile, facultatively anaerobic coccobacilli originally described in relation to their isolation from stool and wounds of human patients (CDC group DF-3). More recently, Dysgonomonas have been found to be widely distributed in terrestrial environments and are particularly enriched in insect systems. Their prevalence in xylophagous insects such as termites and wood-feeding cockroaches, as well as in soil-fed microbial fuel cells, elicit interest in lignocellulose degradation and biofuel production, respectively. Their occurrence in mosquito and fruit fly have implications relating to symbiosis, host immunology and developmental biology. Additionally, their presence in termite, mosquito and nematode present novel opportunities for pest and vector control. Currently, the absolute growth requirements of Dysgonomonas are unknown, and they are commonly cultured under anaerobic conditions on complex media containing blood, peptones, tryptones, and yeast, plant or meat extracts. Restrictive and undefined culturing conditions preclude physiological and genetic studies, and thus further understanding of their metabolic potential. Here we describe the requirements for growth of termite-derived Dysgonomonas isolates and create parallel complex, defined and minimal media that permit vigorous and reliable aerobic growth. Furthermore, we show that these media can be used to easily enrich for Dysgonomonas isolates from densely-colonized and microbially-diverse environmental samples.
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Affiliation(s)
- Charles M Bridges
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Daniel J Gage
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
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Dulay H, Tabares M, Kashefi K, Reguera G. Cobalt Resistance via Detoxification and Mineralization in the Iron-Reducing Bacterium Geobacter sulfurreducens. Front Microbiol 2020; 11:600463. [PMID: 33324382 PMCID: PMC7726332 DOI: 10.3389/fmicb.2020.600463] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022] Open
Abstract
Bacteria in the genus Geobacter thrive in iron- and manganese-rich environments where the divalent cobalt cation (CoII) accumulates to potentially toxic concentrations. Consistent with selective pressure from environmental exposure, the model laboratory representative Geobacter sulfurreducens grew with CoCl2 concentrations (1 mM) typically used to enrich for metal-resistant bacteria from contaminated sites. We reconstructed from genomic data canonical pathways for CoII import and assimilation into cofactors (cobamides) that support the growth of numerous syntrophic partners. We also identified several metal efflux pumps, including one that was specifically upregulated by CoII. Cells acclimated to metal stress by downregulating non-essential proteins with metals and thiol groups that CoII preferentially targets. They also activated sensory and regulatory proteins involved in detoxification as well as pathways for protein and DNA repair. In addition, G. sulfurreducens upregulated respiratory chains that could have contributed to the reductive mineralization of the metal on the cell surface. Transcriptomic evidence also revealed pathways for cell envelope modification that increased metal resistance and promoted cell-cell aggregation and biofilm formation in stationary phase. These complex adaptive responses confer on Geobacter a competitive advantage for growth in metal-rich environments that are essential to the sustainability of cobamide-dependent microbiomes and the sequestration of the metal in hitherto unknown biomineralization reactions.
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Affiliation(s)
- Hunter Dulay
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Marcela Tabares
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Kazem Kashefi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
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55
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Antibacterial Activity of Synthetic Cationic Iron Porphyrins. Antioxidants (Basel) 2020; 9:antiox9100972. [PMID: 33050461 PMCID: PMC7601463 DOI: 10.3390/antiox9100972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 12/28/2022] Open
Abstract
Widespread antibiotic resistance demands new strategies for fighting infections. Porphyrin-based compounds were long ago introduced as photosensitizers for photodynamic therapy, but light-independent antimicrobial activity of such compounds has not been systematically explored. The results of this study demonstrate that synthetic cationic amphiphilic iron N-alkylpyridylporphyrins exert strong bactericidal action at concentrations as low as 5 μM. Iron porphyrin, FeTnHex-2-PyP, which is well tolerated by laboratory animals, efficiently killed Gram-negative and Gram-positive microorganisms. Its bactericidal activity was oxygen-independent and was controlled by the lipophilicity and accumulation of the compound in bacterial cells. Such behavior is in contrast with the anionic gallium protoporphyrin IX, whose efficacy depends on cellular heme uptake systems. Under aerobic conditions, however, the activity of FeTnHex-2-PyP was limited by its destruction due to redox-cycling. Neither iron released from the Fe-porphyrin nor other decomposition products were the cause of the bactericidal activity. FeTnHex-2-PyP was as efficient against antibiotic-sensitive E. coli and S. aureus as against their antibiotic-resistant counterparts. Our data demonstrate that development of amphiphilic, positively charged metalloporphyrins might be a promising approach in the introduction of new weapons against antibiotic-resistant strains.
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56
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Akhter F, Womack E, Vidal JE, Le Breton Y, McIver KS, Pawar S, Eichenbaum Z. Hemoglobin stimulates vigorous growth of Streptococcus pneumoniae and shapes the pathogen's global transcriptome. Sci Rep 2020; 10:15202. [PMID: 32938947 PMCID: PMC7494912 DOI: 10.1038/s41598-020-71910-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022] Open
Abstract
Streptococcus pneumoniae (Spn) must acquire iron from the host to establish infection. We examined the impact of hemoglobin, the largest iron reservoir in the body, on pneumococcal physiology. Supplementation with hemoglobin allowed Spn to resume growth in an iron-deplete medium. Pneumococcal growth with hemoglobin was unusually robust, exhibiting a prolonged logarithmic growth, higher biomass, and extended viability in both iron-deplete and standard medium. We observed the hemoglobin-dependent response in multiple serotypes, but not with other host proteins, free iron, or heme. Remarkably, hemoglobin induced a sizable transcriptome remodeling, effecting virulence and metabolism in particular genes facilitating host glycoconjugates use. Accordingly, Spn was more adapted to grow on the human α − 1 acid glycoprotein as a sugar source with hemoglobin. A mutant in the hemoglobin/heme-binding protein Spbhp-37 was impaired for growth on heme and hemoglobin iron. The mutant exhibited reduced growth and iron content when grown in THYB and hemoglobin. In summary, the data show that hemoglobin is highly beneficial for Spn cultivation in vitro and suggest that hemoglobin might drive the pathogen adaptation in vivo. The hemoglobin receptor, Spbhp-37, plays a role in mediating the positive influence of hemoglobin. These novel findings provide intriguing insights into pneumococcal interactions with its obligate human host.
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Affiliation(s)
- Fahmina Akhter
- Department of Biology, Georgia State University, Atlanta, GA, USA
| | - Edroyal Womack
- Department of Biology, Georgia State University, Atlanta, GA, USA
| | - Jorge E Vidal
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Yoann Le Breton
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park (UMCP), College Park, MD, USA.,Wound Infections Department, Bacterial Diseases Branch, The Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Kevin S McIver
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park (UMCP), College Park, MD, USA
| | - Shrikant Pawar
- Department of Biology, Georgia State University, Atlanta, GA, USA.,Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
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Keppel M, Hünnefeld M, Filipchyk A, Viets U, Davoudi CF, Krüger A, Mack C, Pfeifer E, Polen T, Baumgart M, Bott M, Frunzke J. HrrSA orchestrates a systemic response to heme and determines prioritization of terminal cytochrome oxidase expression. Nucleic Acids Res 2020; 48:6547-6562. [PMID: 32453397 PMCID: PMC7337898 DOI: 10.1093/nar/gkaa415] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/26/2020] [Accepted: 05/05/2020] [Indexed: 01/02/2023] Open
Abstract
Heme is a multifaceted molecule. While serving as a prosthetic group for many important proteins, elevated levels are toxic to cells. The complexity of this stimulus has shaped bacterial network evolution. However, only a small number of targets controlled by heme-responsive regulators have been described to date. Here, we performed chromatin affinity purification and sequencing to provide genome-wide insights into in vivo promoter occupancy of HrrA, the response regulator of the heme-regulated two-component system HrrSA of Corynebacterium glutamicum. Time-resolved profiling revealed dynamic binding of HrrA to more than 200 different genomic targets encoding proteins associated with heme biosynthesis, the respiratory chain, oxidative stress response and cell envelope remodeling. By repression of the extracytoplasmic function sigma factor sigC, which activates the cydABCD operon, HrrA prioritizes the expression of genes encoding the cytochrome bc1-aa3 supercomplex. This is also reflected by a significantly decreased activity of the cytochrome aa3 oxidase in the ΔhrrA mutant. Furthermore, our data reveal that HrrA also integrates the response to heme-induced oxidative stress by activating katA encoding the catalase. These data provide detailed insights in the systemic strategy that bacteria have evolved to respond to the versatile signaling molecule heme.
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Affiliation(s)
- Marc Keppel
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Max Hünnefeld
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Andrei Filipchyk
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Ulrike Viets
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Cedric-Farhad Davoudi
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Aileen Krüger
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Christina Mack
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Eugen Pfeifer
- Microbial Evolutionary Genomics, Institute Pasteur, 75015 Paris, France
| | - Tino Polen
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Meike Baumgart
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Michael Bott
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Julia Frunzke
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
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Abstract
In this issue of Cell Host & Microbe, publications from Bushman et al. (2020) and Knippel et al. (2020) outline elements of host epithelial damage or inflammation that Clostridioides difficile subverts, enabling continued growth. These mechanisms provide insight into how this important pathogen influences the gut environment to promote its metabolic strategy during infection.
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Affiliation(s)
- Matthew L Jenior
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA; Department of Medicine, Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA, USA; Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
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Zhao X, Zhou J, Du G, Chen J. Recent Advances in the Microbial Synthesis of Hemoglobin. Trends Biotechnol 2020; 39:286-297. [PMID: 32912649 DOI: 10.1016/j.tibtech.2020.08.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/27/2020] [Accepted: 08/11/2020] [Indexed: 01/08/2023]
Abstract
Hemoglobin is a cofactor-containing protein with heme that plays important roles in transporting and storing oxygen. Hemoglobins have been widely applied as acellular oxygen carriers, bioavailable iron-supplying agents, and food-grade coloring and flavoring agents. To meet increasing demands and overcome the drawbacks of chemical extraction, the biosynthesis of hemoglobin has become an attractive alternative. Several hemoglobins have recently been synthesized by various microorganisms through metabolic engineering and synthetic biology. In this review, we summarize the novel strategies that have been used to biosynthesize hemoglobin. These strategies can also serve as references for producing other heme-binding proteins.
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Affiliation(s)
- Xinrui Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Laboratory of Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Laboratory of Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
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60
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Verplaetse E, André-Leroux G, Duhutrel P, Coeuret G, Chaillou S, Nielsen-Leroux C, Champomier-Vergès MC. Heme Uptake in Lactobacillus sakei Evidenced by a New Energy Coupling Factor (ECF)-Like Transport System. Appl Environ Microbiol 2020; 86:e02847-19. [PMID: 32680867 PMCID: PMC7480364 DOI: 10.1128/aem.02847-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 07/05/2020] [Indexed: 12/27/2022] Open
Abstract
Lactobacillus sakei is a nonpathogenic lactic acid bacterium and a natural inhabitant of meat ecosystems. Although red meat is a heme-rich environment, L. sakei does not need iron or heme for growth, although it possesses a heme-dependent catalase. Iron incorporation into L. sakei from myoglobin and hemoglobin was previously shown by microscopy and the L. sakei genome reveals the complete equipment for iron and heme transport. Here, we report the characterization of a five-gene cluster (from lsa1836 to lsa1840 [lsa1836-1840]) encoding a putative metal iron ABC transporter. Interestingly, this cluster, together with a heme-dependent catalase gene, is also conserved in other species from the meat ecosystem. Our bioinformatic analyses revealed that the locus might correspond to a complete machinery of an energy coupling factor (ECF) transport system. We quantified in vitro the intracellular heme in the wild type (WT) and in our Δlsa1836-1840 deletion mutant using an intracellular heme sensor and inductively coupled plasma mass spectrometry for quantifying incorporated 57Fe heme. We showed that in the WT L. sakei, heme accumulation occurs rapidly and massively in the presence of hemin, while the deletion mutant was impaired in heme uptake; this ability was restored by in trans complementation. Our results establish the main role of the L. sakei Lsa1836-1840 ECF-like system in heme uptake. Therefore, this research outcome sheds new light on other possible functions of ECF-like systems.IMPORTANCELactobacillus sakei is a nonpathogenic bacterial species exhibiting high fitness in heme-rich environments such as meat products, although it does not need iron or heme for growth. Heme capture and utilization capacities are often associated with pathogenic species and are considered virulence-associated factors in the infected hosts. For these reasons, iron acquisition systems have been deeply studied in such species, while for nonpathogenic bacteria the information is scarce. Genomic data revealed that several putative iron transporters are present in the genome of the lactic acid bacterium L. sakei In this study, we demonstrate that one of them is an ECF-like ABC transporter with a functional role in heme transport. Such evidence has not yet been brought for an ECF; therefore, our study reveals a new class of heme transport system.
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Affiliation(s)
- Emilie Verplaetse
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | | | - Philippe Duhutrel
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Gwendoline Coeuret
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Stéphane Chaillou
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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Kornitzer D, Roy U. Pathways of heme utilization in fungi. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118817. [PMID: 32777371 DOI: 10.1016/j.bbamcr.2020.118817] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 02/08/2023]
Abstract
Iron acquisition is challenging in most environments. As an alternative to elemental iron, organisms can take up iron-protoporphyrin IX, or heme. Heme can be found in decaying organic matter and is particularly prevalent in animal hosts. Fungi have evolved at least three distinct endocytosis-mediated heme uptake systems, which have been studied in detail in the organisms Candida albicans, Cryptococcus neoformans and Schizosaccharomyces pombe. Here we summarize the known molecular details of these three uptake systems that enable parasitic and saprophytic fungi to take advantage of external heme as either cellular iron or heme sources.
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Affiliation(s)
- Daniel Kornitzer
- Department of Molecular Microbiology, B. Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 31096, Israel.
| | - Udita Roy
- Department of Molecular Microbiology, B. Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 31096, Israel
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Cesinger MR, Thomason MK, Edrozo MB, Halsey CR, Reniere ML. Listeria monocytogenes SpxA1 is a global regulator required to activate genes encoding catalase and heme biosynthesis enzymes for aerobic growth. Mol Microbiol 2020; 114:230-243. [PMID: 32255216 PMCID: PMC7496741 DOI: 10.1111/mmi.14508] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 12/24/2022]
Abstract
An imbalance of cellular oxidants and reductants causes redox stress, which must be rapidly detected to restore homeostasis. In bacteria, the Firmicutes encode conserved Spx-family transcriptional regulators that modulate transcription in response to redox stress. SpxA1 is an Spx-family orthologue in the intracellular pathogen Listeria monocytogenes that is essential for aerobic growth and pathogenesis. Here, we investigated the role of SpxA1 in growth and virulence by identifying genes regulated by SpxA1 in broth and during macrophage infection. We found SpxA1-activated genes encoding heme biosynthesis enzymes and catalase (kat) were required for L. monocytogenes aerobic growth in rich medium. An Spx-recognition motif previously defined in Bacillus subtilis was identified in the promoters of SpxA1-activated genes and proved necessary for the proper activation of two genes, indicating this regulation by SpxA1 is likely direct. Together, these findings elucidated the mechanism of spxA1 essentiality in vitro and demonstrated that SpxA1 is required for basal expression of scavenging enzymes to combat redox stress generated in the presence of oxygen.
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Affiliation(s)
- Monica R. Cesinger
- Department of MicrobiologySchool of MedicineUniversity of WashingtonSeattleWAUSA
| | - Maureen K. Thomason
- Department of MicrobiologySchool of MedicineUniversity of WashingtonSeattleWAUSA
| | - Mauna B. Edrozo
- Department of MicrobiologySchool of MedicineUniversity of WashingtonSeattleWAUSA
| | - Cortney R. Halsey
- Department of MicrobiologySchool of MedicineUniversity of WashingtonSeattleWAUSA
| | - Michelle L. Reniere
- Department of MicrobiologySchool of MedicineUniversity of WashingtonSeattleWAUSA
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Optimization of hydrogenobyrinic acid biosynthesis in Escherichia coli using multi-level metabolic engineering strategies. Microb Cell Fact 2020; 19:118. [PMID: 32487216 PMCID: PMC7268678 DOI: 10.1186/s12934-020-01377-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/25/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Hydrogenobyrinic acid is a key intermediate of the de-novo aerobic biosynthesis pathway of vitamin B12. The introduction of a heterologous de novo vitamin B12 biosynthesis pathway in Escherichia coli offers an alternative approach for its production. Although E. coli avoids major limitations that currently faced by industrial producers of vitamin B12, such as long growth cycles, the insufficient supply of hydrogenobyrinic acid restricts industrial vitamin B12 production. RESULTS By designing combinatorial ribosomal binding site libraries of the hemABCD genes in vivo, we found that their optimal relative translational initiation rates are 10:1:1:5. The transcriptional coordination of the uroporphyrinogen III biosynthetic module was realized by promoter engineering of the hemABCD operon. Knockdown of competitive heme and siroheme biosynthesis pathways by RBS engineering enhanced the hydrogenobyrinic acid titer to 20.54 and 15.85 mg L-1, respectively. Combined fine-tuning of the heme and siroheme biosynthetic pathways enhanced the hydrogenobyrinic acid titer to 22.57 mg L-1, representing a remarkable increase of 1356.13% compared with the original strain FH215-HBA. CONCLUSIONS Through multi-level metabolic engineering strategies, we achieved the metabolic balance of the uroporphyrinogen III biosynthesis pathway, eliminated toxicity due to by-product accumulation, and finally achieved a high HBA titer of 22.57 mg L-1 in E. coli. This lays the foundation for high-yield production of vitamin B12 in E. coli and will hopefully accelerate its industrial production.
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Ribič U, Jakše J, Toplak N, Koren S, Kovač M, Klančnik A, Jeršek B. Transporters and Efflux Pumps Are the Main Mechanisms Involved in Staphylococcus epidermidis Adaptation and Tolerance to Didecyldimethylammonium Chloride. Microorganisms 2020; 8:E344. [PMID: 32121333 PMCID: PMC7143832 DOI: 10.3390/microorganisms8030344] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 01/28/2023] Open
Abstract
Staphylococcus epidermidis cleanroom strains are often exposed to sub-inhibitory concentrations of disinfectants, including didecyldimethylammonium chloride (DDAC). Consequently, they can adapt or even become tolerant to them. RNA-sequencing was used to investigate adaptation and tolerance mechanisms of S. epidermidis cleanroom strains (SE11, SE18), with S. epidermidis SE11Ad adapted and S. epidermidis SE18To tolerant to DDAC. Adaptation to DDAC was identified with up-regulation of genes mainly involved in transport (thioredoxin reductase [pstS], the arsenic efflux pump [gene ID, SE0334], sugar phosphate antiporter [uhpT]), while down-regulation was seen for the Agr system (agrA, arC, agrD, psm, SE1543), for enhanced biofilm formation. Tolerance to DDAC revealed the up-regulation of genes associated with transporters (L-cysteine transport [tcyB]; uracil permease [SE0875]; multidrug transporter [lmrP]; arsenic efflux pump [arsB]); the down-regulation of genes involved in amino-acid biosynthesis (lysine [dapE]; histidine [hisA]; methionine [metC]), and an enzyme involved in peptidoglycan, and therefore cell wall modifications (alanine racemase [SE1079]). We show for the first time the differentially expressed genes in DDAC-adapted and DDAC-tolerant S. epidermidis strains, which highlight the complexity of the responses through the involvement of different mechanisms.
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Affiliation(s)
- Urška Ribič
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (U.R.); (A.K.)
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia;
| | - Nataša Toplak
- Omega d.o.o., Dolinškova 8, SI-1000 Ljubljana, Slovenia; (N.T.); (S.K.); (M.K.)
| | - Simon Koren
- Omega d.o.o., Dolinškova 8, SI-1000 Ljubljana, Slovenia; (N.T.); (S.K.); (M.K.)
| | - Minka Kovač
- Omega d.o.o., Dolinškova 8, SI-1000 Ljubljana, Slovenia; (N.T.); (S.K.); (M.K.)
| | - Anja Klančnik
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (U.R.); (A.K.)
| | - Barbara Jeršek
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia; (U.R.); (A.K.)
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65
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Zhang L, Hendrickson RC, Meikle V, Lefkowitz EJ, Ioerger TR, Niederweis M. Comprehensive analysis of iron utilization by Mycobacterium tuberculosis. PLoS Pathog 2020; 16:e1008337. [PMID: 32069330 PMCID: PMC7058343 DOI: 10.1371/journal.ppat.1008337] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/05/2020] [Accepted: 01/20/2020] [Indexed: 12/16/2022] Open
Abstract
Iron is essential for nearly all bacterial pathogens, including Mycobacterium tuberculosis (Mtb), but is severely limited in the human host. To meet its iron needs, Mtb secretes siderophores, small molecules with high affinity for iron, and takes up iron-loaded mycobactins (MBT) and carboxymycobactins (cMBT), from the environment. Mtb is also capable of utilizing heme and hemoglobin which contain more than 70% of the iron in the human body. However, many components of these iron acquisition pathways are still unknown. In this study, a high-density transposon mutagenesis coupled with deep sequencing (TnSeq) showed that Mtb exhibits nearly opposite requirements for 165 genes in the presence of heme and hemoglobin versus MBT and cMBT as iron sources. The ESX-3 secretion system was assessed as essential for siderophore-mediated iron uptake and, surprisingly, also for heme utilization by Mtb. Predictions derived from the TnSeq analysis were validated by growth experiments with isogenic Mtb mutants. These results showed that (i) the efflux pump MmpL5 plays a dominant role in siderophore secretion, (ii) the Rv2047c protein is essential for growth of Mtb in the presence of mycobactin, and (iii) the transcriptional repressor Zur is required for heme utilization by Mtb. The novel genetic determinants of iron utilization revealed in this study will stimulate further experiments in this important area of Mtb physiology.
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Affiliation(s)
- Lei Zhang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - R. Curtis Hendrickson
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Virginia Meikle
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Elliot J. Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
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66
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Garber AI, Nealson KH, Okamoto A, McAllister SM, Chan CS, Barco RA, Merino N. FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies. Front Microbiol 2020; 11:37. [PMID: 32082281 PMCID: PMC7005843 DOI: 10.3389/fmicb.2020.00037] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/09/2020] [Indexed: 01/15/2023] Open
Abstract
Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth's crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and surge in publicly available sequence data has made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition, iron redox cycling, iron storage, and magnetosome formation in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) based on genes related to iron acquisition, storage, and reduction/oxidation in Bacteria and Archaea. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate provided datasets with respect to iron-related genes and gene neighborhood. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. We validated FeGenie against a selected set of 28 isolate genomes and showcase its utility in exploring iron genes present in 27 metagenomes, 4 isolate genomes from human oral biofilms, and 17 genomes from candidate organisms, including members of the candidate phyla radiation. We show that FeGenie accurately identifies iron genes in isolates. Furthermore, analysis of metagenomes using FeGenie demonstrates that the iron gene repertoire and abundance of each environment is correlated with iron richness. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie's database will be maintained and continually updated as new genes are discovered. FeGenie is freely available: https://github.com/Arkadiy-Garber/FeGenie.
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Affiliation(s)
- Arkadiy I. Garber
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Department of Earth Sciences, University of Delaware, Newark, DE, United States
| | - Kenneth H. Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, Tsukuba, Japan
| | - Sean M. McAllister
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States
| | - Clara S. Chan
- Department of Earth Sciences, University of Delaware, Newark, DE, United States
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States
| | - Roman A. Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Nancy Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
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67
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Staphylococcus aureus small colony variants impair host immunity by activating host cell glycolysis and inducing necroptosis. Nat Microbiol 2019; 5:141-153. [PMID: 31686028 PMCID: PMC10184863 DOI: 10.1038/s41564-019-0597-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/19/2019] [Indexed: 01/29/2023]
Abstract
Staphylococcus aureus small colony variants (SCVs) are frequently associated with chronic infection, yet they lack expression of many virulence determinants associated with the pathogenicity of wild-type strains. We found that both wild-type S. aureus and a ΔhemB SCV prototype potently activate glycolysis in host cells. Glycolysis and the generation of mitochondrial reactive oxygen species were sufficient to induce necroptosis, a caspase-independent mechanism of host cell death that failed to eradicate S. aureus and instead promoted ΔhemB SCV pathogenicity. To support ongoing glycolytic activity, the ΔhemB SCV induced over a 100-fold increase in the expression of fumC, which encodes an enzyme that catalyses the degradatin of fumarate, an inhibitor of glycolysis. Consistent with fumC-dependent depletion of local fumarate, the ΔhemB SCV failed to elicit trained immunity and protection from a secondary infectious challenge in the skin. The reliance of the S. aureus SCV population on glycolysis accounts for much of its role in the pathogenesis of S. aureus skin infection.
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68
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Uchida T, Dojun N, Ota K, Sekine Y, Nakamura Y, Umetsu S, Ishimori K. Role of conserved arginine in the heme distal site of HutZ from Vibrio cholerae in the heme degradation reaction. Arch Biochem Biophys 2019; 677:108165. [PMID: 31689379 DOI: 10.1016/j.abb.2019.108165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/25/2019] [Accepted: 10/30/2019] [Indexed: 10/25/2022]
Abstract
HutZ from Vibrio cholerae is a dimeric enzyme that catalyzes degradation of heme. The highly conserved Arg92 residue in the HutZ family is proposed to interact with an iron-bound water molecule in the distal heme pocket. To clarify the specific role of Arg92 in the heme degradation reaction, the residue was substituted with alanine, leucine, histidine or lysine to modulate electrostatic interactions with iron-bound ligand. All four Arg92 mutants reacted with hydrogen peroxide to form verdoheme, a prominent intermediate in the heme degradation process. However, when ascorbic acid was used as an electron source, iron was not released even at pH 6.0 despite a decrease in the Soret band, indicating that non-enzymatic heme degradation occurred. Comparison of the rates of heme reduction, ligand binding and verdoheme formation suggested that proton transfer to the reduced oxyferrous heme, a potential rate-limiting step of heme degradation in HutZ, is hampered by mutation. In our previous study, we found that the increase in the distance between heme and Trp109 from 16 to 18 Å upon lowering the pH from 8.0 to 6.0 leads to activation of ascorbic acid-assisted heme degradation by HutZ. The distance in Arg92 mutants was >19 Å at pH 6.0, suggesting that subunit-subunit interactions at this pH are not suitable for heme degradation, similar to Asp132 and His63 mutants. These results suggest that interactions of Arg92 with heme-bound ligand induce alterations in the distance between subunits, which plays a key role in controlling the heme degradation activity of HutZ.
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Affiliation(s)
- Takeshi Uchida
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan.
| | - Nobuhiko Dojun
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kazuki Ota
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yukari Sekine
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yuina Nakamura
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Sayaka Umetsu
- Division of Chemistry, School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Koichiro Ishimori
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
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69
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Tamura K, Sugimoto H, Shiro Y, Sugita Y. Chemo-Mechanical Coupling in the Transport Cycle of a Heme ABC Transporter. J Phys Chem B 2019; 123:7270-7281. [PMID: 31362510 DOI: 10.1021/acs.jpcb.9b04356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The heme importer from pathogenic bacteria is a member of the ATP-binding cassette (ABC) transporter family, which uses the energy of ATP-binding and hydrolysis for extensive conformational changes. Previous studies have indicated that conformational changes after heme translocation are triggered by ATP-binding to nucleotide binding domains (NBDs) and then, in turn, induce conformational transitions of the transmembrane domains (TMDs). In this study, we applied a template-based iterative all-atom molecular dynamics (MD) simulation to predict the ATP-bound outward-facing conformation of the Burkholderia cenocepacia heme importer BhuUV-T. The resulting model showed a stable conformation of the TMD with the cytoplasmic gate in the closed state and the periplasmic gate in the open state. Furthermore, targeted MD simulation predicted the intermediate structure of an occluded form (Occ) with bound ATP, in which both ends of the heme translocation channel are closed. The MD simulation of the predicted Occ revealed that Ser147 on the ABC signature motifs (LSGG[Q/E]) of NBDs occasionally flips and loses the active conformation required for ATP-hydrolysis. The flipping motion was found to be coupled to the inter-NBD distance. Our results highlight the functional significance of the signature motif of ABC transporters in regulation of ATPase and chemo-mechanical coupling mechanism.
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Affiliation(s)
- Koichi Tamura
- Computational Biophysics Research Team , RIKEN Center for Computational Science , 6-7-1 minatojima-Minamimachi, Chuo-ku , Kobe , Hyogo 650-0047 , Japan
| | - Hiroshi Sugimoto
- Graduate School of Life Science , University of Hyogo , 3-2-1 Kouto, Kamigori , Ako , Hyogo 678-1297 , Japan.,Synchrotron Radiation Life Science Instrumentation Team , RIKEN SPring-8 Center , 1-1-1 Kouto , Sayo , Hyogo 679-5148 , Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science , University of Hyogo , 3-2-1 Kouto, Kamigori , Ako , Hyogo 678-1297 , Japan
| | - Yuji Sugita
- Computational Biophysics Research Team , RIKEN Center for Computational Science , 6-7-1 minatojima-Minamimachi, Chuo-ku , Kobe , Hyogo 650-0047 , Japan.,Theoretical Molecular Science Laboratory , RIKEN Cluster for Pioneering Research , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan.,Laboratory for Biomolecular Function Simulation , RIKEN Center for Biosystems Dynamics Research , 6-7-1 minatojima-Minamimachi, Chuo-ku , Kobe , Hyogo 650-0047 , Japan
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70
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Uchida T, Ota K, Sekine Y, Dojun N, Ishimori K. Subunit-subunit interactions play a key role in the heme-degradation reaction of HutZ from Vibrio cholerae. Dalton Trans 2019; 48:3973-3983. [PMID: 30834412 DOI: 10.1039/c9dt00604d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
HutZ, a dimeric protein, from Vibrio cholerae is a protein that catalyzes the oxygen-dependent degradation of heme. Interestingly, the ascorbic acid-supported heme-degradation activity of HutZ depends on pH: less than 10% of heme is degraded by HutZ at pH 8.0, but nearly 90% of heme is degraded at pH 6.0. We examined here pH-dependent conformational changes in HutZ using fluorescence spectroscopy. Trp109 is estimated to be located approximately 21 Å from heme and is present in a different subunit containing a heme axial ligand. Thus, we postulated that the distance between heme and Trp109 reflects subunit-subunit orientational changes. On the basis of resonance energy transfer from Trp109 to heme, we estimated the distance between heme and Trp109 to be approximately 17 Å at pH 8.0, while the distance increased by less than 2 Å at pH 6.0. We presumed that such changes led to a decrease in electron donation from the proximal histidine, resulting in enhancement of the heme-degradation activity. To confirm this scenario, we mutated Ala31, located at the dimer interface, to valine to alter the distance through the subunit-subunit interaction. The distance between heme and Trp109 for the A31V mutant was elongated to 24-27 Å. Although resonance Raman spectra and reduction rate of heme suggested that this mutation resulted in diminished electron donation from the heme axial ligand, ascorbic acid-supported heme-degradation activity was not observed. Based on our findings, it can be proposed that the relative positioning of two protomers is important in determining the heme degradation rate by HutZ.
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Affiliation(s)
- Takeshi Uchida
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
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71
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Clark J, Terwilliger A, Nguyen C, Green S, Nobles C, Maresso A. Heme catabolism in the causative agent of anthrax. Mol Microbiol 2019; 112:515-531. [PMID: 31063630 DOI: 10.1111/mmi.14270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2019] [Indexed: 12/23/2022]
Abstract
A challenge common to all bacterial pathogens is to acquire nutrients from hostile host environments. Iron is an important cofactor required for essential cellular processes such as DNA repair, energy production and redox balance. Within a mammalian host, most iron is sequestered within heme, which in turn is predominantly bound by hemoglobin. While little is understood about the mechanisms by which bacterial hemophores attain heme from host-hemoglobin, even less is known about intracellular heme processing. Bacillus anthracis, the causative agent of anthrax, displays a remarkable ability to grow in mammalian hosts. Hypothesizing this pathogen harbors robust ways to catabolize heme, we characterize two new intracellular heme-binding proteins that are distinct from the previously described IsdG heme monooxygenase. The first of these, HmoA, binds and degrades heme, is necessary for heme detoxification and facilitates growth on heme iron sources. The second protein, HmoB, binds and degrades heme too, but is not necessary for heme utilization or virulence. The loss of both HmoA and IsdG renders B. anthracis incapable of causing anthrax disease. The additional loss of HmoB in this background increases clearance of bacilli in lungs, which is consistent with this protein being important for survival in alveolar macrophages.
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Affiliation(s)
- Justin Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Austen Terwilliger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Chinh Nguyen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Sabrina Green
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Chris Nobles
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anthony Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
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72
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The effects of novel heme oxygenase inhibitors on the growth of Pseudomonas aeruginosa. Microb Pathog 2019; 129:64-67. [DOI: 10.1016/j.micpath.2019.01.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/19/2018] [Accepted: 01/30/2019] [Indexed: 11/24/2022]
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73
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Richard KL, Kelley BR, Johnson JG. Heme Uptake and Utilization by Gram-Negative Bacterial Pathogens. Front Cell Infect Microbiol 2019; 9:81. [PMID: 30984629 PMCID: PMC6449446 DOI: 10.3389/fcimb.2019.00081] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/08/2019] [Indexed: 02/06/2023] Open
Abstract
Iron is a transition metal utilized by nearly all forms of life for essential cellular processes, such as DNA synthesis and cellular respiration. During infection by bacterial pathogens, the host utilizes various strategies to sequester iron in a process termed, nutritional immunity. To circumvent these defenses, Gram-negative pathogens have evolved numerous mechanisms to obtain iron from heme. In this review we outline the systems that exist in several Gram-negative pathogens that are associated with heme transport and utilization, beginning with hemolysis and concluding with heme degradation. In addition, Gram-negative pathogens must also closely regulate the intracellular concentrations of iron and heme, since high levels of iron can lead to the generation of toxic reactive oxygen species. As such, we also provide several examples of regulatory pathways that control heme utilization, showing that co-regulation with other cellular processes is complex and often not completely understood.
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Affiliation(s)
- Kaylie L Richard
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | - Brittni R Kelley
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | - Jeremiah G Johnson
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
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74
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Keppel M, Piepenbreier H, Gätgens C, Fritz G, Frunzke J. Toxic but tasty - temporal dynamics and network architecture of heme-responsive two-component signaling in Corynebacterium glutamicum. Mol Microbiol 2019; 111:1367-1381. [PMID: 30767351 PMCID: PMC6850329 DOI: 10.1111/mmi.14226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2019] [Indexed: 01/24/2023]
Abstract
Heme is an essential cofactor and alternative iron source for almost all bacterial species but may cause severe toxicity upon elevated levels and consequently, regulatory mechanisms coordinating heme homeostasis represent an important fitness trait. A remarkable scenario is found in several corynebacterial species, e.g. Corynebacterium glutamicum and Corynebacterium diphtheriae, which dedicate two paralogous, heme-responsive two-component systems, HrrSA and ChrSA, to cope with the Janus nature of heme. Here, we combined experimental reporter profiling with a quantitative mathematical model to understand how this particular regulatory network architecture shapes the dynamic response to heme. Our data revealed an instantaneous activation of the detoxification response (hrtBA) upon stimulus perception and we found that kinase activity of both kinases contribute to this fast onset. Furthermore, instant deactivation of the PhrtBA promoter is achieved by a strong ChrS phosphatase activity upon stimulus decline. While the activation of detoxification response is uncoupled from further factors, heme utilization is additionally governed by the global iron regulator DtxR integrating information on iron availability into the regulatory network. Altogether, our data provide comprehensive insights how TCS cross-regulation and network hierarchy shape the temporal dynamics of detoxification (hrtBA) and utilization (hmuO) as part of a global homeostatic response to heme.
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Affiliation(s)
- Marc Keppel
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, 52425, Germany
| | - Hannah Piepenbreier
- LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Marburg, 35032, Germany
| | - Cornelia Gätgens
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, 52425, Germany
| | - Georg Fritz
- LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Marburg, 35032, Germany
| | - Julia Frunzke
- Institute of Bio- und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, 52425, Germany
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75
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Uchida T, Dojun N, Sekine Y, Ishimori K. Role of His63 in HutZ from Vibrio cholerae in the heme degradation reaction and heme binding. Dalton Trans 2019; 48:5408-5416. [DOI: 10.1039/c9dt00926d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
His63 of HutZ from Vibrio cholerae does not contribute to regioselectivity of heme degradation but plays a key role in maintaining the orientation of subunits for HutZ to function in heme degradation.
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Affiliation(s)
- Takeshi Uchida
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo 060-0810
- Japan
| | - Nobuhiko Dojun
- Graduate School of Chemical Sciences and Engineering
- Hokkaido University
- Sapporo 060-8628
- Japan
| | - Yukari Sekine
- Graduate School of Chemical Sciences and Engineering
- Hokkaido University
- Sapporo 060-8628
- Japan
| | - Koichiro Ishimori
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo 060-0810
- Japan
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76
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Andersen SB, Ghoul M, Marvig RL, Lee ZB, Molin S, Johansen HK, Griffin AS. Privatisation rescues function following loss of cooperation. eLife 2018; 7:e38594. [PMID: 30558711 PMCID: PMC6298776 DOI: 10.7554/elife.38594] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/17/2018] [Indexed: 12/11/2022] Open
Abstract
A single cheating mutant can lead to the invasion and eventual eradication of cooperation from a population. Consequently, cheat invasion is often considered equal to extinction in empirical and theoretical studies of cooperator-cheat dynamics. But does cheat invasion necessarily equate extinction in nature? By following the social dynamics of iron metabolism in Pseudomonas aeruginosa during cystic fibrosis lung infection, we observed that individuals evolved to replace cooperation with a 'private' behaviour. Phenotypic assays showed that cooperative iron acquisition frequently was upregulated early in infection, which, however, increased the risk of cheat invasion. With whole-genome sequencing we showed that if, and only if, cooperative iron acquisition is lost from the population, a private system was upregulated. The benefit of upregulation depended on iron availability. These findings highlight the importance of social dynamics of natural populations and emphasizes the potential impact of past social interaction on the evolution of private traits.
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Affiliation(s)
- Sandra Breum Andersen
- Department of ZoologyUniversity of OxfordOxfordUnited Kingdom
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
| | - Melanie Ghoul
- Department of ZoologyUniversity of OxfordOxfordUnited Kingdom
| | | | - Zhuo-Bin Lee
- Department of ZoologyUniversity of OxfordOxfordUnited Kingdom
| | - Søren Molin
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
| | - Helle Krogh Johansen
- Department of Clinical MicrobiologyRigshospitaletCopenhagenDenmark
- Department of Clinical Medicine, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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Chao A, Sieminski PJ, Owens CP, Goulding CW. Iron Acquisition in Mycobacterium tuberculosis. Chem Rev 2018; 119:1193-1220. [PMID: 30474981 DOI: 10.1021/acs.chemrev.8b00285] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The highly contagious disease tuberculosis (TB) is caused by the bacterium Mycobacterium tuberculosis (Mtb), which has been evolving drug resistance at an alarming rate. Like all human pathogens, Mtb requires iron for growth and virulence. Consequently, Mtb iron transport is an emerging drug target. However, the development of anti-TB drugs aimed at these metabolic pathways has been restricted by the dearth of information on Mtb iron acquisition. In this Review, we describe the multiple strategies utilized by Mtb to acquire ferric iron and heme iron. Mtb iron uptake is a complex process, requiring biosynthesis and subsequent export of Mtb siderophores, followed by ferric iron scavenging and ferric-siderophore import into Mtb. Additionally, Mtb possesses two possible heme uptake pathways and an Mtb-specific mechanism of heme degradation that yields iron and novel heme-degradation products. We conclude with perspectives for potential therapeutics that could directly target Mtb heme and iron uptake machineries. We also highlight how hijacking Mtb heme and iron acquisition pathways for drug import may facilitate drug transport through the notoriously impregnable Mtb cell wall.
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Affiliation(s)
| | | | - Cedric P Owens
- Schmid College of Science and Technology , Chapman University , Orange , California 92866 , United States
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78
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Jaworska K, Nieckarz M, Ludwiczak M, Raczkowska A, Brzostek K. OmpR-Mediated Transcriptional Regulation and Function of Two Heme Receptor Proteins of Yersinia enterocolitica Bio-Serotype 2/O:9. Front Cell Infect Microbiol 2018; 8:333. [PMID: 30294593 PMCID: PMC6158557 DOI: 10.3389/fcimb.2018.00333] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 08/29/2018] [Indexed: 12/26/2022] Open
Abstract
We show that Yersinia enterocolitica strain Ye9 (bio-serotype 2/O:9) utilizes heme-containing molecules as an iron source. The Ye9 genome contains two multigenic clusters, hemPRSTUV-1 and hemPRST-2, encoding putative heme receptors HemR1 and HemR2, that share 62% amino acid identity. Expression of these proteins in an Escherichia coli mutant defective in heme biosynthesis allowed this strain to use hemin and hemoglobin as a source of porphyrin. The hemPRSTUV-1 and hemPRST-2 clusters are organized as operons, expressed from the phem−1 and weaker phem−2 promoters, respectively. Expression of both operons is negatively regulated by iron and the iron-responsive transcriptional repressor Fur. In addition, OmpR, the response regulator of two component system (TCSs) EnvZ/OmpR, represses transcription of both operons through interaction with binding sequences overlapping the −35 region of their promoters. Western blot analysis of the level of HemR1 in ompR, fur, and ompRfur mutants, showed an additive effect of these mutations, indicating that OmpR may regulate HemR expression independently of Fur. However, the effect of OmpR on the activity of the phem−1 promoter and on HemR1 production was observed in both iron-depleted and iron-replete conditions, i.e., when Fur represses the iron-regulated promoter. In addition, a hairpin RNA thermometer, composed of four uracil residues (FourU) that pair with the ribosome-binding site in the 5′-untranslated region (5′-UTR) of hemR1 was predicted by in silico analysis. However, thermoregulated expression of HemR1 could not be demonstrated. Taken together, these data suggest that Fur and OmpR control iron/heme acquisition via a complex mechanism based on negative regulation of hemR1 and hemR2 at the transcriptional level. This interplay could fine-tune the level of heme receptor proteins to allow Y. enterocolitica to fulfill its iron/heme requirements without over-accumulation, which might be important for pathogenic growth within human hosts.
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Affiliation(s)
- Karolina Jaworska
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Marta Nieckarz
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Marta Ludwiczak
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Adrianna Raczkowska
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Katarzyna Brzostek
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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79
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Kalidasan V, Joseph N, Kumar S, Hamat RA, Neela VK. The 'Checkmate' for Iron Between Human Host and Invading Bacteria: Chess Game Analogy. Indian J Microbiol 2018; 58:257-267. [PMID: 30013269 PMCID: PMC6023815 DOI: 10.1007/s12088-018-0740-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 05/05/2018] [Indexed: 12/13/2022] Open
Abstract
Iron is an essential nutrient for all living organisms with critical roles in many biological processes. The mammalian host maintains the iron requirements by dietary intake, while the invading pathogenic bacteria compete with the host to obtain those absorbed irons. In order to limit the iron uptake by the bacteria, the human host employs numerous iron binding proteins and withholding defense mechanisms that capture iron from the microbial invaders. To counteract, the bacteria cope with the iron limitation imposed by the host by expressing various iron acquisition systems, allowing them to achieve effective iron homeostasis. The armamentarium used by the human host and invading bacteria, leads to the dilemma of who wins the ultimate war for iron.
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Affiliation(s)
- V. Kalidasan
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (43400 UPM), Serdang, Selangor Darul Ehsan, Malaysia
| | - Narcisse Joseph
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (43400 UPM), Serdang, Selangor Darul Ehsan, Malaysia
| | - Suresh Kumar
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (43400 UPM), Serdang, Selangor Darul Ehsan, Malaysia
| | - Rukman Awang Hamat
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (43400 UPM), Serdang, Selangor Darul Ehsan, Malaysia
| | - Vasantha Kumari Neela
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (43400 UPM), Serdang, Selangor Darul Ehsan, Malaysia
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80
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Zhao XR, Choi KR, Lee SY. Metabolic engineering of Escherichia coli for secretory production of free haem. Nat Catal 2018. [DOI: 10.1038/s41929-018-0126-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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81
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Videira MAM, Lobo SAL, Silva LSO, Palmer DJ, Warren MJ, Prieto M, Coutinho A, Sousa FL, Fernandes F, Saraiva LM. Staphylococcus aureushaem biosynthesis and acquisition pathways are linked through haem monooxygenase IsdG. Mol Microbiol 2018; 109:385-400. [DOI: 10.1111/mmi.14060] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Marco A. M. Videira
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
| | - Susana A. L. Lobo
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
- iBET, Instituto de Biologia Experimental e Tecnológica; Oeiras Portugal
| | - Liliana S. O. Silva
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
| | - David J. Palmer
- School of Biosciences; University of Kent, Giles Lane; Canterbury UK
| | - Martin J. Warren
- School of Biosciences; University of Kent, Giles Lane; Canterbury UK
| | - Manuel Prieto
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico; Universidade de Lisboa; Lisboa Portugal
| | - Ana Coutinho
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico; Universidade de Lisboa; Lisboa Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências; Universidade de Lisboa; Lisboa Portugal
| | - Filipa L. Sousa
- Department of Ecogenomics and Systems Biology; University of Vienna; Vienna Austria
| | - Fábio Fernandes
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico; Universidade de Lisboa; Lisboa Portugal
- Research Unit on Applied Molecular Biosciences−Rede de Química e Tecnologia (UCIBIO-REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; Caparica Portugal
| | - Lígia M. Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier; Universidade Nova de Lisboa; Oeiras Portugal
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82
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Ixodes scapularis does not harbor a stable midgut microbiome. ISME JOURNAL 2018; 12:2596-2607. [PMID: 29946195 DOI: 10.1038/s41396-018-0161-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 04/19/2018] [Accepted: 05/09/2018] [Indexed: 11/08/2022]
Abstract
Hard ticks of the order Ixodidae serve as vectors for numerous human pathogens, including the causative agent of Lyme Disease Borrelia burgdorferi. Tick-associated microbes can influence pathogen colonization, offering the potential to inhibit disease transmission through engineering of the tick microbiota. Here, we investigate whether B. burgdorferi encounters abundant bacteria within the midgut of wild adult Ixodes scapularis, its primary vector. Through the use of controlled sequencing methods and confocal microscopy, we find that the majority of field-collected adult I. scapularis harbor limited internal microbial communities that are dominated by endosymbionts. A minority of I. scapularis ticks harbor abundant midgut bacteria and lack B. burgdorferi. We find that the lack of a stable resident midgut microbiota is not restricted to I. scapularis since extension of our studies to I. pacificus, Amblyomma maculatum, and Dermacentor spp showed similar patterns. Finally, bioinformatic examination of the B. burgdorferi genome revealed the absence of genes encoding known interbacterial interaction pathways, a feature unique to the Borrelia genus within the phylum Spirochaetes. Our results suggest that reduced selective pressure from limited microbial populations within ticks may have facilitated the evolutionary loss of genes encoding interbacterial competition pathways from Borrelia.
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83
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Peherstorfer S, Brewitz HH, Paul George AA, Wißbrock A, Adam JM, Schmitt L, Imhof D. Insights into mechanism and functional consequences of heme binding to hemolysin-activating lysine acyltransferase HlyC from Escherichia coli. Biochim Biophys Acta Gen Subj 2018; 1862:1964-1972. [PMID: 29908817 DOI: 10.1016/j.bbagen.2018.06.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 01/01/2023]
Abstract
BACKGROUND Tight regulation of heme homeostasis is a critical mechanism in pathogenic bacteria since heme functions as iron source and prosthetic group, but is also toxic at elevated concentrations. Hemolysin-activating lysine-acyltransferase (HlyC) from Escherichia coli is crucial for maturation of hemolysin A, which lyses several mammalian cells including erythrocytes liberating large amounts of heme for bacterial uptake. A possible impact and functional consequences of the released heme on events employing bacterial HlyC have remained unexplored. METHODS Heme binding to HlyC was investigated using UV/vis and SPR spectroscopy. Functional impact of heme association was examined using an in vitro hemolysis assay. The interaction was further studied by homology modeling, molecular docking and dynamics simulations. RESULTS We identified HlyC as potential heme-binding protein possessing heme-regulatory motifs. Using wild-type protein and a double alanine mutant we demonstrated that heme binds to HlyC via histidine 151 (H151). We could show further that heme inhibits the enzymatic activity of wild-type HlyC. Computational studies illustrated potential interaction sites in addition to H151 confirming the results from spectroscopy indicating more than one heme-binding site. CONCLUSIONS Taken together, our results reveal novel insights into heme-protein interactions and regulation of a component of the heme uptake system in one of the major causative agents of urinary tract infections in humans. GENERAL SIGNIFICANCE This study points to a possible novel mechanism of regulation as present in many uropathogenic E. coli strains at an early stage of heme iron acquisition from erythrocytes for subsequent internalization by the bacterial heme-uptake machinery.
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Affiliation(s)
- Sandra Peherstorfer
- Institute of Biochemistry, University of Düsseldorf, 40255 Düsseldorf, Germany
| | - Hans Henning Brewitz
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany
| | - Ajay Abisheck Paul George
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany
| | - Amelie Wißbrock
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany
| | - Jana Maria Adam
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, University of Düsseldorf, 40255 Düsseldorf, Germany.
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany.
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84
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Abstract
Transition metals are required cofactors for many proteins that are critical for life, and their concentration within cells is carefully maintained to avoid both deficiency and toxicity. To defend against bacterial pathogens, vertebrate immune proteins sequester metals, in particular zinc, iron, and manganese, as a strategy to limit bacterial acquisition of these necessary nutrients in a process termed "nutritional immunity." In response, bacteria have evolved elegant strategies to access metals and counteract this host defense. In mammals, metal abundance can drastically shift due to changes in dietary intake or absorption from the intestinal tract, disrupting the balance between host and pathogen in the fight for metals and altering susceptibility to disease. This review describes the current understanding of how dietary metals modulate host-microbe interactions and the subsequent impact on the outcome of disease.
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Affiliation(s)
- Christopher A Lopez
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA.
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85
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Schwiesow L, Mettert E, Wei Y, Miller HK, Herrera NG, Balderas D, Kiley PJ, Auerbuch V. Control of hmu Heme Uptake Genes in Yersinia pseudotuberculosis in Response to Iron Sources. Front Cell Infect Microbiol 2018. [PMID: 29520342 PMCID: PMC5827684 DOI: 10.3389/fcimb.2018.00047] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite the mammalian host actively sequestering iron to limit pathogenicity, heme (or hemin when oxidized) and hemoproteins serve as important sources of iron for many bloodborne pathogens. The HmuRSTUV hemin uptake system allows Yersinia species to uptake and utilize hemin and hemoproteins as iron sources. HmuR is a TonB-dependent outer membrane receptor for hemin and hemoproteins. HmuTUV comprise a inner membrane ABC transporter that transports hemin and hemoproteins from the periplasmic space into the bacterial cytoplasm, where it is degraded by HmuS. Here we show that hmuSTUV but not hmuR are expressed under iron replete conditions, whereas hmuR as well as hmuSTUV are expressed under iron limiting conditions, suggesting complex transcriptional control. Indeed, expression of hmuSTUV in the presence of inorganic iron, but not in the presence of hemin, requires the global regulator IscR acting from a promoter in the intergenic region between hmuR and hmuS. This effect of IscR appears to be direct by binding a site mapped by DNaseI footprinting. In contrast, expression of hmuR under iron limiting conditions requires derepression of the ferric uptake regulator Fur acting from the hmuR promoter, as Fur binding upstream of hmuR was demonstrated biochemically. Differential expression by both Fur and IscR would facilitate maximal hemin uptake and utilization when iron and heme availability is low while maintaining the capacity for periplasmic removal and cytosolic detoxification of heme under a wider variety of conditions. We also demonstrate that a Y. pseudotuberculosis ΔiscR mutant has a survival defect when incubated in whole blood, in which iron is sequestered by heme-containing proteins. Surprisingly, this phenotype was independent of the Hmu system, the type III secretion system, complement, and the ability of Yersinia to replicate intracellularly. These results suggest that IscR regulates multiple virulence factors important for Yersinia survival and growth in mammalian tissues and reveal a surprising complexity of heme uptake expression and function under differing conditions of iron.
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Affiliation(s)
- Leah Schwiesow
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Erin Mettert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Yahan Wei
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Halie K Miller
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Natalia G Herrera
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - David Balderas
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Patricia J Kiley
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Victoria Auerbuch
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, United States
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86
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Kawano H, Miyamoto K, Yasunobe M, Murata M, Yamahata E, Yamaguchi R, Miyaki Y, Tsuchiya T, Tanabe T, Funahashi T, Tsujibo H. Identification of the heme acquisition system in Vibrio vulnificus M2799. Microb Pathog 2018; 117:100-108. [PMID: 29432914 DOI: 10.1016/j.micpath.2018.02.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/09/2018] [Accepted: 02/09/2018] [Indexed: 01/16/2023]
Abstract
Vibrio vulnificus, the causative agent of serious, often fatal, infections in humans, requires iron for its pathogenesis. As such, it obtains iron via both vulnibactin and heme-mediated iron-uptake systems. In this study, we identified the heme acquisition system in V. vulnificus M2799. The nucleotide sequences of the genes encoding heme receptors HupA and HvtA and the ATP-binding cassette (ABC) transport system proteins HupB, HupC, and HupD were determined, and then used in the construction of deletion mutants developed from a Δics strain, which could not synthesize vulnibactin. Growth experiments using these mutants indicated that HupA and HvtA are major and minor heme receptors, respectively. The expressions of two proteins were analyzed by the quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR). Furthermore, complementation analyses confirmed that the HupBCD proteins are the only ABC transport system shared by both the HupA and HvtA receptors. This is the first genetic evidence that the HupBCD proteins are essential for heme acquisition by V. vulnificus. Further investigation showed that hupA, hvtA, and hupBCD are regulated by Fur. The qRT-PCR analysis of the heme receptor genes revealed that HupR, a LysR-family positive transcriptional activator, upregulates the expression of hupA, but not hvtA. In addition, ptrB was co-transcribed with hvtA, and PtrB had no influence on growth in low-iron CM9 medium supplemented with hemin, hemoglobin, or cytochrome C.
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Affiliation(s)
- Hiroaki Kawano
- Department of Microbiology, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Katsushiro Miyamoto
- Department of Microbiology, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Megumi Yasunobe
- Department of Microbiology, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Masahiro Murata
- Department of Microbiology, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Eri Yamahata
- Department of Microbiology, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Ryo Yamaguchi
- Department of Microbiology, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Yuta Miyaki
- Department of Microbiology, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Takahiro Tsuchiya
- Department of Microbiology, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Tomotaka Tanabe
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime 790-8578, Japan
| | - Tatsuya Funahashi
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime 790-8578, Japan
| | - Hiroshi Tsujibo
- Department of Microbiology, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
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87
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Keppel M, Davoudi E, Gätgens C, Frunzke J. Membrane Topology and Heme Binding of the Histidine Kinases HrrS and ChrS in Corynebacterium glutamicum. Front Microbiol 2018; 9:183. [PMID: 29479345 PMCID: PMC5812335 DOI: 10.3389/fmicb.2018.00183] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 01/26/2018] [Indexed: 01/11/2023] Open
Abstract
The HrrSA and the ChrSA two-component systems play a central role in the coordination of heme homeostasis in the Gram-positive soil bacterium Corynebacterium glutamicum and the prominent pathogen Corynebacterium diphtheriae, both members of the Corynebacteriaceae. In this study, we have performed a comparative analysis of the membrane topology and heme-binding characteristics of the histidine kinases HrrS and ChrS of C. glutamicum. While the cytoplasmic catalytic domains are highly conserved between HrrS and ChrS, the N-terminal sensing parts share only minor sequence similarity. PhoA and LacZ fusions of the N-terminal sensor domains of HrrS and ChrS revealed that both proteins are embedded into the cytoplasmic membrane via six α-helices. Although the overall membrane topology appeared to be conserved, target gene profiling indicated a higher sensitivity of the ChrS system to low heme levels (< 1 μM). In vitro, solubilized and purified full-length proteins bound heme in a 1:1 stoichiometry per monomer. Alanine-scanning of conserved amino acid residues in the N-terminal sensor domain revealed three aromatic residues (Y112, F115, and F118), which apparently contribute to heme binding of HrrS. Exchange of either one or all three residues resulted in an almost abolished heme binding of HrrS in vitro. In contrast, ChrS mutants only displayed a red shift of the soret band from 406 to 418 nm suggesting an altered set of ligands in the triple mutant. In line with target gene profiling, these in vitro studies suggest distinct differences in the heme-protein interface of HrrS and ChrS. Since the membrane topology mapping displayed no extensive loop regions and alanine-scanning revealed potential heme-binding residues in α-helix number four, we propose an intramembrane sensing mechanism for both proteins. Overall, we present a first comparative analysis of the ChrS and HrrS kinases functioning as transient heme sensors in the Corynebacteriaceae.
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Affiliation(s)
- Marc Keppel
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Eva Davoudi
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Cornelia Gätgens
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
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88
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Choi SR, Britigan BE, Switzer B, Hoke T, Moran D, Narayanasamy P. In Vitro Efficacy of Free and Nanoparticle Formulations of Gallium(III) meso-Tetraphenylporphyrine against Mycobacterium avium and Mycobacterium abscessus and Gallium Biodistribution in Mice. Mol Pharm 2018; 15:1215-1225. [DOI: 10.1021/acs.molpharmaceut.7b01036] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Seoung-ryoung Choi
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Bradley E. Britigan
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
- Department of Internal Medicine, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
- Research Service, Veterans Affairs Medical Center-Nebraska Western Iowa, Omaha, Nebraska 68105, United States
| | - Barbara Switzer
- Department of Internal Medicine, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
- Research Service, Veterans Affairs Medical Center-Nebraska Western Iowa, Omaha, Nebraska 68105, United States
| | - Traci Hoke
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
- Department of Internal Medicine, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
- Research Service, Veterans Affairs Medical Center-Nebraska Western Iowa, Omaha, Nebraska 68105, United States
| | - David Moran
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Prabagaran Narayanasamy
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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89
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Fyrestam J, Östman C. Determination of heme in microorganisms using HPLC-MS/MS and cobalt(III) protoporphyrin IX inhibition of heme acquisition in Escherichia coli. Anal Bioanal Chem 2017; 409:6999-7010. [PMID: 29043383 PMCID: PMC5717118 DOI: 10.1007/s00216-017-0610-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/11/2017] [Accepted: 08/28/2017] [Indexed: 11/27/2022]
Abstract
One of the main threats to the achievements in modern medicine is antimicrobial resistance. Molecular targeting of bacterial acquisition mechanisms of heme has been suggested to be an alternative to antibiotics. In the present study, HPLC-MS/MS combined with a simple clean-up based on liquid-liquid extraction has been developed and evaluated for simultaneous determination of heme and porphyrin heme precursors in microorganisms. Experimental design was used to optimize the extraction parameters, to obtain a method with high recovery, low matrix effects, and high precision. The effects of additives in the culture medium on the biosynthesis of heme were studied using Escherichia coli as a model microorganism. 5-Aminolaevulinic acid and hemin increased the heme concentration in E. coli by a factor of 1.5 and 4.5, respectively. Addition of 5-aminolaevulinic acid bypassed the E. coli negative feedback control of heme biosynthesis, which led to high amounts of intracellular porphyrins. The high heme concentration obtained when hemin was used as a culture additive shows that E. coli has an uptake of heme from its surroundings. In contrast, addition of cobalt protoporphyrin IX to the growth medium reduced the amount of heme in E. coli, demonstrating this compound's ability to mimic real heme and inhibit the heme acquisition mechanisms.
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Affiliation(s)
- Jonas Fyrestam
- Division of Analytical and Toxicological Chemistry, Department of Environmental Science and Analytical Chemistry, Stockholm University, Svante arrheniusväg 16C, 106 91, Stockholm, Sweden
| | - Conny Östman
- Division of Analytical and Toxicological Chemistry, Department of Environmental Science and Analytical Chemistry, Stockholm University, Svante arrheniusväg 16C, 106 91, Stockholm, Sweden.
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90
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Malavia D, Lehtovirta-Morley LE, Alamir O, Weiß E, Gow NAR, Hube B, Wilson D. Zinc Limitation Induces a Hyper-Adherent Goliath Phenotype in Candida albicans. Front Microbiol 2017; 8:2238. [PMID: 29184547 PMCID: PMC5694484 DOI: 10.3389/fmicb.2017.02238] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/31/2017] [Indexed: 01/01/2023] Open
Abstract
Pathogenic microorganisms often face acute micronutrient limitation during infection due to the action of host-mediated nutritional immunity. The human fungal pathogen Candida albicans is polymorphic and its morphological plasticity is one of its most widely recognized pathogenicity attributes. Here we investigated the effect of zinc, iron, manganese, and copper limitation on C. albicans morphology. Restriction of zinc specifically resulted in the formation of enlarged, spherical yeasts, a phenotype which we term Goliath cells. This cellular response to zinc restriction was conserved in C. albicans, C. dubliniensis and C. tropicalis, but not in C. parapsilosis, C. lusitaniae or Debaryomyces hansenii, suggesting that it may have emerged in the last common ancestor of these related pathogenic species. Cell wall analysis revealed proportionally more chitin exposure on the Goliath cell surface. Importantly, these cells were hyper-adherent, suggesting a possible role in pathogenicity. Interestingly, the zincophore-encoding gene PRA1 was expressed by Goliath cells in zinc limited media and lack of Pra1 inhibited both cellular enlargement and adhesion. Goliath cells represent a further layer of Candida phenotypic plasticity.
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Affiliation(s)
- Dhara Malavia
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Aberdeen Fungal Group, Aberdeen, United Kingdom
| | - Laura E Lehtovirta-Morley
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Aberdeen Fungal Group, Aberdeen, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Omran Alamir
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Aberdeen Fungal Group, Aberdeen, United Kingdom
| | - Elisabeth Weiß
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Neil A R Gow
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Aberdeen Fungal Group, Aberdeen, United Kingdom
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Center for Sepsis Control and Care, University Hospital, Jena, Germany.,Institute of Microbiology, Microbial Pathogenicity, Friedrich Schiller University, Jena, Germany
| | - Duncan Wilson
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Aberdeen Fungal Group, Aberdeen, United Kingdom
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91
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Identification of Staphylococcus aureus Factors Required for Pathogenicity and Growth in Human Blood. Infect Immun 2017; 85:IAI.00337-17. [PMID: 28808156 PMCID: PMC5649012 DOI: 10.1128/iai.00337-17] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 08/05/2017] [Indexed: 12/20/2022] Open
Abstract
Staphylococcus aureus is a human commensal but also has devastating potential as an opportunistic pathogen. S. aureus bacteremia is often associated with an adverse outcome. To identify potential targets for novel control approaches, we have identified S. aureus components that are required for growth in human blood. An ordered transposon mutant library was screened, and 9 genes involved specifically in hemolysis or growth on human blood agar were identified by comparing the mutants to the parental strain. Three genes (purA, purB, and pabA) were subsequently found to be required for pathogenesis in the zebrafish embryo infection model. The pabA growth defect was specific to the red blood cell component of human blood, showing no difference from the parental strain in growth in human serum, human plasma, or sheep or horse blood. PabA is required in the tetrahydrofolate (THF) biosynthesis pathway. The pabA growth defect was found to be due to a combination of loss of THF-dependent dTMP production by the ThyA enzyme and increased demand for pyrimidines in human blood. Our work highlights pabA and the pyrimidine salvage pathway as potential targets for novel therapeutics and suggests a previously undefined role for a human blood factor in the activity of sulfonamide antibiotics.
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92
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Sgheiza V, Novick B, Stanton S, Pierce J, Kalmeta B, Holmquist MF, Grimaldi K, Bren KL, Michel LV. Covalent bonding of heme to protein prevents heme capture by nontypeable Haemophilus influenzae. FEBS Open Bio 2017; 7:1778-1783. [PMID: 29123985 PMCID: PMC5666386 DOI: 10.1002/2211-5463.12324] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/15/2017] [Accepted: 09/19/2017] [Indexed: 12/31/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) are Gram‐negative pathogens that contribute to a variety of diseases, including acute otitis media and chronic obstructive pulmonary disease. As NTHi have an absolute requirement for heme during aerobic growth, these bacteria have to scavenge heme from their human hosts. These heme sources can range from free heme to heme bound to proteins, such as hemoglobin. To test the impact of heme structural factors on heme acquisition by NTHi, we prepared a series of heme sources that systematically vary in heme exposure and covalent binding of heme to peptide/protein and tested the ability of NTHi to use these sources to support growth. Results from this study suggest that NTHi can utilize protein‐associated heme only if it is noncovalently attached to the protein.
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Affiliation(s)
- Valerie Sgheiza
- School of Chemistry and Materials Science Rochester Institute of Technology NY USA
| | - Bethany Novick
- School of Chemistry and Materials Science Rochester Institute of Technology NY USA
| | - Sarah Stanton
- School of Chemistry and Materials Science Rochester Institute of Technology NY USA
| | - Jeanetta Pierce
- School of Chemistry and Materials Science Rochester Institute of Technology NY USA
| | - Breanne Kalmeta
- School of Chemistry and Materials Science Rochester Institute of Technology NY USA
| | | | - Kyle Grimaldi
- School of Chemistry and Materials Science Rochester Institute of Technology NY USA
| | - Kara L Bren
- Department of Chemistry University of Rochester NY USA
| | - Lea Vacca Michel
- School of Chemistry and Materials Science Rochester Institute of Technology NY USA
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93
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Naoe Y, Nakamura N, Rahman MM, Tosha T, Nagatoishi S, Tsumoto K, Shiro Y, Sugimoto H. Structural basis for binding and transfer of heme in bacterial heme-acquisition systems. Proteins 2017; 85:2217-2230. [PMID: 28913898 DOI: 10.1002/prot.25386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 08/21/2017] [Accepted: 09/11/2017] [Indexed: 01/10/2023]
Abstract
Periplasmic heme-binding proteins (PBPs) in Gram-negative bacteria are components of the heme acquisition system. These proteins shuttle heme across the periplasmic space from outer membrane receptors to ATP-binding cassette (ABC) heme importers located in the inner-membrane. In the present study, we characterized the structures of PBPs found in the pathogen Burkholderia cenocepacia (BhuT) and in the thermophile Roseiflexus sp. RS-1 (RhuT) in the heme-free and heme-bound forms. The conserved motif, in which a well-conserved Tyr interacts with the nearby Arg coordinates on heme iron, was observed in both PBPs. The heme was recognized by its surroundings in a variety of manners including hydrophobic interactions and hydrogen bonds, which was confirmed by isothermal titration calorimetry. Furthermore, this study of 3 forms of BhuT allowed the first structural comparison and showed that the heme-binding cleft of BhuT adopts an "open" state in the heme-free and 2-heme-bound forms, and a "closed" state in the one-heme-bound form with unique conformational changes. Such a conformational change might adjust the interaction of the heme(s) with the residues in PBP and facilitate the transfer of the heme into the translocation channel of the importer.
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Affiliation(s)
- Youichi Naoe
- Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Nozomi Nakamura
- Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.,Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo, 678-1297, Japan
| | - Md Mahfuzur Rahman
- Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.,Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo, 678-1297, Japan
| | - Takehiko Tosha
- Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Satoru Nagatoishi
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8656, Japan.,Laboratory of Medical Proteomics, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Yoshitsugu Shiro
- Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.,Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo, 678-1297, Japan
| | - Hiroshi Sugimoto
- Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.,Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo, 678-1297, Japan
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94
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Constante M, Fragoso G, Calvé A, Samba-Mondonga M, Santos MM. Dietary Heme Induces Gut Dysbiosis, Aggravates Colitis, and Potentiates the Development of Adenomas in Mice. Front Microbiol 2017; 8:1809. [PMID: 28983289 PMCID: PMC5613120 DOI: 10.3389/fmicb.2017.01809] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 09/05/2017] [Indexed: 12/15/2022] Open
Abstract
Dietary heme can be used by colonic bacteria equipped with heme-uptake systems as a growth factor and thereby impact on the microbial community structure. The impact of heme on the gut microbiota composition may be particularly pertinent in chronic inflammation such as in inflammatory bowel disease (IBD), where a strong association with gut dysbiosis has been consistently reported. In this study we investigated the influence of dietary heme on the gut microbiota and inferred metagenomic composition, and on chemically induced colitis and colitis-associated adenoma development in mice. Using 16S rRNA gene sequencing, we found that mice fed a diet supplemented with heme significantly altered their microbiota composition, characterized by a decrease in α-diversity, a reduction of Firmicutes and an increase of Proteobacteria, particularly Enterobacteriaceae. These changes were similar to shifts seen in dextran sodium sulfate (DSS)-treated mice to induce colitis. In addition, dietary heme, but not systemically delivered heme, contributed to the exacerbation of DSS-induced colitis and facilitated adenoma formation in the azoxymethane/DSS colorectal cancer (CRC) mouse model. Using inferred metagenomics, we found that the microbiota alterations elicited by dietary heme resulted in non-beneficial functional shifts, which were also characteristic of DSS-induced colitis. Furthermore, a reduction in fecal butyrate levels was found in mice fed the heme supplemented diet compared to mice fed the control diet. Iron metabolism genes known to contribute to heme release from red blood cells, heme uptake, and heme exporter proteins, were significantly enriched, indicating a shift toward favoring the growth of bacteria able to uptake heme and protect against its toxicity. In conclusion, our data suggest that luminal heme, originating from dietary components or gastrointestinal bleeding in IBD and, to lesser extent in CRC, directly contributes to microbiota dysbiosis. Thus, luminal heme levels may further exacerbate colitis through the modulation of the gut microbiota and its metagenomic functional composition. Our data may have implications in the development of novel targets for therapeutic approaches aimed at lowering gastrointestinal heme levels through heme chelation or degradation using probiotics and nutritional interventions.
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Affiliation(s)
- Marco Constante
- Département de Médecine, Université de Montréal, MontréalQC, Canada.,Nutrition and Microbiome Laboratory, Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, MontréalQC, Canada
| | - Gabriela Fragoso
- Nutrition and Microbiome Laboratory, Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, MontréalQC, Canada
| | - Annie Calvé
- Nutrition and Microbiome Laboratory, Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, MontréalQC, Canada
| | - Macha Samba-Mondonga
- Nutrition and Microbiome Laboratory, Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, MontréalQC, Canada
| | - Manuela M Santos
- Département de Médecine, Université de Montréal, MontréalQC, Canada.,Nutrition and Microbiome Laboratory, Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, MontréalQC, Canada
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95
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Balaban CL, Banchio C, Ceccarelli EA. TAT-mediated transduction of bacterial redox proteins generates a cytoprotective effect on neuronal cells. PLoS One 2017; 12:e0184617. [PMID: 28886198 PMCID: PMC5591030 DOI: 10.1371/journal.pone.0184617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/28/2017] [Indexed: 12/23/2022] Open
Abstract
Cell penetrating peptides, also known as protein transduction domains, have the capacity to ubiquitously cross cellular membranes carrying many different cargos with negligible cytotoxicity. As a result, they have emerged as a powerful tool for macromolecular delivery-based therapies. In this study, catalytically active bacterial Ferredoxin-NADP+ reductase (LepFNR) and Heme oxygenase (LepHO) fused to the HIV TAT-derived protein transduction peptide (TAT) were efficiently transduced to neuroblastoma SHSY-5Y cells. Proteins entered the cells through an endocytic pathway showing a time/concentration dependent mechanism that was clearly modulated by the nature of the cargo protein. Since ferredoxin-NADP+ reductases and heme oxygenases have been implicated in mechanisms of oxidative stress defense, neuroblastoma cells simultaneously transduced with TAT-LepFNR and TAT-LepHO were challenged by H2O2 incubations to judge the cytoprotective power of these bacterial enzymes. Accumulation of reactive oxygen species was significantly reduced in these transduced neuronal cells. Moreover, measurements of metabolic viability, membrane integrity, and cell survival indicated that these cells showed a better tolerance to oxidative stress. Our results open the possibility for the application of transducible active redox proteins to overcome the damage elicited by oxidative stress in cells and tissues.
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Affiliation(s)
- Cecilia L. Balaban
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Rosario, Argentina
| | - Claudia Banchio
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Rosario, Argentina
| | - Eduardo A. Ceccarelli
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Rosario, Argentina
- * E-mail:
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96
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Sharpton T, Lyalina S, Luong J, Pham J, Deal EM, Armour C, Gaulke C, Sanjabi S, Pollard KS. Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice. mSystems 2017; 2:e00036-17. [PMID: 28904997 PMCID: PMC5585689 DOI: 10.1128/msystems.00036-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/08/2017] [Indexed: 02/08/2023] Open
Abstract
The gut microbiome is linked to inflammatory bowel disease (IBD) severity and altered in late-stage disease. However, it is unclear how gut microbial communities change over the course of IBD development, especially in regard to function. To investigate microbiome-mediated disease mechanisms and discover early biomarkers of IBD, we conducted a longitudinal metagenomic investigation in an established mouse model of IBD, where damped transforming growth factor β (TGF-β) signaling in T cells leads to peripheral immune activation, weight loss, and severe colitis. IBD development is associated with abnormal gut microbiome temporal dynamics, including damped acquisition of functional diversity and significant differences in abundance trajectories for KEGG modules such as glycosaminoglycan degradation, cellular chemotaxis, and type III and IV secretion systems. Most differences between sick and control mice emerge when mice begin to lose weight and heightened T cell activation is detected in peripheral blood. However, levels of lipooligosaccharide transporter abundance diverge prior to immune activation, indicating that it could be a predisease indicator or microbiome-mediated disease mechanism. Taxonomic structure of the gut microbiome also significantly changes in association with IBD development, and the abundances of particular taxa, including several species of Bacteroides, correlate with immune activation. These discoveries were enabled by our use of generalized linear mixed-effects models to test for differences in longitudinal profiles between healthy and diseased mice while accounting for the distributions of taxon and gene counts in metagenomic data. These findings demonstrate that longitudinal metagenomics is useful for discovering the potential mechanisms through which the gut microbiome becomes altered in IBD. IMPORTANCE IBD patients harbor distinct microbial communities with functional capabilities different from those seen with healthy people. But is this cause or effect? Answering this question requires data on changes in gut microbial communities leading to disease onset. By performing weekly metagenomic sequencing and mixed-effects modeling on an established mouse model of IBD, we identified several functional pathways encoded by the gut microbiome that covary with host immune status. These pathways are novel early biomarkers that may either enable microbes to live inside an inflamed gut or contribute to immune activation in IBD mice. Future work will validate the potential roles of these microbial pathways in host-microbe interactions and human disease. This study was novel in its longitudinal design and focus on microbial pathways, which provided new mechanistic insights into the role of gut microbes in IBD development.
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Affiliation(s)
- Thomas Sharpton
- Department of Microbiology, Oregon State University, Corvallis, Oregon
- Department of Statistics, Oregon State University, Corvallis, Oregon
| | | | - Julie Luong
- Gladstone Institutes, San Francisco, California, USA
| | - Joey Pham
- Gladstone Institutes, San Francisco, California, USA
| | - Emily M. Deal
- Gladstone Institutes, San Francisco, California, USA
| | - Courtney Armour
- Department of Microbiology, Oregon State University, Corvallis, Oregon
| | | | - Shomyseh Sanjabi
- Gladstone Institutes, San Francisco, California, USA
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, California, USA
- Department of Epidemiology & Biostatistics, Institute for Human Genetics, and Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
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97
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The Small Protein HemP Is a Transcriptional Activator for the Hemin Uptake Operon in Burkholderia multivorans ATCC 17616. Appl Environ Microbiol 2017. [PMID: 28625994 DOI: 10.1128/aem.00479-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Iron and heme play very important roles in various metabolic functions in bacteria, and their intracellular homeostasis is maintained because high concentrations of free forms of these molecules greatly facilitate the Fenton reaction-mediated production of large amounts of reactive oxygen species that severely damage various biomolecules. The ferric uptake regulator (Fur) from Burkholderiamultivorans ATCC 17616 is an iron-responsive global transcriptional regulator, and its fur deletant exhibits pleiotropic phenotypes. In this study, we found that the phenotypes of the fur deletant were suppressed by an additional mutation in hemP The transcription of hemP was negatively regulated by Fur under iron-replete conditions and was constitutive in the fur deletant. Growth of a hemP deletant was severely impaired in a medium containing hemin as the sole iron source, demonstrating the important role of HemP in hemin utilization. HemP was required as a transcriptional activator that specifically binds the promoter-containing region upstream of a Fur-repressive hmuRSTUV operon, which encodes the proteins for hemin uptake. A hmuR deletant was still able to grow using hemin as the sole iron source, albeit at a rate clearly lower than that of the wild-type strain. These results strongly suggested (i) the involvement of HmuR in hemin uptake and (ii) the presence in ATCC 17616 of at least part of other unknown hemin uptake systems whose expression depends on the HemP function. Our in vitro analysis also indicated high-affinity binding of HemP to hemin, and such a property might modulate transcriptional activation of the hmu operon.IMPORTANCE Although the hmuRSTUV genes for the utilization of hemin as a sole iron source have been identified in a few Burkholderia strains, the regulatory expression of these genes has remained unknown. Our analysis in this study using B. multivorans ATCC 17616 showed that its HemP protein is required for expression of the hmuRSTUV operon, and the role of HemP in betaproteobacterial species was elucidated for the first time, to our knowledge, in this study. The HemP protein was also found to have two additional properties that have not been reported for functional homologues in other species; one is that HemP is able to bind to the promoter-containing region of the hmu operon to directly activate its transcription, and the other is that HemP is also required for the expression of an unknown hemin uptake system.
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98
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Abstract
Iron is an essential micronutrient for both microbes and humans alike. For well over half a century we have known that this element, in particular, plays a pivotal role in health and disease and, most especially, in shaping host-pathogen interactions. Intracellular iron concentrations serve as a critical signal in regulating the expression not only of high-affinity iron acquisition systems in bacteria, but also of toxins and other noted virulence factors produced by some major human pathogens. While we now are aware of many strategies that the host has devised to sequester iron from invading microbes, there are as many if not more sophisticated mechanisms by which successful pathogens overcome nutritional immunity imposed by the host. This review discusses some of the essential components of iron sequestration and scavenging mechanisms of the host, as well as representative Gram-negative and Gram-positive pathogens, and highlights recent advances in the field. Last, we address how the iron acquisition strategies of pathogenic bacteria may be exploited for the development of novel prophylactics or antimicrobials.
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99
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Hameed A, Al-Rashida M, Alharthy RD, Uroos M, Mughal EU, Ali SA, Khan KM. Small molecules as activators in medicinal chemistry (2000-2016). Expert Opin Ther Pat 2017; 27:1089-1110. [PMID: 28673105 DOI: 10.1080/13543776.2017.1349103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
INTRODUCTION From therapeutic point of view, it is often beneficial to enhance the expression of certain enzymes whose low expression is responsible for the observed ailment. Small molecules as activators of several enzymes have great biological potential as anti-microbial and anti-cancer agents, for the treatment of diabetes, obesity, metabolic disorders, and for the treatment of neurological disorders including Alzheimer's disease. This review covers patents describing small molecules as activators, and provides structural leads for the design of even more potent activators. Area covered: This review is focused on small molecules that have been explored as activators of enzymes in the last and current decade (2000-2016). Expert opinion: The ability to modulate activity of enzymes has long been a quest of medicinal chemistry. This has been the impetus behind the development of a plethora of drugs as enzyme inhibitors. However only a few enzyme activators as drugs have made it to the market. Disorders characterized by supressed enzyme activity can be treated by enhancing the activity of a specific enzyme.
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Affiliation(s)
- Abdul Hameed
- a H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences , University of Karachi , Karachi , Pakistan
| | - Mariya Al-Rashida
- b Department of Chemistry , Forman Christian College (A Chartered University) , Lahore , Pakistan
| | - Rima D Alharthy
- c Department of Chemistry, Science and Arts College , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Maliha Uroos
- d Institute of Chemistry , University of the Punjab , Lahore , Pakistan
| | | | - Syed Abid Ali
- a H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences , University of Karachi , Karachi , Pakistan
| | - Khalid Mohammed Khan
- a H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences , University of Karachi , Karachi , Pakistan
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100
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Sterkel M, Oliveira JHM, Bottino-Rojas V, Paiva-Silva GO, Oliveira PL. The Dose Makes the Poison: Nutritional Overload Determines the Life Traits of Blood-Feeding Arthropods. Trends Parasitol 2017; 33:633-644. [PMID: 28549573 DOI: 10.1016/j.pt.2017.04.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 04/20/2017] [Accepted: 04/27/2017] [Indexed: 12/21/2022]
Abstract
Vertebrate blood composition is heavily biased towards proteins, and hemoglobin, which is a hemeprotein, is by far the most abundant protein. Typically, hematophagous insects ingest blood volumes several times their weight before the blood meal. This barbarian feast offers an abundance of nutrients, but the degradation of blood proteins generates toxic concentrations of amino acids and heme, along with unparalleled microbiota growth. Despite this challenge, hematophagous arthropods have successfully developed mechanisms that bypass the toxicity of these molecules. While these adaptations allow hematophagous arthropods to tolerate their diet, they also constitute a unique mode of operation for cell signaling, immunity, and metabolism, the study of which may offer insights into the biology of disease vectors and may lead to novel vector-specific control methods.
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Affiliation(s)
- Marcos Sterkel
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - José Henrique M Oliveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Vanessa Bottino-Rojas
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Gabriela O Paiva-Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Brazil
| | - Pedro L Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Brazil.
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