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Zhang J, Liang Q, Mu D, Lian F, Gong Y, Ye M, Chen G, Ye Y, Du Z. Cultivating the uncultured: Harnessing the "sandwich agar plate" approach to isolate heme-dependent bacteria from marine sediment. MLIFE 2024; 3:143-155. [PMID: 38827516 PMCID: PMC11139205 DOI: 10.1002/mlf2.12093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/18/2023] [Accepted: 10/10/2023] [Indexed: 06/04/2024]
Abstract
In the classical microbial isolation technique, the isolation process inevitably destroys all microbial interactions and thus makes it difficult to culture the many microorganisms that rely on these interactions for survival. In this study, we designed a simple coculture technique named the "sandwich agar plate method," which maintains microbial interactions throughout the isolation and pure culture processes. The total yield of uncultured species in sandwich agar plates based on eight helper strains was almost 10-fold that of the control group. Many uncultured species displayed commensal lifestyles. Further study found that heme was the growth-promoting factor of some marine commensal bacteria. Subsequent genomic analysis revealed that heme auxotrophies were common in various biotopes and prevalent in many uncultured microbial taxa. Moreover, our study supported that the survival strategies of heme auxotrophy in different habitats varied considerably. These findings highlight that cocultivation based on the "sandwich agar plate method" could be developed and used to isolate more uncultured bacteria.
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Affiliation(s)
- Jing Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
| | | | - Da‐Shuai Mu
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
- Shandong University‐Weihai Research Institute of Industrial TechnologyWeihaiChina
| | | | - Ya Gong
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
| | - Mengqi Ye
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
| | - Guan‐Jun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
| | - Yuqi Ye
- Marine CollegeShandong UniversityWeihaiChina
| | - Zong‐Jun Du
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
- Shandong University‐Weihai Research Institute of Industrial TechnologyWeihaiChina
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2
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Graf J, Schöpperle M, Pernil R, Schleiff E. Two TonB-dependent outer membrane transporters involved in heme uptake in Anabaena sp. PCC 7120. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:16-28. [PMID: 38234586 PMCID: PMC10792254 DOI: 10.15698/mic2024.01.812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 11/03/2023] [Accepted: 11/13/2023] [Indexed: 01/19/2024]
Abstract
Low availability of micronutrients such as iron has enforced the evolution of uptake systems in all kingdoms of life. In Gram-negative bacteria, outer membrane, periplasmatic and plasma membrane localized proteins facilitate the uptake of iron-loaded chelators, which are energized by TonB proteins. The specificity of different uptake systems likely depends either on the endogenously produced siderophore or on the bioavailability of iron-chelator complexes in the environment. Hence, an uptake system for schizokinen produced by the model cyanobacterium Anabaena sp. PCC 7120 exists, while bioinformatics analysis suggests the existence of additional systems, likely for uptake of xenosiderophores. Consistently, proteins encoded by alr2153 (hutA1) and alr3242 (hutA2) are assigned as outer membrane heme transporters. Indeed, Anabaena sp. PCC 7120 can utilize external heme as an iron source. The addition of heme resulted in an induction of genes involved in heme degradation and chlorophyll a synthesis and in an increase of the chlorophyll a content. Moreover, iron starvation induced the expression of hutA1, while the addition of heme led to its repression. Remarkably, the addition of a high concentration of heme but not iron starvation resulted in hutA2 induction. Plasmid insertion mutants of both genes exhibited a reduced capacity to recover from iron starvation by heme addition, which indicates a dependence of heme uptake on functional HutA1 and HutA2 proteins. The structural model generated by bioinformatics methods is further in agreement with a role in heme uptake. Thus, we provide evidence that Anabaena sp. PCC 7120 uses a heme uptake system in parallel to other iron acquisition systems.
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Affiliation(s)
- Julia Graf
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
| | - Martin Schöpperle
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
- Current address: Lonza Cologne GmbH, Köln, Germany:
| | - Rafael Pernil
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, 60438 Frankfurt, Germany
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Max von Laue Str. 11, 60438 Frankfurt, Germany
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3
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Hassan IZ, Qekwana DN, Naidoo V. Do Pathogenic Escherichia coli Isolated from Gallus gallus in South Africa Carry Co-Resistance Toward Colistin and Carbapenem Antimicrobials? Foodborne Pathog Dis 2023; 20:388-397. [PMID: 37471208 DOI: 10.1089/fpd.2023.0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023] Open
Abstract
Colistin and carbapenems are critically important antimicrobials often used as a last resort to manage multidrug-resistant bacterial infections in humans. With limited alternatives, resistance to these antimicrobials is of concern as organisms could potentially spread horizontally rendering treatments ineffective. The aim of this study was to investigate co-resistance to colistin and carbapenems among Escherichia coli isolated from poultry in South Africa. Forty-six E. coli strains obtained from clinical cases of breeder and broiler chickens were used. In addition to other antibiotics, all the isolates were tested against colistin and carbapenems using broth microdilution. Multiplex polymerase chain reactions were used to investigate the presence of colistin (mcr-1 to 5) and carbapenem (blaOXA-48, blaNDM-1, and blaVIM) resistance genes. Isolates exhibiting colistin resistance (>2 μg/mL) underwent a whole-genome sequencing analysis. Resistance to colistin (10.9%) and cefepime (6.5%) was noted with all colistin-resistant strains harboring the mcr-1 gene. None of the E. coli isolates were resistant to carbapenems nor carried the other resistant genes (mcr-2 to 5, blaOXA-48, blaNDM-1, and blaVIM). The mcr-1-positive strains belonged to sequence types ST117 and ST156 and carried virulence genes ompA, aslA, fdeC, fimH, iroN, iutA, tsh, pic, ast A and set 1A/1B. In conclusion, clinical E. coli strains from chickens in this study possessed mobile resistance genes for colistin and several other clinically relevant antimicrobials but not carbapenems. Additionally, they belonged to sequence types in addition to carrying virulence factors often associated with human extraintestinal pathogenic E. coli infections. Thus, the potential risk of transmitting these strains to humans cannot be underestimated especially if sick birds are dispatched into the thriving poorly regulated Cornish hen industry. The need for routine veterinary surveillance and monitoring of antimicrobial resistance, antimicrobial use and the importance of strengthening regulations guiding the informal poultry sector remains important.
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Affiliation(s)
- Ibrahim Zubairu Hassan
- Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Daniel N Qekwana
- Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Vinny Naidoo
- Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
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4
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Ray S, Gaudet R. Structures and coordination chemistry of transporters involved in manganese and iron homeostasis. Biochem Soc Trans 2023; 51:897-923. [PMID: 37283482 PMCID: PMC10330786 DOI: 10.1042/bst20210699] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/08/2023]
Abstract
A repertoire of transporters plays a crucial role in maintaining homeostasis of biologically essential transition metals, manganese, and iron, thus ensuring cell viability. Elucidating the structure and function of many of these transporters has provided substantial understanding into how these proteins help maintain the optimal cellular concentrations of these metals. In particular, recent high-resolution structures of several transporters bound to different metals enable an examination of how the coordination chemistry of metal ion-protein complexes can help us understand metal selectivity and specificity. In this review, we first provide a comprehensive list of both specific and broad-based transporters that contribute to cellular homeostasis of manganese (Mn2+) and iron (Fe2+ and Fe3+) in bacteria, plants, fungi, and animals. Furthermore, we explore the metal-binding sites of the available high-resolution metal-bound transporter structures (Nramps, ABC transporters, P-type ATPase) and provide a detailed analysis of their coordination spheres (ligands, bond lengths, bond angles, and overall geometry and coordination number). Combining this information with the measured binding affinity of the transporters towards different metals sheds light into the molecular basis of substrate selectivity and transport. Moreover, comparison of the transporters with some metal scavenging and storage proteins, which bind metal with high affinity, reveal how the coordination geometry and affinity trends reflect the biological role of individual proteins involved in the homeostasis of these essential transition metals.
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Affiliation(s)
- Shamayeeta Ray
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, U.S.A
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, U.S.A
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5
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Llauger M, Arnau J, Albano-Gaglio M, Bover-Cid S, Martín B, Bou R. Utilization of Porcine Livers through the Formation of Zn-Protoporphyrin Pigment Optimized by a Response Surface Methodology. Foods 2023; 12:foods12091903. [PMID: 37174439 PMCID: PMC10178239 DOI: 10.3390/foods12091903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
There is a growing demand for clean-label products. This study aimed to obtain a food-grade coloring ingredient for meat products based on the formation of Zn-protoporphyrin from porcine livers, thus contributing to the development of nitrite-free products. First, the effects of sodium disulfite and acetic, ascorbic, and lactic acids on the formation of Zn-protoporphyrin and the total microbial count were studied. The combination of ascorbic and acetic acids resulted in a higher Zn-protoporphyrin content than acetic acid alone, and microbial levels were maintained (ca. 3 log CFU/mL). Second, a response surface methodology was used to maximize Zn-protoporphyrin while maintaining microbiological food standards. To that end, the effects of pH (4.2-5.4), incubation time (3-30 h), and temperature (25-50 °C) were studied. The selected conditions for Zn-protoporphyrin formation involved anaerobic incubation at pH 4.8 and 45 °C for 24 h. The safety was validated through challenge testing for relevant pathogens (Listeria monocytogenes, Salmonella spp., and Clostridium perfringens). A significant reduction (>6 log units) was observed in the selected conditions for L. monocytogenes and Salmonella, whereas C. perfringens spores remained at the inoculated levels. The optimized procedure is proven to be microbiologically safe, and may improve the color of nitrite-free meat products.
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Affiliation(s)
- Mar Llauger
- Food Safety and Functionality Program, Institute of Agrifood Research and Technology (IRTA), Finca Camps i Armet s/n, 17121 Monells, Spain
| | - Jacint Arnau
- Food Quality and Technology Program, Institute of Agrifood Research and Technology (IRTA), Finca Camps i Armet s/n, 17121 Monells, Spain
| | - Michela Albano-Gaglio
- Food Quality and Technology Program, Institute of Agrifood Research and Technology (IRTA), Finca Camps i Armet s/n, 17121 Monells, Spain
| | - Sara Bover-Cid
- Food Safety and Functionality Program, Institute of Agrifood Research and Technology (IRTA), Finca Camps i Armet s/n, 17121 Monells, Spain
| | - Belén Martín
- Food Safety and Functionality Program, Institute of Agrifood Research and Technology (IRTA), Finca Camps i Armet s/n, 17121 Monells, Spain
| | - Ricard Bou
- Food Quality and Technology Program, Institute of Agrifood Research and Technology (IRTA), Finca Camps i Armet s/n, 17121 Monells, Spain
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Cui F, Fan R, Wang D, Li J, Li T. Research progress on iron uptake pathways and mechanisms of foodborne microorganisms and their application in the food sector. Crit Rev Food Sci Nutr 2023:1-19. [PMID: 37099732 DOI: 10.1080/10408398.2023.2204491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Iron is one of the essential nutrients for almost all microorganisms. Under iron-limited conditions, bacteria can secrete siderophores to the outside world to absorb iron for survival. This process requires the coordinated action of energy-transducing proteins, transporters, and receptors. The spoilage factors of some spoilage bacteria and the pathogenic mechanism of pathogenic bacteria are also closely related to siderophores. Meanwhile, some siderophores have also gradually evolved toward beneficial aspects. First, a variety of siderophores are classified into three aspects. In addition, representative iron uptake systems of Gram-negative and Gram-positive bacteria are described in detail to understand the common and specific pathways of iron uptake by various bacteria. In particular, the causes of siderophore-induced bacterial pathogenicity and the methods and mechanisms of inhibiting bacterial iron absorption under the involvement of siderophores are presented. Then, the application of siderophores in the food sector is mainly discussed, such as improving the food quality of dairy products and meat, inhibiting the attack of pathogenic bacteria on food, improving the plant growth environment, and promoting plant growth. Finally, this review highlights the unresolved fate of siderophores in the iron uptake system and emphasizes further development of siderophore-based substitutes for traditional drugs, new antibiotic-resistance drugs, and vaccines in the food and health sectors.
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Affiliation(s)
- Fangchao Cui
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Rongsen Fan
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Dangfeng Wang
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
- College of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jianrong Li
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Tingting Li
- Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, Dalian, China
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7
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Akhtar AA, Turner DP. The role of bacterial ATP-binding cassette (ABC) transporters in pathogenesis and virulence: Therapeutic and vaccine potential. Microb Pathog 2022; 171:105734. [PMID: 36007845 DOI: 10.1016/j.micpath.2022.105734] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/24/2022]
Abstract
The ATP-binding cassette (ABC) transporter superfamily is found in all domains of life, facilitating critical biological processes through the translocation of a wide variety of substrates from, ions to proteins, across cellular membranes in an ATP-coupled process. The role of ABC transporters in eukaryotes has been well established: the facilitation of genetic diseases and multi-drug resistance (MDR) in cancer patients. In contrast, the role of ABC transporters in prokaryotes has been ambiguous due to their diverse functions and the sheer number of organisms in which they reside. This review examines the role of bacterial ABC transporters in pathogenesis and virulence, and their potential for therapeutic and vaccine application. We demonstrate how ABC transporters play a vital role in the virulence and pathogenesis of several pathogenic bacteria through the import of essential molecules, such as metal ions, amino acids, peptides, vitamins and osmoprotectants, as well as, the export of virulent determinants involved in glycoconjugate biosynthesis and Type I secretion. Furthermore, ABC exporters facilitate the persistence of pathogenic bacteria through the export of toxic xenobiotic substances, thus, contributing to the development of antimicrobial resistance. We also show that ABC transporters display considerable potential for therapeutic application through immunisation and resistance reversal. In conclusion, bacterial ABC transporters play an immense role in virulence and pathogenesis and display desirable traits for clinical use, therefore, potentially aiding in the battle against MDR.
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Affiliation(s)
- Armaan A Akhtar
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom.
| | - David Pj Turner
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
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8
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Tu P, Chi L, Bian X, Gao B, Ru H, Lu K. A Black Raspberry-Rich Diet Protects From Dextran Sulfate Sodium-Induced Intestinal Inflammation and Host Metabolic Perturbation in Association With Increased Aryl Hydrocarbon Receptor Ligands in the Gut Microbiota of Mice. Front Nutr 2022; 9:842298. [PMID: 35734371 PMCID: PMC9208328 DOI: 10.3389/fnut.2022.842298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Dietary modulation of the gut microbiota recently received considerable attention, and ligand activation of aryl hydrocarbon receptor (AHR) plays a pivotal role in intestinal immunity. Importantly, black raspberry (BRB, Rubus occidentalis) is associated with a variety of beneficial health effects. We aim to investigate effects of a BRB-rich diet on dextran sulfate sodium (DSS)-induced intestinal inflammation and to determine whether its consequent anti-inflammatory effects are relevant to modulation of the gut microbiota, especially its production of AHR ligands. A mouse model of DSS-induced intestinal inflammation was used in the present study. C57BL/6J mice were fed either AIN-76A or BRB diet. Composition and functions of the gut microbiota were assessed by 16S rRNA sequencing and comparative metagenome analysis. Metabolic profiles of host and the gut microbiome were assessed by serum and fecal metabolomic profiling and identification. BRB diet was found to ameliorate DSS-induced intestinal inflammation and host metabolic perturbation. BRB diet also protected from DSS-induced perturbation in diversity and composition in the gut microbiota. BRB diet promoted AHR ligand production by the gut microbiota, as revealed by increased levels of fecal AHR activity in addition to increased levels of two known AHR ligands, hemin and biliverdin. Accordingly, enrichment of bacterial genes and pathways responsible for production of hemin and biliverdin were found, specific gut bacteria that are highly correlated with abundances of hemin and biliverdin were also identified. BRB dietary intervention ameliorated intestinal inflammation in mice in association with promotion of AHR ligand production by the gut microbiota.
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Affiliation(s)
- Pengcheng Tu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Liang Chi
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Xiaoming Bian
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, United States
| | - Bei Gao
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, United States
| | - Hongyu Ru
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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9
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Roth-Walter F. Iron-Deficiency in Atopic Diseases: Innate Immune Priming by Allergens and Siderophores. FRONTIERS IN ALLERGY 2022; 3:859922. [PMID: 35769558 PMCID: PMC9234869 DOI: 10.3389/falgy.2022.859922] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/03/2022] [Indexed: 12/12/2022] Open
Abstract
Although iron is one of the most abundant elements on earth, about a third of the world's population are affected by iron deficiency. Main drivers of iron deficiency are beside the chronic lack of dietary iron, a hampered uptake machinery as a result of immune activation. Macrophages are the principal cells distributing iron in the human body with their iron restriction skewing these cells to a more pro-inflammatory state. Consequently, iron deficiency has a pronounced impact on immune cells, favoring Th2-cell survival, immunoglobulin class switching and primes mast cells for degranulation. Iron deficiency during pregnancy increases the risk of atopic diseases in children, while both children and adults with allergy are more likely to have anemia. In contrast, an improved iron status seems to protect against allergy development. Here, the most important interconnections between iron metabolism and allergies, the effect of iron deprivation on distinct immune cell types, as well as the pathophysiology in atopic diseases are summarized. Although the main focus will be humans, we also compare them with innate defense and iron sequestration strategies of microbes, given, particularly, attention to catechol-siderophores. Similarly, the defense and nutritional strategies in plants with their inducible systemic acquired resistance by salicylic acid, which further leads to synthesis of flavonoids as well as pathogenesis-related proteins, will be elaborated as both are very important for understanding the etiology of allergic diseases. Many allergens, such as lipocalins and the pathogenesis-related proteins, are able to bind iron and either deprive or supply iron to immune cells. Thus, a locally induced iron deficiency will result in immune activation and allergic sensitization. However, the same proteins such as the whey protein beta-lactoglobulin can also transport this precious micronutrient to the host immune cells (holoBLG) and hinder their activation, promoting tolerance and protecting against allergy. Since 2019, several clinical trials have also been conducted in allergic subjects using holoBLG as a food for special medical purposes, leading to a reduction in the allergic symptom burden. Supplementation with nutrient-carrying lipocalin proteins can circumvent the mucosal block and nourish selectively immune cells, therefore representing a new dietary and causative approach to compensate for functional iron deficiency in allergy sufferers.
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Affiliation(s)
- Franziska Roth-Walter
- Comparative Medicine, The Interuniversity Messerli Research Institute, University of Veterinary Medicine Vienna, Medical University Vienna, University of Vienna, Vienna, Austria
- Institute of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
- *Correspondence: Franziska Roth-Walter ;
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10
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Banerjee S, Chanakira MN, Hall J, Kerkan A, Dasgupta S, Martin DW. A review on bacterial redox dependent iron transporters and their evolutionary relationship. J Inorg Biochem 2022; 229:111721. [PMID: 35033753 DOI: 10.1016/j.jinorgbio.2022.111721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/05/2023]
Abstract
Iron is an essential yet toxic micronutrient and its transport across biological membranes is tightly regulated in all living organisms. One such iron transporter, the Ftr-type permeases, is found in both eukaryotic and prokaryotic cells. These Ftr-type transporters are required for iron transport, predicted to form α-helical transmembrane structures, and conserve two ArgGluxxGlu (x = any amino acid) motifs. In the yeast Ftr transporter (Ftr1p), a ferroxidase (Fet3p) is required for iron transport in an oxidation coupled transport step. None of the bacterial Ftr-type transporters (EfeU and FetM from E. coli; cFtr from Campylobacter jejuni; FtrC from Brucella, Bordetella, and Burkholderia spp.) contain a ferroxidase protein. Bioinformatics report predicted periplasmic EfeO and FtrB (from the EfeUOB and FtrABCD systems) as novel cupredoxins. The Cu2+ binding and the ferrous oxidation properties of these proteins are uncharacterized and the other two bacterial Ftr-systems are expressed without any ferroxidase/cupredoxin, leading to controversy about the mode of function of these transporters. Here, we review published data on Ftr-type transporters to gain insight into their functional diversity. Based on original bioinformatics data presented here evolutionary relations between these systems are presented.
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Affiliation(s)
- Sambuddha Banerjee
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA.
| | - Mina N Chanakira
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Jonathan Hall
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Alexa Kerkan
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Saumya Dasgupta
- Department of Chemistry, Amity Institute of Applied Sciences, Amity University Kolkata, WB 700135, India
| | - Daniel W Martin
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
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11
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Iron-Utilization System in Vibrio vulnificus M2799. Mar Drugs 2021; 19:md19120710. [PMID: 34940709 PMCID: PMC8706444 DOI: 10.3390/md19120710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/10/2021] [Accepted: 12/16/2021] [Indexed: 11/16/2022] Open
Abstract
Vibrio vulnificus is a Gram-negative pathogenic bacterium that causes serious infections in humans and requires iron for growth. A clinical isolate, V. vulnificus M2799, secretes a catecholate siderophore, vulnibactin, that captures ferric ions from the environment. In the ferric-utilization system in V. vulnificus M2799, an isochorismate synthase (ICS) and an outer membrane receptor, VuuA, are required under low-iron conditions, but alternative proteins FatB and VuuB can function as a periplasmic-binding protein and a ferric-chelate reductase, respectively. The vulnibactin-export system is assembled from TolCV1 and several RND proteins, including VV1_1681. In heme acquisition, HupA and HvtA serve as specific outer membrane receptors and HupB is a sole periplasmic-binding protein, unlike FatB in the ferric-vulnibactin utilization system. We propose that ferric-siderophore periplasmic-binding proteins and ferric-chelate reductases are potential targets for drug discovery in infectious diseases.
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12
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Heme auxotrophy in abundant aquatic microbial lineages. Proc Natl Acad Sci U S A 2021; 118:2102750118. [PMID: 34785591 DOI: 10.1073/pnas.2102750118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 01/22/2023] Open
Abstract
Heme, a porphyrin ring complexed with iron, is a metalloprosthetic group of numerous proteins involved in diverse metabolic and respiratory processes across all domains of life, and is thus considered essential for respiring organisms. Several microbial groups are known to lack the de novo heme biosynthetic pathway and therefore require exogenous heme from the environment. These heme auxotroph groups are largely limited to pathogens, symbionts, or microorganisms living in nutrient-replete conditions, whereas the complete absence of heme biosynthesis is extremely rare in free-living organisms. Here, we show that the acI lineage, a predominant and ubiquitous free-living bacterial group in freshwater habitats, is auxotrophic for heme, based on the experimental or genomic evidence. We found that two recently cultivated acI isolates require exogenous heme for their growth. One of the cultured acI isolates also exhibited auxotrophy for riboflavin. According to whole-genome analyses, all (n = 20) isolated acI strains lacked essential enzymes necessary for heme biosynthesis, indicating that heme auxotrophy is a conserved trait in this lineage. Analyses of >24,000 representative genomes for species clusters of the Genome Taxonomy Database revealed that heme auxotrophy is widespread across abundant but not-yet-cultivated microbial groups, including Patescibacteria, Marinisomatota (SAR406), Actinomarinales (OM1), and Marine groups IIb and III of Euryarchaeota Our findings indicate that heme auxotrophy is a more common phenomenon than previously thought, and may lead to use of heme as a growth factor to increase the cultured microbial diversity.
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13
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Martínez-Ruiz EB, Cooper M, Barrero-Canosa J, Haryono MAS, Bessarab I, Williams RBH, Szewzyk U. Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation. BMC Genomics 2021; 22:464. [PMID: 34157973 PMCID: PMC8218464 DOI: 10.1186/s12864-021-07766-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 06/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cylindrospermopsin is a highly persistent cyanobacterial secondary metabolite toxic to humans and other living organisms. Strain OF001 and A210 are manganese-oxidizing bacteria (MOB) able to transform cylindrospermopsin during the oxidation of Mn2+. So far, the enzymes involved in manganese oxidation in strain OF001 and A210 are unknown. Therefore, we analyze the genomes of two cylindrospermopsin-transforming MOB, Pseudomonas sp. OF001 and Rubrivivax sp. A210, to identify enzymes that could catalyze the oxidation of Mn2+. We also investigated specific metabolic features related to pollutant degradation and explored the metabolic potential of these two MOB with respect to the role they may play in biotechnological applications and/or in the environment. RESULTS Strain OF001 encodes two multicopper oxidases and one haem peroxidase potentially involved in Mn2+ oxidation, with a high similarity to manganese-oxidizing enzymes described for Pseudomonas putida GB-1 (80, 83 and 42% respectively). Strain A210 encodes one multicopper oxidase potentially involved in Mn2+ oxidation, with a high similarity (59%) to the manganese-oxidizing multicopper oxidase in Leptothrix discophora SS-1. Strain OF001 and A210 have genes that might confer them the ability to remove aromatic compounds via the catechol meta- and ortho-cleavage pathway, respectively. Based on the genomic content, both strains may grow over a wide range of O2 concentrations, including microaerophilic conditions, fix nitrogen, and reduce nitrate and sulfate in an assimilatory fashion. Moreover, the strain A210 encodes genes which may convey the ability to reduce nitrate in a dissimilatory manner, and fix carbon via the Calvin cycle. Both MOB encode CRISPR-Cas systems, several predicted genomic islands, and phage proteins, which likely contribute to their genome plasticity. CONCLUSIONS The genomes of Pseudomonas sp. OF001 and Rubrivivax sp. A210 encode sequences with high similarity to already described MCOs which may catalyze manganese oxidation required for cylindrospermopsin transformation. Furthermore, the analysis of the general metabolism of two MOB strains may contribute to a better understanding of the niches of cylindrospermopsin-removing MOB in natural habitats and their implementation in biotechnological applications to treat water.
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Affiliation(s)
- Erika Berenice Martínez-Ruiz
- Chair of Environmental Microbiology, Technische Universität Berlin, Institute of Environmental Technology, Straße des 17. Juni 135, 10623, Berlin, Germany.
| | - Myriel Cooper
- Chair of Environmental Microbiology, Technische Universität Berlin, Institute of Environmental Technology, Straße des 17. Juni 135, 10623, Berlin, Germany.
| | - Jimena Barrero-Canosa
- Chair of Environmental Microbiology, Technische Universität Berlin, Institute of Environmental Technology, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Mindia A S Haryono
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 119077, Singapore
| | - Irina Bessarab
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 119077, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 119077, Singapore
| | - Ulrich Szewzyk
- Chair of Environmental Microbiology, Technische Universität Berlin, Institute of Environmental Technology, Straße des 17. Juni 135, 10623, Berlin, Germany
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14
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Khasheii B, Mahmoodi P, Mohammadzadeh A. Siderophores: Importance in bacterial pathogenesis and applications in medicine and industry. Microbiol Res 2021; 250:126790. [PMID: 34098495 DOI: 10.1016/j.micres.2021.126790] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/14/2021] [Accepted: 05/24/2021] [Indexed: 12/21/2022]
Abstract
Iron is an essential element for all microorganisms. Siderophores are low-weight, high-affinity iron chelating molecules produced in response to iron deficiency by Gram-positive and Gram-negative bacteria which also known as essential virulence factors of bacteria. Several studies have indicated that defective production and/or function of these molecules as well as iron acquisition systems in pathogens are associated with a reduction in pathogenicity of bacteria. Because of their potential role in various biological pathways, siderophores have been received special attention as secondary metabolites. Siderophores can detect iron levels in a variety of environments with a biosensor function. In medicine, siderophores are used to deliver antibiotics (Trojan horse strategy) to resistant bacteria and to treat diseases such as cancer and malaria. In this review, we discuss the iron acquisition pathways in Gram-positive and -negative bacteria, importance of siderophore production in pathogenesis of bacteria, classification of siderophores, and main applications of siderophores in medicine and industry.
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Affiliation(s)
- Behnoush Khasheii
- Department of Pathobiology, Faculty of Veterinary Science, Bu-Ali Sina University, Hamedan, Iran
| | - Pezhman Mahmoodi
- Department of Pathobiology, Faculty of Veterinary Science, Bu-Ali Sina University, Hamedan, Iran.
| | - Abdolmajid Mohammadzadeh
- Department of Pathobiology, Faculty of Veterinary Science, Bu-Ali Sina University, Hamedan, Iran
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15
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Klebba PE, Newton SMC, Six DA, Kumar A, Yang T, Nairn BL, Munger C, Chakravorty S. Iron Acquisition Systems of Gram-negative Bacterial Pathogens Define TonB-Dependent Pathways to Novel Antibiotics. Chem Rev 2021; 121:5193-5239. [PMID: 33724814 PMCID: PMC8687107 DOI: 10.1021/acs.chemrev.0c01005] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Iron is an indispensable metabolic cofactor in both pro- and eukaryotes, which engenders a natural competition for the metal between bacterial pathogens and their human or animal hosts. Bacteria secrete siderophores that extract Fe3+ from tissues, fluids, cells, and proteins; the ligand gated porins of the Gram-negative bacterial outer membrane actively acquire the resulting ferric siderophores, as well as other iron-containing molecules like heme. Conversely, eukaryotic hosts combat bacterial iron scavenging by sequestering Fe3+ in binding proteins and ferritin. The variety of iron uptake systems in Gram-negative bacterial pathogens illustrates a range of chemical and biochemical mechanisms that facilitate microbial pathogenesis. This document attempts to summarize and understand these processes, to guide discovery of immunological or chemical interventions that may thwart infectious disease.
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Affiliation(s)
- Phillip E Klebba
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Salete M C Newton
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - David A Six
- Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States
| | - Ashish Kumar
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Taihao Yang
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Brittany L Nairn
- Department of Biological Sciences, Bethel University, 3900 Bethel Drive, St. Paul, Minnesota 55112, United States
| | - Colton Munger
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Somnath Chakravorty
- Jacobs School of Medicine and Biomedical Sciences, SUNY Buffalo, Buffalo, New York 14203, United States
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16
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Gamage SMK, Lee KTW, Dissabandara DLO, Lam AKY, Gopalan V. Dual role of heme iron in cancer; promotor of carcinogenesis and an inducer of tumour suppression. Exp Mol Pathol 2021; 120:104642. [PMID: 33905708 DOI: 10.1016/j.yexmp.2021.104642] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/14/2021] [Accepted: 04/22/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE Heme is a crucial compound for cell survival but is also equipped with the potential to be toxic and carcinogenic to cells. However, with the recent advancement of knowledge regarding ferroptosis, the iron mediated cell death, heme can be postulated to induce tumour suppression through ferroptosis. This review summarizes the literature on the carcinogenic and anticarcinogenic properties of heme with specific emphasis on the alterations observed on heme synthesis, metabolism and transport in tumour cells. METHODS Literature search was performed in PubMed data base using the MeSH terms 'heme iron or heme', 'cancer or carcinogenesis' and 'tumour suppression' or 'anticarcinogenic properties. Out of 189 results, 166 were relevant to the current review. RESULTS Heme supports carcinogenesis via modulation of immune cell function, promoting inflammation and gut dysbiosis, impeding tumour suppressive potential of P53 gene, promoting cellular cytotoxicity and reactive oxygen species generation and modulating Nfr2 /HO-1 axis. The carcinogenic and anticarcinogenic properties of heme are both dose and oxygen concentration dependant. At low doses, heme is harmless and even helpful in maintaining the much-needed redox balance within the cell. However, when heme exceeds physiological concentrations, it could initiate and propagate carcinogenesis, due to its ability to produce reactive oxygen species (ROS). The same phenomenon of heme mediated ROS generation could be manipulated to initiate tumour suppression via ferroptosis, but the therapeutic doses are yet to be determined. CONCLUSION Heme iron possesses powerful carcinogenic and anticarcinogenic properties which are dosage and oxygen availability dependant.
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Affiliation(s)
- Sujani M K Gamage
- Cancer Molecular Pathology, School of Medicine, Griffith University, Gold Coast, Queensland 4222, Australia; Department of Anatomy, Faculty of Medicine, University of Peradeniya, Sri Lanka
| | - Katherine T W Lee
- Cancer Molecular Pathology, School of Medicine, Griffith University, Gold Coast, Queensland 4222, Australia
| | - D Lakal O Dissabandara
- Cancer Molecular Pathology, School of Medicine, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Alfred King-Yin Lam
- Cancer Molecular Pathology, School of Medicine, Griffith University, Gold Coast, Queensland 4222, Australia.
| | - Vinod Gopalan
- Cancer Molecular Pathology, School of Medicine, Griffith University, Gold Coast, Queensland 4222, Australia.
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17
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A noncanonical heme oxygenase specific for the degradation of c-type heme. J Biol Chem 2021; 296:100666. [PMID: 33862082 PMCID: PMC8131568 DOI: 10.1016/j.jbc.2021.100666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 04/07/2021] [Accepted: 04/12/2021] [Indexed: 11/24/2022] Open
Abstract
Heme oxygenases (HOs) play a critical role in recouping iron from the labile heme pool. The acquisition and liberation of heme iron are especially important for the survival of pathogenic bacteria. All characterized HOs, including those belonging to the HugZ superfamily, preferentially cleave free b-type heme. Another common form of heme found in nature is c-type heme, which is covalently linked to proteinaceous cysteine residues. However, mechanisms for direct iron acquisition from the c-type heme pool are unknown. Here we identify a HugZ homolog from the oligopeptide permease (opp) gene cluster of Paracoccus denitrificans that lacks any observable reactivity with heme b and show that it instead rapidly degrades c-type hemopeptides. This c-type heme oxygenase catalyzes the oxidative cleavage of the model substrate microperoxidase-11 at the β- and/or δ-meso position(s), yielding the corresponding peptide-linked biliverdin, CO, and free iron. X-ray crystallographic analysis suggests that the switch in substrate specificity from b-to c-type heme involves loss of the N-terminal α/β domain and C-terminal loop containing the coordinating histidine residue characteristic of HugZ homologs, thereby accommodating a larger substrate that provides its own iron ligand. These structural features are also absent in certain heme utilization/storage proteins from human pathogens that exhibit low or no HO activity with free heme. This study thus expands the scope of known iron acquisition strategies to include direct oxidative cleavage of heme-containing proteolytic fragments of c-type cytochromes and helps to explain why certain oligopeptide permeases show specificity for the import of heme in addition to peptides.
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18
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Wang M, Nie Y, Wu XL. Extracellular heme recycling and sharing across species by novel mycomembrane vesicles of a Gram-positive bacterium. THE ISME JOURNAL 2021; 15:605-617. [PMID: 33037324 PMCID: PMC8027190 DOI: 10.1038/s41396-020-00800-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/16/2020] [Accepted: 09/28/2020] [Indexed: 12/26/2022]
Abstract
Microbes spontaneously release membrane vesicles (MVs), which play roles in nutrient acquisition and microbial interactions. Iron is indispensable for microbes, but is a difficult nutrient to acquire. However, whether MVs are also responsible for efficient iron uptake and therefore involved in microbial interaction remains to be elucidated. Here, we used a Gram-positive strain, Dietzia sp. DQ12-45-1b, to analyze the function of its MVs in heme-iron recycling and sharing between species. We determined the structure and constituent of MVs and showed that DQ12-45-1b releases MVs originating from the mycomembrane. When comparing proteomes of MVs between iron-limiting and iron-rich conditions, we found that under iron-limiting conditions, heme-binding proteins are enriched. Next, we proved that MVs participate in extracellular heme capture and transport, especially in heme recycling from environmental hemoproteins. Finally, we found that the heme carried in MVs is utilized by multiple species, and we further verified that membrane fusion efficiency and species evolutionary distance determine heme delivery. Together, our findings strongly suggest that MVs act as a newly identified pathway for heme recycling, and represent a public good shared between phylogenetically closely related species.
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Affiliation(s)
- Meng Wang
- College of Engineering, Peking University, 100871, Beijing, China
| | - Yong Nie
- College of Engineering, Peking University, 100871, Beijing, China.
| | - Xiao-Lei Wu
- College of Engineering, Peking University, 100871, Beijing, China.
- Institute of Ocean Research, Peking University, 100871, Beijing, China.
- Institute of Ecology, Peking University, 100871, Beijing, China.
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19
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Fan D, Fang Q. Siderophores for medical applications: Imaging, sensors, and therapeutics. Int J Pharm 2021; 597:120306. [PMID: 33540031 DOI: 10.1016/j.ijpharm.2021.120306] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 01/07/2023]
Abstract
Siderophores are low-molecular-weight chelators produced by microorganisms to scavenge iron from the environment and deliver it to cells via specific receptors. Tremendous researches on the molecular basis of siderophore regulation, synthesis, secretion, and uptake have inspired their diverse applications in the medical field. Replacing iron with radionuclides in siderophores, such as the most prominent Ga-68 for positron emission tomography (PET), carves out ways for targeted imaging of infectious diseases and cancers. Additionally, the high affinity of siderophores for metal ions or microorganisms makes them a potent detecting moiety in sensors that can be used for diagnosis. As for therapeutics, the notable Trojan horse-inspired siderophore-antibiotic conjugates demonstrate enhanced toxicity against multi-drug resistant (MDR) pathogens. Besides, siderophores can tackle iron overload diseases and, when combined with moieties such as hydrogels and nanoparticles, a wide spectrum of iron-induced diseases and even cancers. In this review, we briefly outline the related mechanisms, before summarizing the siderophore-based applications in imaging, sensors, and therapeutics.
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Affiliation(s)
- Di Fan
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory of Nanophotonic Materials and Devices, CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
| | - Qiaojun Fang
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory of Nanophotonic Materials and Devices, CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China; Sino-Danish Center for Education and Research, Beijing 101408, PR China.
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20
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Chhabra R, Saha A, Chamani A, Schneider N, Shah R, Nanjundan M. Iron Pathways and Iron Chelation Approaches in Viral, Microbial, and Fungal Infections. Pharmaceuticals (Basel) 2020; 13:E275. [PMID: 32992923 PMCID: PMC7601909 DOI: 10.3390/ph13100275] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/13/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
Iron is an essential element required to support the health of organisms. This element is critical for regulating the activities of cellular enzymes including those involved in cellular metabolism and DNA replication. Mechanisms that underlie the tight control of iron levels are crucial in mediating the interaction between microorganisms and their host and hence, the spread of infection. Microorganisms including viruses, bacteria, and fungi have differing iron acquisition/utilization mechanisms to support their ability to acquire/use iron (e.g., from free iron and heme). These pathways of iron uptake are associated with promoting their growth and virulence and consequently, their pathogenicity. Thus, controlling microorganismal survival by limiting iron availability may prove feasible through the use of agents targeting their iron uptake pathways and/or use of iron chelators as a means to hinder development of infections. This review will serve to assimilate findings regarding iron and the pathogenicity of specific microorganisms, and furthermore, find whether treating infections mediated by such organisms via iron chelation approaches may have potential clinical benefit.
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Affiliation(s)
| | | | | | | | | | - Meera Nanjundan
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620, USA; (R.C.); (A.S.); (A.C.); (N.S.); (R.S.)
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21
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Khan D, Lee D, Gulten G, Aggarwal A, Wofford J, Krieger I, Tripathi A, Patrick JW, Eckert DM, Laganowsky A, Sacchettini J, Lindahl P, Bankaitis VA. A Sec14-like phosphatidylinositol transfer protein paralog defines a novel class of heme-binding proteins. eLife 2020; 9:57081. [PMID: 32780017 PMCID: PMC7462610 DOI: 10.7554/elife.57081] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/10/2020] [Indexed: 01/02/2023] Open
Abstract
Yeast Sfh5 is an unusual member of the Sec14-like phosphatidylinositol transfer protein (PITP) family. Whereas PITPs are defined by their abilities to transfer phosphatidylinositol between membranes in vitro, and to stimulate phosphoinositide signaling in vivo, Sfh5 does not exhibit these activities. Rather, Sfh5 is a redox-active penta-coordinate high spin FeIII hemoprotein with an unusual heme-binding arrangement that involves a co-axial tyrosine/histidine coordination strategy and a complex electronic structure connecting the open shell iron d-orbitals with three aromatic ring systems. That Sfh5 is not a PITP is supported by demonstrations that heme is not a readily exchangeable ligand, and that phosphatidylinositol-exchange activity is resuscitated in heme binding-deficient Sfh5 mutants. The collective data identify Sfh5 as the prototype of a new class of fungal hemoproteins, and emphasize the versatility of the Sec14-fold as scaffold for translating the binding of chemically distinct ligands to the control of diverse sets of cellular activities.
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Affiliation(s)
- Danish Khan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
| | - Dongju Lee
- Department of Molecular and Cellular Medicine, Texas A&M Health Sciences Center, College Station, United States
| | - Gulcin Gulten
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
| | - Anup Aggarwal
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
| | - Joshua Wofford
- Department of Chemistry, Texas A&M University, College Station, United States.,Department of Chemistry, Charleston Southern University, North Charleston, United States
| | - Inna Krieger
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
| | - Ashutosh Tripathi
- Department of Molecular and Cellular Medicine, Texas A&M Health Sciences Center, College Station, United States
| | - John W Patrick
- Department of Chemistry, Texas A&M University, College Station, United States
| | - Debra M Eckert
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, United States
| | - James Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
| | - Paul Lindahl
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States.,Department of Chemistry, Texas A&M University, College Station, United States
| | - Vytas A Bankaitis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States.,Department of Molecular and Cellular Medicine, Texas A&M Health Sciences Center, College Station, United States.,Department of Chemistry, Texas A&M University, College Station, United States
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22
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Iron acquisition system of Sphingobium sp. strain SYK-6, a degrader of lignin-derived aromatic compounds. Sci Rep 2020; 10:12177. [PMID: 32699224 PMCID: PMC7376174 DOI: 10.1038/s41598-020-68984-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/03/2020] [Indexed: 11/23/2022] Open
Abstract
Iron, an essential element for all organisms, acts as a cofactor of enzymes in bacterial degradation of recalcitrant aromatic compounds. The bacterial family, Sphingomonadaceae comprises various degraders of recalcitrant aromatic compounds; however, little is known about their iron acquisition system. Here, we investigated the iron acquisition system in a model bacterium capable of degrading lignin-derived aromatics, Sphingobium sp. strain SYK-6. Analyses of SYK-6 mutants revealed that FiuA (SLG_34550), a TonB-dependent receptor (TBDR), was the major outer membrane iron transporter. Three other TBDRs encoded by SLG_04340, SLG_04380, and SLG_10860 also participated in iron uptake, and tonB2 (SLG_34540), one of the six tonB comprising the Ton complex which enables TBDR-mediated transport was critical for iron uptake. The ferrous iron transporter FeoB (SLG_36840) played an important role in iron uptake across the inner membrane. The promoter activities of most of the iron uptake genes were induced under iron-limited conditions, and their regulation is controlled by SLG_29410 encoding the ferric uptake regulator, Fur. Although feoB, among all the iron uptake genes identified is highly conserved in Sphingomonad strains, the outer membrane transporters seem to be diversified. Elucidation of the iron acquisition system promises better understanding of the bacterial degradation mechanisms of aromatic compounds.
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23
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AlMatar M, Albarri O, Makky EA, Var I, Köksal F. A Glance on the Role of Bacterial Siderophore from the Perspectives of Medical and Biotechnological Approaches. Curr Drug Targets 2020; 21:1326-1343. [PMID: 32564749 DOI: 10.2174/1389450121666200621193018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/10/2020] [Accepted: 05/20/2020] [Indexed: 11/22/2022]
Abstract
Iron, which is described as the most basic component found in nature, is hard to be assimilated by microorganisms. It has become increasingly complicated to obtain iron from nature as iron (II) in the presence of oxygen oxidized to press (III) oxide and hydroxide, becoming unsolvable at neutral pH. Microorganisms appeared to produce organic molecules known as siderophores in order to overcome this condition. Siderophore's essential function is to connect with iron (II) and make it dissolvable and enable cell absorption. These siderophores, apart from iron particles, have the ability to chelate various other metal particles that have collocated away to focus the use of siderophores on wound care items. There is a severe clash between the host and the bacterial pathogens during infection. By producing siderophores, small ferric iron-binding molecules, microorganisms obtain iron. In response, host immune cells produce lipocalin 2 to prevent bacterial reuptake of siderophores loaded with iron. Some bacteria are thought to produce lipocalin 2-resistant siderophores to counter this risk. The aim of this article is to discuss the recently described roles and applications of bacterial siderophore.
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Affiliation(s)
- Manaf AlMatar
- Faculty of Industrial Sciences & Technology, Universiti Malaysia Pahang (UMP), Gambang, 26300 Kuantan, Malaysia
| | - Osman Albarri
- Department of Biotechnology, Institute of Natural and Applied Sciences (Fen Bilimleri Enstitusu) Cukurova University, Adana, Turkey
| | - Essam A Makky
- Faculty of Industrial Sciences & Technology, Universiti Malaysia Pahang (UMP), Gambang, 26300 Kuantan, Malaysia
| | - Işıl Var
- Department of Food Engineering, Agricultural Faculty, Cukurova University, Adana, Turkey
| | - Fatih Köksal
- Department of Medical Microbiology, Faculty of Medicine, Cukurova University, Adana, Turkey
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24
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Thøgersen R, Castro-Mejía JL, Kræmer Sundekilde U, H Hansen L, Gray N, Kuhnle G, Rye Jørgensen N, Kornerup Hansen A, Sandris Nielsen D, Bertram HC. Inulin and milk mineral fortification of a pork sausage exhibits distinct effects on the microbiome and biochemical activity in the gut of healthy rats. Food Chem 2020; 331:127291. [PMID: 32559598 DOI: 10.1016/j.foodchem.2020.127291] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 05/06/2020] [Accepted: 06/07/2020] [Indexed: 01/10/2023]
Abstract
This study investigated inulin and calcium-rich milk mineral incorporation into a pork sausage in order to examine the effects on microbiome and biochemical activity in the gastrointestinal tract upon ingestion. Rats (n = 48) were fed one of four sausages; a pork sausage enriched with 1) inulin (6.0%) and milk mineral (3%), 2) inulin (6.0%), 3) milk mineral (3%) or 4) control sausages without enrichment. NMR-based metabolomics revealed that inulin-enrichment increased the fecal concentration of short-chain fatty acids (SCFAs). Milk mineral-enrichment also increased SCFA concentrations, although less pronounced. In addition, milk mineral reduced the concentration of nitroso compounds in feces and small intestinal content. Combined enrichment with both inulin and milk mineral showed no cumulative effect on SCFA formation and seemed to oppose the milk mineral-induced reduction of nitroso compound formation. 16S rRNA gene amplicon sequencing indicated that alterations of the gut microbiome contributed to the observed effects.
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Affiliation(s)
- Rebekka Thøgersen
- Department of Food Science, Aarhus University, Agro Food Park 48, DK-8200 Aarhus N, Denmark
| | - Josué L Castro-Mejía
- Department of Food Science, Faculty of Science, University of Copenhagen, Denmark
| | | | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Nicola Gray
- Department of Food & Nutritional Sciences, University of Reading, United Kingdom; Australian National Phenome Centre, Health Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Gunter Kuhnle
- Department of Food & Nutritional Sciences, University of Reading, United Kingdom
| | - Niklas Rye Jørgensen
- Department of Clinical Biochemistry, Rigshospitalet, Glostrup, Denmark; OPEN, Odense Patient Data Explorative Network, Odense University Hospital/Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Axel Kornerup Hansen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | - Hanne Christine Bertram
- Department of Food Science, Aarhus University, Agro Food Park 48, DK-8200 Aarhus N, Denmark.
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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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The Jekyll and Hyde Symbiont: Could Wolbachia Be a Nutritional Mutualist? J Bacteriol 2020; 202:JB.00589-19. [PMID: 31659008 DOI: 10.1128/jb.00589-19] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The most common intracellular symbiont on the planet-Wolbachia pipientis-is infamous largely for the reproductive manipulations induced in its host. However, more recent evidence suggests that this bacterium may also serve as a nutritional mutualist in certain host backgrounds and for certain metabolites. We performed a large-scale analysis of conserved gene content across all sequenced Wolbachia genomes to infer potential nutrients made by these symbionts. We review and critically evaluate the prior research supporting a beneficial role for Wolbachia and suggest future experiments to test hypotheses of metabolic provisioning.
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Cooper RO, Cressler CE. Characterization of key bacterial species in the Daphnia magna microbiota using shotgun metagenomics. Sci Rep 2020; 10:652. [PMID: 31959775 PMCID: PMC6971282 DOI: 10.1038/s41598-019-57367-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 12/24/2019] [Indexed: 12/28/2022] Open
Abstract
The keystone zooplankton Daphnia magna has recently been used as a model system for understanding host-microbiota interactions. However, the bacterial species present and functions associated with their genomes are not well understood. In order to understand potential functions of these species, we combined 16S rRNA sequencing and shotgun metagenomics to characterize the whole-organism microbiota of Daphnia magna. We assembled five potentially novel metagenome-assembled genomes (MAGs) of core bacteria in Daphnia magna. Genes involved in host colonization and immune system evasion were detected across the MAGs. Some metabolic pathways were specific to some MAGs, including sulfur oxidation, nitrate reduction, and flagellar assembly. Amino acid exporters were identified in MAGs identified as important for host fitness, and pathways for key vitamin biosynthesis and export were identified across MAGs. In total, our examination of functions in these MAGs shows a diversity of nutrient acquisition and metabolism pathways present that may benefit the host, as well as genomic signatures of host association and immune system evasion.
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Affiliation(s)
- Reilly O Cooper
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA.
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28
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Muraki N, Kitatsuji C, Okamoto Y, Uchida T, Ishimori K, Aono S. Structural basis for the heme transfer reaction in heme uptake machinery from Corynebacteria. Chem Commun (Camb) 2019; 55:13864-13867. [PMID: 31670736 DOI: 10.1039/c9cc07369h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystal structures of the conserved region domains of HtaA and HtaB, which act as heme binding/transport proteins in the heme uptake machinery in Corynebacterium glutamicum, are determined for the first time. The molecular mechanism of heme transfer among these proteins is proposed based on the spectroscopic and structural analyses.
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Affiliation(s)
- Norifumi Muraki
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787, Japan.
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Page MGP. The Role of Iron and Siderophores in Infection, and the Development of Siderophore Antibiotics. Clin Infect Dis 2019; 69:S529-S537. [PMID: 31724044 PMCID: PMC6853763 DOI: 10.1093/cid/ciz825] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Iron is an essential nutrient for bacterial growth, replication, and metabolism. Humans store iron bound to various proteins such as hemoglobin, haptoglobin, transferrin, ferritin, and lactoferrin, limiting the availability of free iron for pathogenic bacteria. However, bacteria have developed various mechanisms to sequester or scavenge iron from the host environment. Iron can be taken up by means of active transport systems that consist of bacterial small molecule siderophores, outer membrane siderophore receptors, the TonB-ExbBD energy-transducing proteins coupling the outer and the inner membranes, and inner membrane transporters. Some bacteria also express outer membrane receptors for iron-binding proteins of the host and extract iron directly from these for uptake. Ultimately, iron is acquired and transported into the bacterial cytoplasm. The siderophores are small molecules produced and released by nearly all bacterial species and are classified according to the chemical nature of their iron-chelating group (ie, catechol, hydroxamate, α-hydroxyl-carboxylate, or mixed types). Siderophore-conjugated antibiotics that exploit such iron-transport systems are under development for the treatment of infections caused by gram-negative bacteria. Despite demonstrating high in vitro potency against pathogenic multidrug-resistant bacteria, further development of several candidates had stopped due to apparent adaptive resistance during exposure, lack of consistent in vivo efficacy, or emergence of side effects in the host. However, cefiderocol, with an optimized structure, has advanced and has been investigated in phase 1 to 3 clinical trials. This article discusses the mechanisms implicated in iron uptake and the challenges associated with the design and utilization of siderophore-mimicking antibiotics.
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Affiliation(s)
- Malcom G P Page
- Life Sciences and Chemistry, Jacobs University, Bremen gGmbh, Bremen, Germany
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Iron: an essential nutrient for Aspergillus fumigatus and a fulcrum for pathogenesis. Curr Opin Infect Dis 2019; 31:506-511. [PMID: 30379731 DOI: 10.1097/qco.0000000000000487] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
PURPOSE OF REVIEW Aspergillus fumigatus is a ubiquitous saprophytic fungus that can cause life-threatening invasive aspergillosis in immunocompromised patients. Apart from the immune status of the host only a few characterized virulence factors have been identified. In this review, we describe the role of iron in the manifestation of A. fumigatus virulence. RECENT FINDINGS We gathered recent clinical evidence suggesting that tissue iron overload increases the risk of invasive aspergillosis occurrence. Furthermore, we summarize the mechanisms that A. fumigatus employs to achieve iron homeostasis and their importance in A. fumigatus proliferation in vitro. We describe two recent in-vivo models that clearly demonstrate the importance of iron in A. fumigatus growth and invasion. SUMMARY Based on these recent findings, therapy aimed at managing A. fumigatus iron homeostasis locally could make conditions more favorable to the host.
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Choi SR, Britigan BE, Narayanasamy P. Dual Inhibition of Klebsiella pneumoniae and Pseudomonas aeruginosa Iron Metabolism Using Gallium Porphyrin and Gallium Nitrate. ACS Infect Dis 2019; 5:1559-1569. [PMID: 31264851 DOI: 10.1021/acsinfecdis.9b00100] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Iron- and heme-uptake pathways and metabolism are promising targets for the development of new antimicrobial agents, as their disruption would lead to nutritional iron starvation and inhibition of bacterial growth. Salts of gallium(III) (Ga), an iron mimetic metal, disrupt iron-dependent biological processes by binding iron-utilizing proteins and competing with iron for uptake by bacterial siderophore-mediated iron uptake systems. Ga porphyrins, heme mimetic complexes, disrupt heme-utilizing hemoproteins. Because Ga(NO3)3 and Ga porphyrin disrupt different pathways of bacterial ion acquisition and utilization, we hypothesized that if used in combination, they would result in enhanced antimicrobial activity. Antimicrobial activity of Ga porphyrins (Ga protoporphyrin, GaPP, or Ga mesoporphyrin, GaMP) alone and in combination with Ga(NO3)3 were evaluated against Pseudomonas aeruginosa, Klebsiella pneumoniae, Acinetobacter baumannii, and methicillin-resistant Staphylococcus aureus (MRSA) under iron-limited conditions. The Ga porphyrin/Ga(NO3)3 combination demonstrated substantial synergism against K. pneumoniae, P. aeruginosa, and MRSA. Time-kill assays revealed that the synergistic combination of GaPP/Ga(NO3)3 was bacteriostatic against K. pneumoniae and MRSA and bactericidal against P. aeruginosa. The GaPP/Ga(NO3)3 combination significantly disrupted K. pneumoniae and P. aeruginosa biofilms on plasma-coated surfaces and increased the survival of Caenorhabditis elegans infected with K. pneumoniae or P. aeruginosa. When assessing the antibacterial activity of the Ga(III)/antibiotic combinations, GaPP/colistin and Ga(NO3)3/colistin combinations also showed synergistic activity against K. pneumoniae and P. aeruginosa. Our results demonstrate that GaPP and Ga(NO3)3 have significant synergistic effects against several important human bacterial pathogens through dual inhibition of iron and heme metabolism.
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Affiliation(s)
- Seoung-ryoung Choi
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Bradley E. Britigan
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 985900 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
- Department of Internal Medicine and Research Service, Veterans Affairs Medical Center—Nebraska Western Iowa, Omaha, Nebraska 68105, United States
| | - Prabagaran Narayanasamy
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, Nebraska 68198, United States
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Dai J, Liu Y, Liu S, Li S, Gao N, Wang J, Zhou J, Qiu D. Differential gene content and gene expression for bacterial evolution and speciation of Shewanella in terms of biosynthesis of heme and heme-requiring proteins. BMC Microbiol 2019; 19:173. [PMID: 31362704 PMCID: PMC6664582 DOI: 10.1186/s12866-019-1549-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/19/2019] [Indexed: 01/31/2023] Open
Abstract
Background Most species of Shewanella harbor two ferrochelatase paralogues for the biosynthesis of c-type cytochromes, which are crucial for their respiratory versatility. In our previous study of the Shewanella loihica PV-4 strain, we found that the disruption of hemH1 but not hemH2 resulted in a significant accumulation of extracellular protoporphyrin IX (PPIX), but it is different in Shewanella oneidensis MR-1. Hence, the function and transcriptional regulation of two ferrochelatase genes, hemH1 and hemH2, are investigated in S. oneidensis MR-1. Result In the present study, deletion of either hemH1 or hemH2 in S. oneidensis MR-1 did not lead to overproduction of extracellular protoporphyrin IX (PPIX) as previously described in the hemH1 mutants of S. loihica PV-4. Moreover, supplement of exogenous hemins made it possible to generate the hemH1 and hemH2 double mutant in MR-1, but not in PV-4. Under aerobic condition, exogenous hemins were required for the growth of MR-1ΔhemH1ΔhemH2, which also overproduced extracellular PPIX. These results suggest that heme is essential for aerobic growth of Shewanella species and MR-1 could also uptake hemin for biosynthesis of essential cytochrome(s) and respiration. Besides, the exogenous hemin mediated CymA cytochrome maturation and the cellular KatB catalase activity. Both hemH paralogues were transcribed in wild-type MR-1, and the hemH2 transcription was remarkably up-regulated in MR-1ΔhemH1 mutant to compensate for the loss of hemH1. The periplasmic glutathione peroxidase gene pgpD, located in the same operon with hemH2, and a large gene cluster coding for iron, heme (hemin) uptake systems are absent in the PV-4 genome. Conclusion Our results indicate that the genetic divergence in gene content and gene expression between these Shewanella species, accounting for the phenotypic difference described here, might be due to their speciation and adaptation to the specific habitats (iron-rich deep-sea vent versus iron-poor freshwater) in which they evolved and the generated mutants could potentially be utilized for commercial production of PPIX. Electronic supplementary material The online version of this article (10.1186/s12866-019-1549-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingcheng Dai
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yaqi Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuangyuan Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuyang Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Na Gao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.,Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94270, USA
| | - Dongru Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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33
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Iron/Heme Metabolism-Targeted Gallium(III) Nanoparticles Are Active against Extracellular and Intracellular Pseudomonas aeruginosa and Acinetobacter baumannii. Antimicrob Agents Chemother 2019; 63:AAC.02643-18. [PMID: 30782994 DOI: 10.1128/aac.02643-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/06/2019] [Indexed: 12/24/2022] Open
Abstract
Iron/heme acquisition systems are critical for microorganisms to acquire iron from the human host, where iron sources are limited due to the nutritional immune system and insolubility of the ferric form of iron. Prior work has shown that a variety of gallium compounds can interfere with bacterial iron acquisition. This study explored the intra- and extracellular antimicrobial activities of gallium protoporphyrin (GaPP), gallium mesoporphyrin (GaMP), and nanoparticles encapsulating GaPP or GaMP against the Gram-negative pathogens Pseudomonas aeruginosa and Acinetobacter baumannii, including clinical isolates. All P. aeruginosa and A. baumannii isolates were susceptible to GaPP and GaMP, with MICs ranging from 0.5 to ∼32 μg/ml in iron-depleted medium. Significant intra- and extracellular growth inhibition was observed against P. aeruginosa cultured in macrophages at a gallium concentration of 3.3 μg/ml (5 μM) of all Ga(III) compounds, including nanoparticles. Nanoparticle formulations showed prolonged activity against both P. aeruginosa and A. baumannii in previously infected macrophages. When the macrophages were loaded with the nanoparticles 3 days prior to infection, there was a 5-fold decrease in growth of P. aeruginosa in the presence of single emulsion F127 copolymer nanoparticles encapsulating GaMP (eFGaMP). In addition, all Ga(III) porphyrins and nanoparticles showed significant intracellular and antibiofilm activity against both pathogens, with the nanoparticles exhibiting intracellular activity for 3 days. Ga nanoparticles also increased the survival rate of Caenorhabditis elegans nematodes infected by P. aeruginosa and A. baumannii Our results demonstrate that Ga nanoparticles have prolonged in vitro and in vivo activities against both P. aeruginosa and A. baumannii, including disruption of their biofilms.
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Donegan RK, Moore CM, Hanna DA, Reddi AR. Handling heme: The mechanisms underlying the movement of heme within and between cells. Free Radic Biol Med 2019; 133:88-100. [PMID: 30092350 PMCID: PMC6363905 DOI: 10.1016/j.freeradbiomed.2018.08.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 02/02/2023]
Abstract
Heme is an essential cofactor and signaling molecule required for virtually all aerobic life. However, excess heme is cytotoxic. Therefore, heme must be safely transported and trafficked from the site of synthesis in the mitochondria or uptake at the cell surface, to hemoproteins in most subcellular compartments. While heme synthesis and degradation are relatively well characterized, little is known about how heme is trafficked and transported throughout the cell. Herein, we review eukaryotic heme transport, trafficking, and mobilization, with a focus on factors that regulate bioavailable heme. We also highlight the role of gasotransmitters and small molecules in heme mobilization and bioavailability, and heme trafficking at the host-pathogen interface.
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Affiliation(s)
- Rebecca K Donegan
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Courtney M Moore
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - David A Hanna
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Amit R Reddi
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, United States; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States; Parker Petit Institute for Bioengineering & Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, United States.
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35
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The role of metal ions in the virulence and viability of bacterial pathogens. Biochem Soc Trans 2019; 47:77-87. [PMID: 30626704 DOI: 10.1042/bst20180275] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/08/2018] [Accepted: 11/29/2018] [Indexed: 01/18/2023]
Abstract
Metal ions fulfil a plethora of essential roles within bacterial pathogens. In addition to acting as necessary cofactors for cellular proteins, making them indispensable for both protein structure and function, they also fulfil roles in signalling and regulation of virulence. Consequently, the maintenance of cellular metal ion homeostasis is crucial for bacterial viability and pathogenicity. It is therefore unsurprising that components of the immune response target and exploit both the essentiality of metal ions and their potential toxicity toward invading bacteria. This review provides a brief overview of the transition metal ions iron, manganese, copper and zinc during infection. These essential metal ions are discussed in the context of host modulation of bioavailability, bacterial acquisition and efflux, metal-regulated virulence factor expression and the molecular mechanisms that contribute to loss of viability and/or virulence during host-imposed metal stress.
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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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37
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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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38
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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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39
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Antigenic Properties of Iron Regulated Proteins in Acinetobacter baumannii: An In Silico Approach. Int J Pept Res Ther 2017. [DOI: 10.1007/s10989-017-9665-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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40
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Hoshino M, Nakakido M, Nagatoishi S, Aikawa C, Nakagawa I, Tsumoto K. Biophysical characterization of the interaction between heme and proteins responsible for heme transfer in Streptococcus pyogenes. Biochem Biophys Res Commun 2017; 493:1109-1114. [DOI: 10.1016/j.bbrc.2017.09.055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 09/12/2017] [Indexed: 10/18/2022]
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41
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Jeschek M, Panke S, Ward TR. Artificial Metalloenzymes on the Verge of New-to-Nature Metabolism. Trends Biotechnol 2017; 36:60-72. [PMID: 29061328 DOI: 10.1016/j.tibtech.2017.10.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 01/13/2023]
Abstract
Residing at the interface of chemistry and biotechnology, artificial metalloenzymes (ArMs) offer an attractive technology to combine the versatile reaction repertoire of transition metal catalysts with the exquisite catalytic features of enzymes. While earlier efforts in this field predominantly comprised studies in well-defined test-tube environments, a trend towards exploiting ArMs in more complex environments has recently emerged. Integration of these artificial biocatalysts in enzymatic cascades and using them in whole-cell biotransformations and in vivo opens up entirely novel prospects for both preparative chemistry and synthetic biology. We highlight selected recent developments with a particular focus on challenges and opportunities in the in vivo application of ArMs.
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Affiliation(s)
- Markus Jeschek
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland.
| | - Sven Panke
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, Basel, Switzerland
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42
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De Serrano LO. Biotechnology of siderophores in high-impact scientific fields. Biomol Concepts 2017; 8:169-178. [DOI: 10.1515/bmc-2017-0016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/29/2017] [Indexed: 01/06/2023] Open
Abstract
AbstractDifferent aspects of bacterial and fungal siderophore biotechnological applications will be discussed. Areas of application presented include, but are not limited to agriculture, medicine, pharmacology, bioremediation, biodegradation and food industry. In agriculture-related applications, siderophores could be employed to enhance plant growth due to their uptake by rhizobia. Siderophores hindered the presence of plant pathogens in biocontrol strategies. Bioremediation studies on siderophores discuss mostly the mobilization of heavy metals and radionuclides; the emulsifying effects of siderophore-producing microorganisms in oil-contaminated environments are also presented. The different applications found in literature based in medicine and pharmacological approaches range from iron overload to drug delivery systems and, more recently, vaccines. Additional research should be done in siderophore production and their metabolic relevance to have a deeper understanding for future biotechnological advances.
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Affiliation(s)
- Luis O. De Serrano
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, MT 59812, USA
- Center for Translational Medicine, University of Montana, 32 Campus Dr., Missoula, MT 59801, USA
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43
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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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44
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Uchida T, Funamizu T, Ogura M, Ishimori K. Heme Iron Coordination Structure of Heme Transport Protein HutB fromVibrio Cholerae. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Takeshi Uchida
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628
| | - Takumi Funamizu
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628
| | - Mariko Ogura
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628
| | - Koichiro Ishimori
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628
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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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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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Onzuka M, Sekine Y, Uchida T, Ishimori K, Ozaki SI. HmuS from Yersinia pseudotuberculosis is a non-canonical heme-degrading enzyme to acquire iron from heme. Biochim Biophys Acta Gen Subj 2017; 1861:1870-1878. [PMID: 28385652 DOI: 10.1016/j.bbagen.2017.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/22/2017] [Accepted: 04/02/2017] [Indexed: 01/28/2023]
Abstract
Some Gram-negative pathogens import host heme into the cytoplasm and utilize it as an iron source for their survival. We report here that HmuS, encoded by the heme utilizing system (hmu) locus, cleaves the protoporphyrin ring to release iron from heme. A liquid chromatography/mass spectrometry analysis revealed that the degradation products of this reaction are two biliverdin isomers that result from transformation of a verdoheme intermediate. This oxidative heme degradation by HmuS required molecular oxygen and electrons supplied by either ascorbate or NADPH. Electrons could not be directly transferred from NADPH to heme; instead, ferredoxin-NADP+ reductase (FNR) functioned as a mediator. Although HmuS does not share amino acid sequence homology with heme oxygenase (HO), a well-known heme-degrading enzyme, absorption and resonance Raman spectral analyses suggest that the heme iron is coordinated with an axial histidine residue and a water molecule in both enzymes. The substitution of axial His196 or distal Arg102 with an alanine residue in HmuS almost completely eliminated heme-degradation activity, suggesting that Fe-His coordination and interaction of a distal residue with water molecules in the heme pocket are important for this activity.
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Affiliation(s)
- Masato Onzuka
- Department of Biological Chemistry, Graduate School of Science and Technology for Innovation, Yamaguchi University, Yoshida, Yamaguchi 753-8515, Japan
| | - Yukari Sekine
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Takeshi Uchida
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Koichiro Ishimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Shin-Ichi Ozaki
- Department of Biological Chemistry, Graduate School of Science and Technology for Innovation, Yamaguchi University, Yoshida, Yamaguchi 753-8515, Japan.
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48
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Direct Heme Uptake by Phytoplankton-Associated Roseobacter Bacteria. mSystems 2017; 2:mSystems00124-16. [PMID: 28083564 PMCID: PMC5225302 DOI: 10.1128/msystems.00124-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/09/2016] [Indexed: 01/19/2023] Open
Abstract
Ecosystem productivity in large regions of the surface ocean is fueled by iron that has been microbially regenerated from biomass. Currently, the specific microbes and molecules that mediate the transfer of recycled iron between microbial trophic levels remain largely unknown. We characterized a marine bacterial heme transporter and verified its role in acquiring heme, an abundant iron-containing enzyme cofactor. We present evidence that after host cell lysis, phytoplankton-associated bacteria directly extract heme and hemoproteins from algal cellular debris in order to fulfill their iron requirements and that the regulation of this process may be modulated by host cues. Direct heme transport, in contrast to multistep extracellular processing of hemoproteins, may allow certain phytoplankton-associated bacteria to rapidly extract iron from decaying phytoplankton, thus efficiently recycling cellular iron into the wider microbial loop. Iron is an essential micronutrient and can limit the growth of both marine phytoplankton and heterotrophic bacterioplankton. In this study, we investigated the molecular basis of heme transport, an organic iron acquisition pathway, in phytoplankton-associated Roseobacter bacteria and explored the potential role of bacterial heme uptake in the marine environment. We searched 153 Roseobacter genomes and found that nearly half contained putative complete heme transport systems with nearly the same synteny. We also examined a publicly available coculture transcriptome and found that Roseobacter strain Sulfitobacter sp. strain SA11 strongly downregulated a putative heme transport gene cluster during mutualistic growth with a marine diatom, suggesting that the regulation of heme transport might be influenced by host cues. We generated a mutant of phytoplankton-associated Roseobacter strain Ruegeria sp. strain TM1040 by insertionally inactivating its homolog of the TonB-dependent heme transporter hmuR and confirmed the role of this gene in the uptake of heme and hemoproteins. We performed competition experiments between iron-limited wild-type and mutant TM1040 strains and found that the wild type maintains a growth advantage when competing with the mutant for iron compounds derived solely from lysed diatom cells. Heme transport systems were largely absent from public marine metagenomes and metatranscriptomes, suggesting that marine bacteria with the potential for heme transport likely have small standing populations in the free-living bacterioplankton. Heme transport is likely a useful strategy for phytoplankton-associated bacteria because it provides direct access to components of the host intracellular iron pool after lysis. IMPORTANCE Ecosystem productivity in large regions of the surface ocean is fueled by iron that has been microbially regenerated from biomass. Currently, the specific microbes and molecules that mediate the transfer of recycled iron between microbial trophic levels remain largely unknown. We characterized a marine bacterial heme transporter and verified its role in acquiring heme, an abundant iron-containing enzyme cofactor. We present evidence that after host cell lysis, phytoplankton-associated bacteria directly extract heme and hemoproteins from algal cellular debris in order to fulfill their iron requirements and that the regulation of this process may be modulated by host cues. Direct heme transport, in contrast to multistep extracellular processing of hemoproteins, may allow certain phytoplankton-associated bacteria to rapidly extract iron from decaying phytoplankton, thus efficiently recycling cellular iron into the wider microbial loop.
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49
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Structural Characterization of Heme Environmental Mutants of CgHmuT that Shuttles Heme Molecules to Heme Transporters. Int J Mol Sci 2016; 17:ijms17060829. [PMID: 27240352 PMCID: PMC4926363 DOI: 10.3390/ijms17060829] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 05/19/2016] [Accepted: 05/24/2016] [Indexed: 01/19/2023] Open
Abstract
Corynebacteria contain a heme uptake system encoded in hmuTUV genes, in which HmuT protein acts as a heme binding protein to transport heme to the cognate transporter HmuUV. The crystal structure of HmuT from Corynebacterium glutamicum (CgHmuT) reveals that heme is accommodated in the central cleft with His141 and Tyr240 as the axial ligands and that Tyr240 forms a hydrogen bond with Arg242. In this work, the crystal structures of H141A, Y240A, and R242A mutants were determined to understand the role of these residues for the heme binding of CgHmuT. Overall and heme environmental structures of these mutants were similar to those of the wild type, suggesting that there is little conformational change in the heme-binding cleft during heme transport reaction with binding and the dissociation of heme. A loss of one axial ligand or the hydrogen bonding interaction with Tyr240 resulted in an increase in the redox potential of the heme for CgHmuT to be reduced by dithionite, though the wild type was not reduced under physiological conditions. These results suggest that the heme environmental structure stabilizes the ferric heme binding in CgHmuT, which will be responsible for efficient heme uptake under aerobic conditions where Corynebacteria grow.
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50
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Sachla AJ, Ouattara M, Romero E, Agniswamy J, Weber IT, Gadda G, Eichenbaum Z. In vitro heme biotransformation by the HupZ enzyme from Group A streptococcus. Biometals 2016; 29:593-609. [PMID: 27154580 DOI: 10.1007/s10534-016-9937-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 05/01/2016] [Indexed: 01/14/2023]
Abstract
In Group A streptococcus (GAS), the metallorepressor MtsR regulates iron homeostasis. Here we describe a new MtsR-repressed gene, which we named hupZ (heme utilization protein). A recombinant HupZ protein was purified bound to heme from Escherichia coli grown in the presence of 5-aminolevulinic acid and iron. HupZ specifically binds heme with stoichiometry of 1:1. The addition of NADPH to heme-bound HupZ (in the presence of cytochrome P450 reductase, NADPH-regeneration system and catalase) triggered progressive decrease of the HupZ Soret band and the appearance of an absorption peak at 660 nm that was resistance to hydrolytic conditions. No spectral changes were observed when ferredoxin and ferredoxin reductase were used as redox partners. Differential spectroscopy with myoglobin or with the ferrous chelator, ferrozine, confirmed that carbon monoxide and free iron are produced during the reaction. ApoHupZ was crystallized as a homodimer with a split β-barrel conformation in each monomer comprising six β strands and three α helices. This structure resembles the split β-barrel domain shared by the members of a recently described family of heme degrading enzymes. However, HupZ is smaller and lacks key residues found in the proteins of the latter group. Phylogenetic analysis places HupZ on a clade separated from those for previously described heme oxygenases. In summary, we have identified a new GAS enzyme-containing split β-barrel and capable of heme biotransformation in vitro; to the best of our knowledge, this is the first enzyme among Streptococcus species with such activity.
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Affiliation(s)
- Ankita J Sachla
- Department of Biology, College of Arts and Sciences, Georgia State University, P.O. Box 4010, Atlanta, GA, 30302-4010, USA
| | - Mahamoudou Ouattara
- Department of Biology, College of Arts and Sciences, Georgia State University, P.O. Box 4010, Atlanta, GA, 30302-4010, USA
| | - Elvira Romero
- Department of Chemistry, College of Arts and Sciences, Georgia State University, Atlanta, GA, 30302-3965, USA
| | - Johnson Agniswamy
- Department of Biology, College of Arts and Sciences, Georgia State University, P.O. Box 4010, Atlanta, GA, 30302-4010, USA
| | - Irene T Weber
- Department of Biology, College of Arts and Sciences, Georgia State University, P.O. Box 4010, Atlanta, GA, 30302-4010, USA.,Department of Chemistry, College of Arts and Sciences, Georgia State University, Atlanta, GA, 30302-3965, USA.,Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, 30303, USA
| | - Giovanni Gadda
- Department of Biology, College of Arts and Sciences, Georgia State University, P.O. Box 4010, Atlanta, GA, 30302-4010, USA.,Department of Chemistry, College of Arts and Sciences, Georgia State University, Atlanta, GA, 30302-3965, USA.,Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, 30303, USA.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303, USA
| | - Zehava Eichenbaum
- Department of Biology, College of Arts and Sciences, Georgia State University, P.O. Box 4010, Atlanta, GA, 30302-4010, USA.
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