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Rugiel M, Janik-Olchawa N, Kowalczyk J, Pomorska K, Sitarz M, Bik E, Horak D, Babic M, Setkowicz Z, Chwiej J. Raman microscopy allows to follow internalization, subcellular accumulation and fate of iron oxide nanoparticles in cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 323:124888. [PMID: 39116589 DOI: 10.1016/j.saa.2024.124888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/05/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024]
Abstract
An important issue in the context of both potenial toxicity of iron oxide nanoparticles (IONP) and their medical applications is tracking of the internalization process of these nanomaterials into living cells, as well as their localization and fate within them. The typical methods used for this purpose are transmission electron microscopy, confocal fluorescence microscopy as well as light-scattering techniques including dark-field microscopy and flow cytometry. All the techniques mentioned have their advantages and disadvantages. Among the problems it is necessary to mention complicated sample preparation, difficult interpretation of experimental data requiring qualified and experienced personnel, different behavior of fluorescently labeled IONP comparing to those label-free or finally the lack of possibility of chemical composition characteristics of nanomaterials. The purpose of the present investigation was the assessment of the usefulness of Raman microscopy for the tracking of the internalization of IONP into cells, as well as the optimization of this process. Moreover, the study focused on identification of the potential differences in the cellular fate of superparamagnetic nanoparticles having magnetite and maghemite core. The Raman spectra of U87MG cells which internalized IONP presented additional bands which position depended on the used laser wavelength. They occurred at the wavenumber range 1700-2400 cm-1 for laser 488 nm and below the wavenumber of 800 cm-1 in case of laser 532 nm. The intensity of the mentioned Raman bands was higher for the green laser (532 nm) and their position, was independent and not characteristic on the primary core material of IONP (magnetite, maghemite). The obtained results showed that Raman microscopy is an excellent, non-destructive and objective technique that allows monitoring the process of internalization of IONP into cells and visualizing such nanoparticles and/or their metabolism products within them at low exposure levels. What is more, the process of tracking IONP using the technique may be further improved by using appropriate wavelength and power of the laser source.
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Affiliation(s)
- Marzena Rugiel
- Faculty of Physics and Applied Computer Science, AGH University of Krakow, Mickiewicza 30, 30-059 Krakow, Poland
| | - Natalia Janik-Olchawa
- Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Krakow, Poland
| | - Julia Kowalczyk
- Faculty of Physics and Applied Computer Science, AGH University of Krakow, Mickiewicza 30, 30-059 Krakow, Poland
| | - Karolina Pomorska
- Faculty of Physics and Applied Computer Science, AGH University of Krakow, Mickiewicza 30, 30-059 Krakow, Poland
| | - Maciej Sitarz
- Faculty of Materials Science and Ceramics, AGH University of Krakow, Mickiewicza 30, 30-059, Krakow, Poland
| | - Ewelina Bik
- Academic Centre for Materials and Nanotechnology, AGH University of Krakow, Mickiewicza 30, 30-059 Krakow, Poland
| | - Daniel Horak
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského 2, 162 00, Prague 6, Czech Republic
| | - Michal Babic
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského 2, 162 00, Prague 6, Czech Republic
| | - Zuzanna Setkowicz
- Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Krakow, Poland
| | - Joanna Chwiej
- Faculty of Physics and Applied Computer Science, AGH University of Krakow, Mickiewicza 30, 30-059 Krakow, Poland.
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2
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Ye D, Nguyen PT, Bourgault S, Couture M. The heme binding protein ChuX is a regulator of heme degradation by the ChuS protein in Escherichia coli O157:H7. J Inorg Biochem 2024; 256:112575. [PMID: 38678912 DOI: 10.1016/j.jinorgbio.2024.112575] [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] [Received: 03/01/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024]
Abstract
Escherichia coli O157:H7 possesses an 8-gene cluster (chu genes) that contains genes involved in heme transport and processing from the human host. Among the chu genes, four encode cytoplasmic proteins (ChuS, ChuX, ChuY and ChuW). ChuX was previously shown to be a heme binding protein and to assist ChuW in heme degradation under anaerobic conditions. The purpose of this work was to investigate if ChuX works in concert with ChuS, which is a protein able to degrade heme by a non-canonical mechanism and release the iron from the porphyrin under aerobic conditions using hydrogen peroxide as the oxidant. We showed that when the heme-bound ChuX and apo-ChuS protein are mixed, heme is efficiently transferred from ChuX to ChuS. Heme-bound ChuX displayed a peroxidase activity with ABTS and H2O2 but not heme-bound ChuS, which is an efficient test to determine the protein to which heme is bound in the ChuS-ChuX complex. We found that ChuX protects heme from chemical oxidation and that it has no heme degradation activity by itself. Unexpectedly, we found that ChuX inhibits heme degradation by ChuS and stops the reaction at an early intermediate. We determined using surface plasmon resonance that ChuX interacts with ChuS and that it forms a relatively stable complex. These results indicate that ChuX in addition to its heme transfer activity is a regulator of ChuS activity, a function that was not described before for any of the heme carrier protein that delivers heme to heme degradation enzymes.
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Affiliation(s)
- Danrong Ye
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Quebec City, QC, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS) and PROTEO, Université Laval, Quebec city, QC, Canada; Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO), Montreal, QC, Canada
| | - Phuong Trang Nguyen
- Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO), Montreal, QC, Canada; Departement of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada
| | - Steve Bourgault
- Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO), Montreal, QC, Canada; Departement of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada
| | - Manon Couture
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Quebec City, QC, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS) and PROTEO, Université Laval, Quebec city, QC, Canada; Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO), Montreal, QC, Canada.
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3
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Keith AD, Sawyer EB, Choy DCY, Xie Y, Biggs GS, Klein OJ, Brear PD, Wales DJ, Barker PD. Combining experiment and energy landscapes to explore anaerobic heme breakdown in multifunctional hemoproteins. Phys Chem Chem Phys 2024; 26:695-712. [PMID: 38053511 DOI: 10.1039/d3cp03897a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
To survive, many pathogens extract heme from their host organism and break down the porphyrin scaffold to sequester the Fe2+ ion via a heme oxygenase. Recent studies have revealed that certain pathogens can anaerobically degrade heme. Our own research has shown that one such pathway proceeds via NADH-dependent heme degradation, which has been identified in a family of hemoproteins from a range of bacteria. HemS, from Yersinia enterocolitica, is the main focus of this work, along with HmuS (Yersinia pestis), ChuS (Escherichia coli) and ShuS (Shigella dysenteriae). We combine experiments, Energy Landscape Theory, and a bioinformatic investigation to place these homologues within a wider phylogenetic context. A subset of these hemoproteins are known to bind certain DNA promoter regions, suggesting not only that they can catalytically degrade heme, but that they are also involved in transcriptional modulation responding to heme flux. Many of the bacterial species responsible for these hemoproteins (including those that produce HemS, ChuS and ShuS) are known to specifically target oxygen-depleted regions of the gastrointestinal tract. A deeper understanding of anaerobic heme breakdown processes exploited by these pathogens could therefore prove useful in the development of future strategies for disease prevention.
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Affiliation(s)
- Alasdair D Keith
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Elizabeth B Sawyer
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Desmond C Y Choy
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Yuhang Xie
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - George S Biggs
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Oskar James Klein
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Paul D Brear
- Department of Biochemistry, University of Cambridge, Sanger Building, Cambridge CB2 1GA, UK
| | - David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Paul D Barker
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
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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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5
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Abstract
We hereby present the first descriptions of human-invasive infections caused by Escherichia marmotae, a recently described species that encompasses the former “Escherichia cryptic clade V.” We describe four cases, one acute sepsis of unknown origin, one postoperative sepsis after cholecystectomy, one spondylodiscitis, and one upper urinary tract infection. Cases were identified through unsystematic queries in a single clinical lab over 6 months. Through genome sequencing of the causative strains combined with available genomes from elsewhere, we demonstrate Es. marmotae to be a likely ubiquitous species containing genotypic virulence traits associated with Escherichia pathogenicity. The invasive isolates were scattered among isolates from a range of nonhuman sources in the phylogenetic analyses, thus indicating inherent virulence in multiple lineages. Pan genome analyses indicate that Es. marmotae has a large accessory genome and is likely to obtain ecologically advantageous traits, such as genes encoding antimicrobial resistance. Reliable identification might be possible by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), but relevant spectra are missing in commercial databases. It can be identified through 16S rRNA gene sequencing. Escherichia marmotae could represent a relatively common human pathogen, and improved diagnostics will provide a better understanding of its clinical importance. IMPORTANCEEscherichia coli is the most common pathogen found in blood cultures and urine and among the most important pathogenic species in the realm of human health. The notion that some of these isolates are not Es. coli but rather another species within the same genus may have implications for what Es. coli constitutes. We only recently have obtained methods to separate the two species, which means that possible differences in important clinical aspects, such as antimicrobial resistance rates, virulence, and phylogenetic structure, may exist. We believe that Es. marmotae as a common pathogen is new merely because we have not looked or bothered to distinguish between the thousands of invasive Escherichia passing through microbiological laboratories each day.
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Brimberry M, Toma MA, Hines KM, Lanzilotta WN. HutW from Vibrio cholerae Is an Anaerobic Heme-Degrading Enzyme with Unique Functional Properties. Biochemistry 2021; 60:699-710. [PMID: 33600151 DOI: 10.1021/acs.biochem.0c00950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Increasing antibiotic resistance, and a growing recognition of the importance of the human microbiome, demand that new therapeutic targets be identified. Characterization of metabolic pathways that are unique to enteric pathogens represents a promising approach. Iron is often the rate-limiting factor for growth, and Vibrio cholerae, the causative agent of cholera, has been shown to contain numerous genes that function in the acquisition of iron from the environment. Included in this arsenal of genes are operons dedicated to obtaining iron from heme and heme-containing proteins. Given the persistence of cholera, an important outstanding question is whether V. cholerae is capable of anaerobic heme degradation as was recently reported for enterohemorrhagic Escherichia coli O157:H7. In this work, we demonstrate that HutW from V. cholerae is a radical S-adenosylmethionine methyl transferase involved in the anaerobic opening of the porphyrin ring of heme. However, in contrast to the enzyme ChuW, found in enterohemorrhagic E. coli O157:H7, there are notable differences in the mechanism and products of the HutW reaction. Of particular interest are data that demonstrate HutW will catalyze ring opening as well as tetrapyrrole reduction and can utilize reduced nicotinamide adenine dinucleotide phosphate as an electron source. The biochemical and biophysical properties of HutW are presented, and the evolutionary implications are discussed.
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7
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Mathew LG, Beattie NR, Pritchett C, Lanzilotta WN. New Insight into the Mechanism of Anaerobic Heme Degradation. Biochemistry 2019; 58:4641-4654. [PMID: 31652058 DOI: 10.1021/acs.biochem.9b00841] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
ChuW, ChuX, and ChuY are contiguous genes downstream from a single promoter that are expressed in the enteric pathogen Escherichia coli O157:H7 when iron is limiting. These genes, and the corresponding proteins, are part of a larger heme uptake and utilization operon that is common to several other enteric pathogens, such as Vibrio cholerae. The aerobic degradation of heme has been well characterized in humans and several pathogenic bacteria, including E. coli O157:H7, but only recently was it shown that ChuW catalyzes the anaerobic degradation of heme to release iron and produce a reactive tetrapyrrole termed "anaerobilin". ChuY has been shown to function as an anaerobilin reductase, in a role that parallels biliverdin reductase. In this work we have employed biochemical and biophysical approaches to further interrogate the mechanism of the anaerobic degradation of heme. We demonstrate that the iron atom of the heme does not participate in the catalytic mechanism of ChuW and that S-adenosyl-l-methionine binding induces conformational changes that favor catalysis. In addition, we show that ChuX and ChuY have synergistic and additive effects on the turnover rate of ChuW. Finally, we have found that ChuS is an effective source of heme or protoporphyrin IX for ChuW under anaerobic conditions. These data indicate that ChuS may have dual functionality in vivo. Specifically, ChuS serves as a heme oxygenase during aerobic metabolism of heme but functions as a cytoplasmic heme storage protein under anaerobic conditions, akin to what has been shown for PhuS (45% sequence identity) from Pseudomonas aeruginosa.
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Affiliation(s)
- Liju G Mathew
- Department of Biochemistry and Molecular Biology & Center for Metalloenzyme Studies , University of Georgia , Athens , Georgia 30602 , United States
| | - Nathaniel R Beattie
- Department of Biochemistry and Molecular Biology & Center for Metalloenzyme Studies , University of Georgia , Athens , Georgia 30602 , United States
| | - Clayton Pritchett
- Department of Biochemistry and Molecular Biology & Center for Metalloenzyme Studies , University of Georgia , Athens , Georgia 30602 , United States
| | - William N Lanzilotta
- Department of Biochemistry and Molecular Biology & Center for Metalloenzyme Studies , University of Georgia , Athens , Georgia 30602 , United States
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8
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Shi YJ, Fang QJ, Huang HQ, Gong CG, Hu YH. HutZ is required for biofilm formation and contributes to the pathogenicity of Edwardsiella piscicida. Vet Res 2019; 50:76. [PMID: 31578154 PMCID: PMC6775658 DOI: 10.1186/s13567-019-0693-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/19/2019] [Indexed: 12/13/2022] Open
Abstract
Edwardsiella piscicida is a severe fish pathogen. Haem utilization systems play an important role in bacterial adversity adaptation and pathogenicity. In this study, a speculative haem utilization protein, HutZEp, was characterized in E. piscicida. hutZEp is encoded with two other genes, hutW and hutX, in an operon that is similar to the haem utilization operon hutWXZ identified in V. cholerae. However, protein activity analysis showed that HutZEp is probably not related to hemin utilization. To explore the biological role of HutZEp, a markerless hutZEp in-frame mutant strain, TX01ΔhutZ, was constructed. Deletion of hutZEp did not significantly affect bacterial growth in normal medium, in iron-deficient conditions, or in the presence of haem but significantly retarded bacterial biofilm growth. The expression of known genes related to biofilm growth was not affected by hutZEp deletion, which indicated that HutZEp was probably a novel factor promoting biofilm formation in E. piscicida. Compared to the wild-type TX01, TX01ΔhutZ exhibited markedly compromised tolerance to acid stress and host serum stress. Pathogenicity analysis showed that inactivation of hutZEp significantly impaired the ability of E. piscicida to invade and reproduce in host cells and to infect host tissue. In contrast to TX01, TX01ΔhutZ was defective in blocking host macrophage activation. The expression of hutZEp was directly regulated by the ferric uptake regulator Fur. This study is the first functional characterization of HutZ in a fish pathogen, and these findings suggested that HutZEp is essential for E. piscicida biofilm formation and contributes to host infection.
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Affiliation(s)
- Yan-Jie Shi
- Ocean College of Hebei Agricultural University, Qinhuangdao, 066000, China.,Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Qing-Jian Fang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Hui-Qin Huang
- Ocean College of Hebei Agricultural University, Qinhuangdao, 066000, China.,Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.,Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou, 571101, China
| | - Chun-Guang Gong
- Ocean College of Hebei Agricultural University, Qinhuangdao, 066000, China.
| | - Yong-Hua Hu
- Ocean College of Hebei Agricultural University, Qinhuangdao, 066000, China. .,Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China. .,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China. .,Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou, 571101, China.
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9
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Pettersen VK, Mosevoll KA, Lindemann PC, Wiker HG. Coordination of Metabolism and Virulence Factors Expression of Extraintestinal Pathogenic Escherichia coli Purified from Blood Cultures of Patients with Sepsis. Mol Cell Proteomics 2016; 15:2890-907. [PMID: 27364158 PMCID: PMC5013306 DOI: 10.1074/mcp.m116.060582] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Indexed: 02/06/2023] Open
Abstract
One of the trademarks of extraintestinal pathogenic Escherichia coli is adaptation of metabolism and basic physiology to diverse host sites. However, little is known how this common human pathogen adapts to permit survival and growth in blood. We used label-free quantitative proteomics to characterize five E. coli strains purified from clinical blood cultures associated with sepsis and urinary tract infections. Further comparison of proteome profiles of the clinical strains and a reference uropathogenic E. coli strain 536 cultivated in blood culture and on two different solid media distinguished cellular features altered in response to the pathogenically relevant condition. The analysis covered nearly 60% of the strains predicted proteomes, and included quantitative description based on label-free intensity scores for 90% of the detected proteins. Statistical comparison of anaerobic and aerobic blood cultures revealed 32 differentially expressed proteins (1.5% of the shared proteins), mostly associated with acquisition and utilization of metal ions critical for anaerobic or aerobic respiration. Analysis of variance identified significantly altered amounts of 47 proteins shared by the strains (2.7%), including proteins involved in vitamin B6 metabolism and virulence. Although the proteomes derived from blood cultures were fairly similar for the investigated strains, quantitative proteomic comparison to the growth on solid media identified 200 proteins with substantially changed levels (11% of the shared proteins). Blood culture was characterized by up-regulation of anaerobic fermentative metabolism and multiple virulence traits, including cell motility and iron acquisition. In a response to the growth on solid media there were increased levels of proteins functional in aerobic respiration, catabolism of medium-specific carbon sources and protection against oxidative and osmotic stresses. These results demonstrate on the expressed proteome level that expression of extraintestinal virulence factors and overall cellular metabolism closely reflects specific growth conditions. Data are available via ProteomeXchange with identifier PXD002912.
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Affiliation(s)
- Veronika Kuchařová Pettersen
- From the ‡The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway;
| | | | - Paul Christoffer Lindemann
- From the ‡The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; ¶Department of Microbiology; Haukeland University Hospital, N-5021 Bergen, Norway
| | - Harald G Wiker
- From the ‡The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; ¶Department of Microbiology; Haukeland University Hospital, N-5021 Bergen, Norway
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10
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Sekine Y, Tanzawa T, Tanaka Y, Ishimori K, Uchida T. Cytoplasmic Heme-Binding Protein (HutX) from Vibrio cholerae Is an Intracellular Heme Transport Protein for the Heme-Degrading Enzyme, HutZ. Biochemistry 2016; 55:884-93. [DOI: 10.1021/acs.biochem.5b01273] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yukari Sekine
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Takehito Tanzawa
- Graduate
School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yoshikazu Tanaka
- Faculty
of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
- PRESTO, Japan Science and Technology Agency, Sapporo 060-0810, Japan
| | - Koichiro Ishimori
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takeshi Uchida
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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11
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Su T, Chi K, Wang K, Guo L, Huang Y. Expression, purification and preliminary crystallographic analysis of a haem-utilizing protein, HutX, from Vibrio cholerae. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:141-4. [PMID: 25664785 DOI: 10.1107/s2053230x14027666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 12/18/2014] [Indexed: 01/04/2023]
Abstract
Vibrio cholerae, the causative agent of cholera, has developed a variety of mechanisms to obtain the limited-availability iron from human hosts. One important method for iron acquisition is through haem-uptake systems. Although the transport of haem has been widely studied, the fate of haem once it enters the cytoplasm remains an open question. Here, preliminary X-ray crystallographic analysis was performed on HutX, a member of the conserved haem-utilization operon from V. cholerae strain N16961. The crystals of HutX were found to belong to the orthorhombic space group C2221, with unit-cell parameters a = 50.1, b = 169.0, c = 81.8 Å. There are two protein molecules in the asymmetric unit, with a corresponding Matthews coefficient VM of 2.06 Å(3) Da(-1) and a solvent content of 40.28%.
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Affiliation(s)
- Tiantian Su
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, 27 Shanda Nanlu, Jinan, Shandong 250100, People's Republic of China
| | - Kaikai Chi
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, 27 Shanda Nanlu, Jinan, Shandong 250100, People's Republic of China
| | - Kang Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, 27 Shanda Nanlu, Jinan, Shandong 250100, People's Republic of China
| | - Liming Guo
- Rizhao Center for Disease Prevention and Control, Rizhao Health Bureau, 136 Beijing Road, Rizhao, Shandong 276826, People's Republic of China
| | - Yan Huang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, 27 Shanda Nanlu, Jinan, Shandong 250100, People's Republic of China
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12
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Wilks A, Ikeda-Saito M. Heme utilization by pathogenic bacteria: not all pathways lead to biliverdin. Acc Chem Res 2014; 47:2291-8. [PMID: 24873177 PMCID: PMC4139177 DOI: 10.1021/ar500028n] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The eukaryotic heme oxygenases (HOs) (E.C. 1.14.99.3) convert heme
to biliverdin, iron, and carbon monoxide (CO) in three successive
oxygenation steps. Pathogenic bacteria require iron for survival and
infection. Extracellular heme uptake from the host plays a critical
role in iron acquisition and virulence. In the past decade, several
HOs required for the release of iron from extracellular heme have
been identified in pathogenic bacteria, including Corynebacterium
diphtheriae, Neisseriae meningitides, and Pseudomonas aeruginosa. The
bacterial enzymes were shown to be structurally and mechanistically
similar to those of the canonical eukaryotic HO enzymes. However,
the recent discovery of the structurally and mechanistically distinct
noncanonical heme oxygenases of Staphylococcus aureus and Mycobacterium tuberculosis has
expanded the reaction manifold of heme degradation. The distinct ferredoxin-like
structural fold and extreme heme ruffling are proposed to give rise
to the alternate heme degradation products in the S.
aureus and M. tuberculosis enzymes. In addition, several “heme-degrading factors”
with no structural homology to either class of HOs have recently been
reported. The identification of these “heme-degrading proteins”
has largely been determined on the basis of in vitro heme degradation
assays. Many of these proteins were reported to produce biliverdin,
although no extensive characterization of the products was performed.
Prior to the characterization of the canonical HO enzymes, the nonenzymatic
degradation of heme and heme proteins in the presence of a reductant
such as ascorbate or hydrazine, a reaction termed “coupled
oxidation”, served as a model for biological heme degradation.
However, it was recognized that there were important mechanistic differences
between the so-called coupled oxidation of heme proteins and enzymatic
heme oxygenation. In the coupled oxidation reaction, the final product,
verdoheme, can readily be converted to biliverdin under hydrolytic
conditions. The differences between heme oxygenation by the canonical
and noncanonical HOs and coupled oxidation will be discussed in the
context of the stabilization of the reactive FeIII–OOH
intermediate and regioselective heme hydroxylation. Thus, in the determination
of heme oxygenase activity in vitro, it is important to ensure that
the reaction proceeds through successive oxygenation steps. We further
suggest that when bacterial heme degradation is being characterized,
a systems biology approach combining genetics, mechanistic enzymology,
and metabolite profiling should be undertaken.
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Affiliation(s)
- Angela Wilks
- Department
of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201-1140, United States
| | - Masao Ikeda-Saito
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University Katahira, Aoba, Sendai 980-8577, Japan
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13
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The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence. PLoS Pathog 2013. [PMID: 23785281 DOI: 10.1371/journal.ppat.1003403.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
While phosphotyrosine modification is an established regulatory mechanism in eukaryotes, it is less well characterized in bacteria due to low prevalence. To gain insight into the extent and biological importance of tyrosine phosphorylation in Escherichia coli, we used immunoaffinity-based phosphotyrosine peptide enrichment combined with high resolution mass spectrometry analysis to comprehensively identify tyrosine phosphorylated proteins and accurately map phosphotyrosine sites. We identified a total of 512 unique phosphotyrosine sites on 342 proteins in E. coli K12 and the human pathogen enterohemorrhagic E. coli (EHEC) O157:H7, representing the largest phosphotyrosine proteome reported to date in bacteria. This large number of tyrosine phosphorylation sites allowed us to define five phosphotyrosine site motifs. Tyrosine phosphorylated proteins belong to various functional classes such as metabolism, gene expression and virulence. We demonstrate for the first time that proteins of a type III secretion system (T3SS), required for the attaching and effacing (A/E) lesion phenotype characteristic for intestinal colonization by certain EHEC strains, are tyrosine phosphorylated by bacterial kinases. Yet, A/E lesion and metabolic phenotypes were unaffected by the mutation of the two currently known tyrosine kinases, Etk and Wzc. Substantial residual tyrosine phosphorylation present in an etk wzc double mutant strongly indicated the presence of hitherto unknown tyrosine kinases in E. coli. We assess the functional importance of tyrosine phosphorylation and demonstrate that the phosphorylated tyrosine residue of the regulator SspA positively affects expression and secretion of T3SS proteins and formation of A/E lesions. Altogether, our study reveals that tyrosine phosphorylation in bacteria is more prevalent than previously recognized, and suggests the involvement of phosphotyrosine-mediated signaling in a broad range of cellular functions and virulence.
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14
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Hansen AM, Chaerkady R, Sharma J, Díaz-Mejía JJ, Tyagi N, Renuse S, Jacob HKC, Pinto SM, Sahasrabuddhe NA, Kim MS, Delanghe B, Srinivasan N, Emili A, Kaper JB, Pandey A. The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence. PLoS Pathog 2013; 9:e1003403. [PMID: 23785281 PMCID: PMC3681748 DOI: 10.1371/journal.ppat.1003403] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 04/22/2013] [Indexed: 01/31/2023] Open
Abstract
While phosphotyrosine modification is an established regulatory mechanism in eukaryotes, it is less well characterized in bacteria due to low prevalence. To gain insight into the extent and biological importance of tyrosine phosphorylation in Escherichia coli, we used immunoaffinity-based phosphotyrosine peptide enrichment combined with high resolution mass spectrometry analysis to comprehensively identify tyrosine phosphorylated proteins and accurately map phosphotyrosine sites. We identified a total of 512 unique phosphotyrosine sites on 342 proteins in E. coli K12 and the human pathogen enterohemorrhagic E. coli (EHEC) O157:H7, representing the largest phosphotyrosine proteome reported to date in bacteria. This large number of tyrosine phosphorylation sites allowed us to define five phosphotyrosine site motifs. Tyrosine phosphorylated proteins belong to various functional classes such as metabolism, gene expression and virulence. We demonstrate for the first time that proteins of a type III secretion system (T3SS), required for the attaching and effacing (A/E) lesion phenotype characteristic for intestinal colonization by certain EHEC strains, are tyrosine phosphorylated by bacterial kinases. Yet, A/E lesion and metabolic phenotypes were unaffected by the mutation of the two currently known tyrosine kinases, Etk and Wzc. Substantial residual tyrosine phosphorylation present in an etk wzc double mutant strongly indicated the presence of hitherto unknown tyrosine kinases in E. coli. We assess the functional importance of tyrosine phosphorylation and demonstrate that the phosphorylated tyrosine residue of the regulator SspA positively affects expression and secretion of T3SS proteins and formation of A/E lesions. Altogether, our study reveals that tyrosine phosphorylation in bacteria is more prevalent than previously recognized, and suggests the involvement of phosphotyrosine-mediated signaling in a broad range of cellular functions and virulence. While phosphotyrosine modification is established in eukaryote cell signaling, it is less characterized in bacteria. Despite that deletion of bacterial tyrosine kinases is known to affect various cellular functions and virulence of bacterial pathogens, few phosphotyrosine proteins are currently known. To gain insight into the extent and biological function of tyrosine phosphorylation in E. coli, we carried out an in-depth phosphotyrosine protein profiling using a mass spectrometry-based proteomics approach. Our study on E. coli K12 and the human pathogen enterohemorrhagic E. coli (EHEC) O157:H7, which is a common cause of food-borne outbreaks of diarrhea, hemorrhagic colitis and hemolytic uremic syndrome, reveal that tyrosine phosphorylation is far more prevalent than previously recognized. Target proteins are involved in a broad range of cellular functions and virulence. Proteins of the type III secretion system (T3SS), required for the attaching and effacing lesion phenotype characteristic for intestinal colonization by EHEC, are tyrosine phosphorylated. The expression of these T3SS proteins and A/E lesion formation is affected by a tyrosine phosphorylated residue on the regulator SspA. Also, our data indicates the presence of hitherto unknown E. coli tyrosine kinases. Overall, tyrosine phosphorylation seems to be involved in controlling cellular core processes and virulence of bacteria.
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Affiliation(s)
- Anne-Marie Hansen
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Raghothama Chaerkady
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jyoti Sharma
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Manipal University, Manipal, India
| | - J. Javier Díaz-Mejía
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
- Department of Biology, Wilfrid Laurier University, Waterloo, Canada
| | - Nidhi Tyagi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Santosh Renuse
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Harrys K. C. Jacob
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Manipal University, Manipal, India
| | - Nandini A. Sahasrabuddhe
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
- Manipal University, Manipal, India
| | - Min-Sik Kim
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
| | | | | | - Andrew Emili
- Department of Biology, Wilfrid Laurier University, Waterloo, Canada
| | - James B. Kaper
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (JBK); (AP)
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (JBK); (AP)
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