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Wawer J, Andrukajtis M, Karczewski J, Zielińska-Jurek A, Piątek R. Fibrillar aggregates in powdered milk. J DAIRY RES 2023; 90:1-5. [PMID: 36694366 DOI: 10.1017/s002202992300002x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
This research paper addresses the hypothesis that powdered milk may contain amyloid fibrils. Amyloids are fibrillar aggregates of proteins. Up to this time, research on the presence of amyloids in food products are scarce. To check the hypothesis we performed thioflavin T fluorescence assay, X-ray powder diffraction, atomic force microscopy and fluorescence microscopy imaging. Our preliminary results show that commercially available milks contain fibrils that have features characteristic to amyloids. The obtained results can be interpreted in two opposite ways. The presence of amyloids could be considered as a hazard due to the fact that food products may induce amyloid related diseases. On the other hand, the presence of amyloids in traditionally consumed foodstuffs could serve as proof that fibrils of food proteins do not pose a threat for consumers.
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Affiliation(s)
- Jarosław Wawer
- Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza Str. 11/12, 80-233 Gdańsk, Poland
| | - Martyna Andrukajtis
- Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza Str. 11/12, 80-233 Gdańsk, Poland
| | - Jakub Karczewski
- Faculty of Applied Physics and Mathematics, Institute of Nanotechnology and Materials Science, Gdańsk University of Technology, Narutowicza Str. 11/12, 80-233 Gdańsk, Poland
| | - Anna Zielińska-Jurek
- Department of Process Engineering and Chemical Technology, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza Str. 11/12, 80-233 Gdańsk, Poland
| | - Rafał Piątek
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza Str. 11/12, 80-233 Gdańsk, Poland
- BioTechMed Center, Gdańsk University of Technology, Narutowicza Str. 11/12, 80-233 Gdańsk, Poland
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Fedorowicz J, Bazar D, Brankiewicz W, Kapica H, Ciura K, Zalewska-Piątek B, Piątek R, Cal K, Mojsiewicz-Pieńkowska K, Sączewski J. Development of Safirinium dyes for new applications: fluorescent staining of bacteria, human kidney cells, and the horny layer of the epidermis. Sci Rep 2022; 12:15098. [PMID: 36065005 PMCID: PMC9445088 DOI: 10.1038/s41598-022-19262-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/26/2022] [Indexed: 11/09/2022] Open
Abstract
Low-molecular synthetic fluorophores are convenient tools in bioimaging applications. Several derivatives of Safirinium dyes as well as their reactive N-hydroxysuccinimide (NHS) esters bearing diverse substituents were synthesized and evaluated experimentally in terms of their lipophilicity by means of reverse-phase and immobilized artificial membrane high-performance liquid chromatography. Subsequently, the selected compounds were employed as novel cellular imaging agents for staining Gram-positive and Gram-negative bacteria, human kidney cell line, as well as human skin tissue. The analyzed dyes allowed for visualization of cellular structures such as mitochondria, endoplasmic reticulum, and cellular nuclei. They proved to be useful in fluorescent staining of stratum corneum, especially in the aspect of xenobiotic exposure and its penetration into the skin. The best results were obtained with the use of moderately lipophilic NHS esters of Safirinium Q. The development of Safirinium dyes is a promising alternative for commercially available dyes since the reported molecules have low molecular masses and exhibit efficient staining and remarkable water solubility. Moreover, they are relatively simple and low-cost in synthesis.
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Affiliation(s)
- Joanna Fedorowicz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), 00014, Helsinki, Finland. .,Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland.
| | - Dagmara Bazar
- Department of Physical Chemistry, Medical University of Gdańsk, Al. Gen. Hallera 107, 80-416, Gdańsk, Poland
| | - Wioletta Brankiewicz
- Department of Pharmaceutical Technology and Biochemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Hanna Kapica
- Department of Physical Chemistry, Medical University of Gdańsk, Al. Gen. Hallera 107, 80-416, Gdańsk, Poland
| | - Krzesimir Ciura
- Department of Physical Chemistry, Medical University of Gdańsk, Al. Gen. Hallera 107, 80-416, Gdańsk, Poland.,QSAR Lab Ltd., Trzy Lipy 3 St., 80-172, Gdańsk, Poland
| | - Beata Zalewska-Piątek
- Department of Molecular Biotechnology and Microbiology, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Rafał Piątek
- Department of Molecular Biotechnology and Microbiology, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland.,BioTechMed Center, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Krzysztof Cal
- Department of Pharmaceutical Technology, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | | | - Jarosław Sączewski
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
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Zalewska-Piątek B, Piątek R. Bacteriophages as Potential Tools for Use in Antimicrobial Therapy and Vaccine Development. Pharmaceuticals (Basel) 2021; 14:331. [PMID: 33916345 PMCID: PMC8066226 DOI: 10.3390/ph14040331] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/19/2021] [Accepted: 04/02/2021] [Indexed: 12/16/2022] Open
Abstract
The constantly growing number of people suffering from bacterial, viral, or fungal infections, parasitic diseases, and cancers prompts the search for innovative methods of disease prevention and treatment, especially based on vaccines and targeted therapy. An additional problem is the global threat to humanity resulting from the increasing resistance of bacteria to commonly used antibiotics. Conventional vaccines based on bacteria or viruses are common and are generally effective in preventing and controlling various infectious diseases in humans. However, there are problems with the stability of these vaccines, their transport, targeted delivery, safe use, and side effects. In this context, experimental phage therapy based on viruses replicating in bacterial cells currently offers a chance for a breakthrough in the treatment of bacterial infections. Phages are not infectious and pathogenic to eukaryotic cells and do not cause diseases in human body. Furthermore, bacterial viruses are sufficient immuno-stimulators with potential adjuvant abilities, easy to transport, and store. They can also be produced on a large scale with cost reduction. In recent years, they have also provided an ideal platform for the design and production of phage-based vaccines to induce protective host immune responses. The most promising in this group are phage-displayed vaccines, allowing for the display of immunogenic peptides or proteins on the phage surfaces, or phage DNA vaccines responsible for expression of target genes (encoding protective antigens) incorporated into the phage genome. Phage vaccines inducing the production of specific antibodies may in the future protect us against infectious diseases and constitute an effective immune tool to fight cancer. Moreover, personalized phage therapy can represent the greatest medical achievement that saves lives. This review demonstrates the latest advances and developments in the use of phage vaccines to prevent human infectious diseases; phage-based therapy, including clinical trials; and personalized treatment adapted to the patient's needs and the type of bacterial infection. It highlights the advantages and disadvantages of experimental phage therapy and, at the same time, indicates its great potential in the treatment of various diseases, especially those resistant to commonly used antibiotics. All the analyses performed look at the rich history and development of phage therapy over the past 100 years.
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Affiliation(s)
- Beata Zalewska-Piątek
- Department of Molecular Biotechnology and Microbiology, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland;
| | - Rafał Piątek
- Department of Molecular Biotechnology and Microbiology, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland;
- BioTechMed Center, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
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Fedorowicz J, Wierzbicka M, Cebrat M, Wiśniewska P, Piątek R, Zalewska-Piątek B, Szewczuk Z, Sączewski J. Application of Safirinium N-Hydroxysuccinimide Esters to Derivatization of Peptides for High-Resolution Mass Spectrometry, Tandem Mass Spectrometry, and Fluorescent Labeling of Bacterial Cells. Int J Mol Sci 2020; 21:ijms21249643. [PMID: 33348897 PMCID: PMC7767236 DOI: 10.3390/ijms21249643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/13/2020] [Accepted: 12/15/2020] [Indexed: 12/16/2022] Open
Abstract
Mass spectrometry methods are commonly used in the identification of peptides and biomarkers. Due to a relatively low abundance of proteins in biological samples, there is a need for the development of novel derivatization methods that would improve MS detection limits. Hence, novel fluorescent N–hydroxysuccinimide esters of dihydro-[1,2,4]triazolo[4,3-a]pyridin-2-ium carboxylates (Safirinium P dyes) have been synthesized. The obtained compounds, which incorporate quaternary ammonium salt moieties, easily react with aliphatic amine groups of peptides, both in solution and on the solid support; thus, they can be applied for derivatization as ionization enhancers. Safirinium tagging experiments with ubiquitin hydrolysate revealed that the sequence coverage level was high (ca. 80%), and intensities of signals were enhanced up to 8-fold, which proves the applicability of the proposed tags in the bottom–up approach. The obtained results confirmed that the novel compounds enable the detection of trace amounts of peptides, and fixed positive charge within the tags results in high ionization efficiency. Moreover, Safirinium NHS esters have been utilized as imaging agents for fluorescent labeling and the microscopic visualization of living cells such as E. coli Top10 bacterial strain.
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Affiliation(s)
- Joanna Fedorowicz
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
- Correspondence: ; Tel.: +48-58-349-1957
| | - Magdalena Wierzbicka
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland; (M.W.); (M.C.); (Z.S.)
| | - Marek Cebrat
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland; (M.W.); (M.C.); (Z.S.)
| | - Paulina Wiśniewska
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (P.W.); (J.S.)
| | - Rafał Piątek
- Department of Molecular Biotechnology and Microbiology, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland; (R.P.); (B.Z.-P.)
| | - Beata Zalewska-Piątek
- Department of Molecular Biotechnology and Microbiology, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland; (R.P.); (B.Z.-P.)
| | - Zbigniew Szewczuk
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland; (M.W.); (M.C.); (Z.S.)
| | - Jarosław Sączewski
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (P.W.); (J.S.)
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Zalewska-Piątek B, Piątek R. Phage Therapy as a Novel Strategy in the Treatment of Urinary Tract Infections Caused by E. Coli. Antibiotics (Basel) 2020; 9:antibiotics9060304. [PMID: 32517088 PMCID: PMC7344395 DOI: 10.3390/antibiotics9060304] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 12/14/2022] Open
Abstract
Urinary tract infections (UTIs) are regarded as one of the most common bacterial infections affecting millions of people, in all age groups, annually in the world. The major causative agent of complicated and uncomplicated UTIs are uropathogenic E. coli strains (UPECs). Huge problems with infections of this type are their chronicity and periodic recurrences. Other disadvantages that are associated with UTIs are accompanying complications and high costs of health care, systematically increasing resistance of uropathogens to routinely used antibiotics, as well as biofilm formation by them. This creates the need to develop new approaches for the prevention and treatment of UTIs, among which phage therapy has a dominant potential to eliminate uropathogens within urinary tract. Due to the growing interest in such therapy in the last decade, the bacteriophages (natural, genetically modified, engineered, or combined with antibiotics or disinfectants) represent an innovative antimicrobial alternative and a strategy for managing the resistance of uropathogenic microorganisms and controlling UTIs.
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Zalewska-Piątek B, Olszewski M, Lipniacki T, Błoński S, Wieczór M, Bruździak P, Skwarska A, Nowicki B, Nowicki S, Piątek R. A shear stress micromodel of urinary tract infection by the Escherichia coli producing Dr adhesin. PLoS Pathog 2020; 16:e1008247. [PMID: 31917805 PMCID: PMC7004390 DOI: 10.1371/journal.ppat.1008247] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 02/06/2020] [Accepted: 11/28/2019] [Indexed: 11/25/2022] Open
Abstract
In this study, we established a dynamic micromodel of urinary tract infection to analyze the impact of UT-segment-specific urinary outflow on the persistence of E. coli colonization. We found that the adherence of Dr+ E. coli to bladder T24 transitional cells and type IV collagen is maximal at lowest shear stress and is reduced by any increase in flow velocity. The analyzed adherence was effective in the whole spectrum of physiological shear stress and was almost irreversible over the entire range of generated shear force. Once Dr+ E. coli bound to host cells or collagen, they did not detach even in the presence of elevated shear stress or of chloramphenicol, a competitive inhibitor of binding. Investigating the role of epithelial surface architecture, we showed that the presence of budding cells–a model microarchitectural obstacle–promotes colonization of the urinary tract by E. coli. We report a previously undescribed phenomenon of epithelial cell “rolling-shedding” colonization, in which the detached epithelial cells reattach to the underlying cell line through a layer of adherent Dr+ E. coli. This rolling-shedding colonization progressed continuously due to “refilling” induced by the flow-perturbing obstacle. The shear stress of fluid containing free-floating bacteria fueled the rolling, while providing an uninterrupted supply of new bacteria to be trapped by the rolling cell. The progressive rolling allows for transfer of briefly attached bacteria onto the underlying monolayer in a repeating cascading event. Uropathogenic E. coli (UPEC) equipped with Dr fimbriae are associated with recurrent and chronic urinary tract infections (UTIs). The fimbriae assembled by the chaperone-usher pathway provide strong host-specific adherence which is, however, strongly modulated by the dynamically changing urine flow in the urinary tract (UT). In this paper, we use a dynamic in vitro micro-model of UTI to analyze the UT segment-specific impact of urinary outflow on the persistence and spread of Dr+ E. coli during host colonization. We conclude that the adhesive envelope formed by Dr fimbriae promotes strong and irreversible multivalent adherence of Dr+ E. coli to host receptors under flow conditions. We also observed that budding host cells–a model of any form of epithelial roughness, including carcinogenesis or physical injuries–facilitate the adherence of bacteria at flow conditions typically found in the UT, and our numerical simulations provided a mechanistic explanation for this effect. Finally, we combined the results to propose a rolling-shedding-refilling colonization model that shows how the wash off of detached colonized host cells may provoke a massive spread of UPEC. Our findings shed new light on UTI development and may be instrumental in the development of novel therapeutics.
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Affiliation(s)
- Beata Zalewska-Piątek
- Department of Molecular Microbiology and Biotechnology, Gdańsk University of Technology, Gdańsk, Poland
| | - Marcin Olszewski
- Department of Molecular Microbiology and Biotechnology, Gdańsk University of Technology, Gdańsk, Poland
| | - Tomasz Lipniacki
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Sławomir Błoński
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Miłosz Wieczór
- Department of Physical Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Piotr Bruździak
- Department of Physical Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Anna Skwarska
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Bogdan Nowicki
- Nowicki Institute for Woman’s Health Research, Brentwood, Tennessee, United States of America
| | - Stella Nowicki
- Nowicki Institute for Woman’s Health Research, Brentwood, Tennessee, United States of America
| | - Rafał Piątek
- Department of Molecular Microbiology and Biotechnology, Gdańsk University of Technology, Gdańsk, Poland
- * E-mail:
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Zalewska-Piątek B, Piątek R, Krawczyk B, Olszewski M. Pathomechanism of urinary tract infections caused by uropathogenic E. coli strains. POSTEP HIG MED DOSW 2019. [DOI: 10.5604/01.3001.0013.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Urinary tract infections (UTIs) are one of the most often and most common bacterial infections affecting even 150 millions of people each year worldwide. The problem of these infections results from chronicity, recurrences and increasing drug resistance of uropathogens causing them. Uropathogenic E. coli strains (UPEC) are the dominant causative agent of UTIs. These strains have many adhesion factors located on the surface of their cells responsible for the initial stage of adherence and colonization of the urinary tract. Among UPEC, the most common virulence factors are monoadhesive pili of type 1 and P and poliadhesins of Dr family, that biogensis is carried out via the conserved secretion pathway of chaperone-usher type (CUP). In addition to urovirulence factors, the UPEC strains developed a number of mechanisms important in pathogenesis of UTIs and enabling them to survive in the urinary tract environment (adhesion, invasion, formation of intracellular aggregates and quiescent bacterial reservoirs, strukturalfilamentation
of bacteria, resistance to antibiotics). Commonly used antibiotic therapy seems to be very effective in the control and treatment of UTIs. However, the increasing multidrug resistance of bacterial strains and the high frequency of recurrences and chronicity of the infections are the basis for the development of alternative therapeutic forms and prevention strategies.
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Affiliation(s)
- Beata Zalewska-Piątek
- Katedra Biotechnologii Molekularnej i Mikrobiologii, Wydział Chemiczny, Politechnika Gdańska, Gdańsk
| | - Rafał Piątek
- Katedra Biotechnologii Molekularnej i Mikrobiologii, Wydział Chemiczny, Politechnika Gdańska, Gdańsk
| | - Beata Krawczyk
- Katedra Biotechnologii Molekularnej i Mikrobiologii, Wydział Chemiczny, Politechnika Gdańska, Gdańsk
| | - Marcin Olszewski
- Katedra Biotechnologii Molekularnej i Mikrobiologii, Wydział Chemiczny, Politechnika Gdańska, Gdańsk
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Wawer J, Szociński M, Olszewski M, Piątek R, Naczk M, Krakowiak J. Influence of the ionic strength on the amyloid fibrillogenesis of hen egg white lysozyme. Int J Biol Macromol 2018; 121:63-70. [PMID: 30290259 DOI: 10.1016/j.ijbiomac.2018.09.165] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/17/2018] [Accepted: 09/25/2018] [Indexed: 10/28/2022]
Abstract
The study investigates the role of the electrostatic interactions in the fibrillation of the hen egg white lysozyme (HEWL). In order to achieve this aim the influence of the cations Na+, Mg2+ and Al3+ on the amyloid fibril formation and amorphous aggregation was tested. The amyloids are formed in the solution without added salt but the Thioflavin T fluorescence gives the false-negative result. In these conditions, the HEWL fibrils are long and curvy. If the ionic strength of the solution is sufficiently high, the formed amyloids are shorter and fragmented. Our study shows that the addition of the aluminium salt promotes protein fibrillation. The amorphous aggregation dominates in the high concentration of electrolyte. The in vitro amyloid fibril formation seems to be regulated by universal mechanisms. The theories implemented in the polymer science or for colloidal solutions give the qualitative description of the aggregation phenomena. However, the specific interactions and the additional effects (e.g. fibril fragmentation) modulate the amyloidogenesis.
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Affiliation(s)
- Jarosław Wawer
- Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza Str. 11/12, Gdańsk 80-233, Poland.
| | - Michał Szociński
- Department of Electrochemistry, Corrosion and Materials Engineering, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza Str. 11/12, Gdańsk 80-233, Poland
| | - Marcin Olszewski
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza Str. 11/12, Gdańsk 80-233, Poland
| | - Rafał Piątek
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza Str. 11/12, Gdańsk 80-233, Poland
| | - Mateusz Naczk
- Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza Str. 11/12, Gdańsk 80-233, Poland
| | - Joanna Krakowiak
- Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza Str. 11/12, Gdańsk 80-233, Poland
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Pilipczuk J, Zalewska-Piątek B, Bruździak P, Czub J, Wieczór M, Olszewski M, Wanarska M, Nowicki B, Augustin-Nowacka D, Piątek R. Role of the disulfide bond in stabilizing and folding of the fimbrial protein DraE from uropathogenic Escherichia coli. J Biol Chem 2017; 292:16136-16149. [PMID: 28739804 PMCID: PMC5625045 DOI: 10.1074/jbc.m117.785477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 07/21/2017] [Indexed: 11/22/2022] Open
Abstract
Dr fimbriae are homopolymeric adhesive organelles of uropathogenic Escherichia coli composed of DraE subunits, responsible for the attachment to host cells. These structures are characterized by enormously high stability resulting from the structural properties of an Ig-like fold of DraE. One feature of DraE and other fimbrial subunits that makes them peculiar among Ig-like domain-containing proteins is a conserved disulfide bond that joins their A and B strands. Here, we investigated how this disulfide bond affects the stability and folding/unfolding pathway of DraE. We found that the disulfide bond stabilizes self-complemented DraE (DraE-sc) by ∼50 kJ mol−1 in an exclusively thermodynamic manner, i.e. by lowering the free energy of the native state and with almost no effect on the free energy of the transition state. This finding was confirmed by experimentally determined folding and unfolding rate constants of DraE-sc and a disulfide bond-lacking DraE-sc variant. Although the folding of both proteins exhibited similar kinetics, the unfolding rate constant changed upon deletion of the disulfide bond by 10 orders of magnitude, from ∼10−17 s−1 to 10−7 s−1. Molecular simulations revealed that unfolding of the disulfide bond-lacking variant is initiated by strands A or G and that disulfide bond-mediated joining of strand A to the core strand B cooperatively stabilizes the whole protein. We also show that the disulfide bond in DraE is recognized by the DraB chaperone, indicating a mechanism that precludes the incorporation of less stable, non-oxidized DraE forms into the fimbriae.
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Affiliation(s)
- Justyna Pilipczuk
- From the Departments of Molecular Biotechnology and Microbiology and
| | | | - Piotr Bruździak
- Physical Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland
| | - Jacek Czub
- Physical Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland
| | - Miłosz Wieczór
- Physical Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland
| | - Marcin Olszewski
- From the Departments of Molecular Biotechnology and Microbiology and
| | - Marta Wanarska
- From the Departments of Molecular Biotechnology and Microbiology and
| | - Bogdan Nowicki
- the Nowicki Institute for Women's Health Research, Brentwood, Tennessee 37027, and
| | | | - Rafał Piątek
- From the Departments of Molecular Biotechnology and Microbiology and
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Olszewski M, Balsewicz J, Nowak M, Maciejewska N, Cyranka-Czaja A, Zalewska-Piątek B, Piątek R, Kur J. Characterization of a Single-Stranded DNA-Binding-Like Protein from Nanoarchaeum equitans--A Nucleic Acid Binding Protein with Broad Substrate Specificity. PLoS One 2015; 10:e0126563. [PMID: 25973760 PMCID: PMC4431734 DOI: 10.1371/journal.pone.0126563] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 04/03/2015] [Indexed: 11/18/2022] Open
Abstract
Background SSB (single-stranded DNA-binding) proteins play an essential role in all living cells and viruses, as they are involved in processes connected with ssDNA metabolism. There has recently been an increasing interest in SSBs, since they can be applied in molecular biology techniques and analytical methods. Nanoarchaeum equitans, the only known representative of Archaea phylum Nanoarchaeota, is a hyperthermophilic, nanosized, obligatory parasite/symbiont of Ignicoccus hospitalis. Results This paper reports on the ssb-like gene cloning, gene expression and characterization of a novel nucleic acid binding protein from Nanoarchaeum equitans archaeon (NeqSSB-like protein). This protein consists of 243 amino acid residues and one OB fold per monomer. It is biologically active as a monomer like as SSBs from some viruses. The NeqSSB-like protein displays a low sequence similarity to the Escherichia coli SSB, namely 10% identity and 29% similarity, and is the most similar to the Sulfolobus solfataricus SSB (14% identity and 32% similarity). The NeqSSB-like protein binds to ssDNA, although it can also bind mRNA and, surprisingly, various dsDNA forms, with no structure-dependent preferences as evidenced by gel mobility shift assays. The size of the ssDNA binding site, which was estimated using fluorescence spectroscopy, is 7±1 nt. No salt-dependent binding mode transition was observed. NeqSSB-like protein probably utilizes a different model for ssDNA binding than the SSB proteins studied so far. This protein is highly thermostable; the half-life of the ssDNA binding activity is 5 min at 100°C and melting temperature (Tm) is 100.2°C as shown by differential scanning calorimetry (DSC) analysis. Conclusion NeqSSB-like protein is a novel highly thermostable protein which possesses a unique broad substrate specificity and is able to bind all types of nucleic acids.
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Affiliation(s)
- Marcin Olszewski
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
- * E-mail:
| | - Jan Balsewicz
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
| | - Marta Nowak
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
| | - Natalia Maciejewska
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
| | - Anna Cyranka-Czaja
- University of Wroclaw, Faculty of Biotechnology, Department of Protein Engineering, 50–138, Wrocław, Poland
| | - Beata Zalewska-Piątek
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
| | - Rafał Piątek
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
| | - Józef Kur
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
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11
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Abstract
Display of heterologous proteins on the surface of micro-organisms has become an increasingly used strategy for a range of applications in microbiology, biotechnology and vaccinology. In this study, the potential of the major structural protein DraE of Escherichia coli Dr fimbriae as a display system for heterologous sequences was tested. One copy of a heterologous sequence mimicking a small P(k) epitope of simian virus 5 was inserted into the draE gene, replacing the N-terminal region of the surface-exposed domain 2 as previously done with the glycoprotein D of herpes simplex virus type 1. The exposure of chimeric proteins on the bacterial surface was detected by immunofluorescence microscopy. Insertion of the heterogenic peptides had no detectable effect on the Ig-barrel structure of the DraE fimbrial subunits, as confirmed by FTIR spectroscopy. Additionally, the affinity of the chimeric fimbriae for DAF and type IV collagen was similar to that of the wild-type Dr fimbriae.
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MESH Headings
- Adhesins, Bacterial/chemistry
- Adhesins, Bacterial/genetics
- Adhesins, Bacterial/metabolism
- Adhesins, Escherichia coli/chemistry
- Adhesins, Escherichia coli/genetics
- Adhesins, Escherichia coli/metabolism
- Collagen/metabolism
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Models, Molecular
- Parainfluenza Virus 5/genetics
- Protein Structure, Tertiary
- Receptors, Immunologic/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Spectroscopy, Fourier Transform Infrared
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Affiliation(s)
- Beata Zalewska
- Department of Microbiology, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Janusz Stangret
- Department of Physical Chemistry, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Katarzyna Bury
- Department of Microbiology, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Marek Wojciechowski
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Józef Kur
- Department of Microbiology, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Rafał Piątek
- Department of Microbiology, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-952 Gdańsk, Poland
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12
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Zalewska B, Piątek R, Bury K, Samet A, Nowicki B, Nowicki S, Kur J. A surface-exposed DraD protein of uropathogenic Escherichia coli bearing Dr fimbriae may be expressed and secreted independently from DraC usher and DraE adhesin. Microbiology (Reading) 2005; 151:2477-2486. [PMID: 16000738 DOI: 10.1099/mic.0.28083-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The dra gene cluster, expressed by uropathogenic Escherichia coli strains, determines bacterial attachment and invasion. The Dr fimbrial structures formed at the bacterial cell surface are composed of DraE subunits. The Dr fimbriae-coding cluster contains six open reading frames – draA, draB, draC, draD, draP and draE – among which the draE gene encodes the structural fimbrial subunit DraE. Very little is known about E. coli surface expression of the draD gene product. The expression of DraD and its role in the biogenesis of Dr fimbriae were determined by constructing mutants in the dra operon and by immunoblot and immunofluorescence experiments. In this study, DraD was found to be a surface-exposed protein. The expression of DraD was independent of the DraC usher and DraE fimbrial subunits. Polymerization of DraE fimbrial subunits into fimbrial structures did not require expression of the DraD protein.
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Affiliation(s)
- Beata Zalewska
- Department of Microbiology, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Rafał Piątek
- Department of Microbiology, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Katarzyna Bury
- Department of Microbiology, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Alfred Samet
- Department of Clinical Microbiology, Public Hospital No. 1, Gdańsk, Poland
| | - Bogdan Nowicki
- Department of Obstetrics and Gynecology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Stella Nowicki
- Department of Obstetrics and Gynecology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Józef Kur
- Department of Microbiology, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-952 Gdańsk, Poland
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13
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Dąbrowski S, Olszewski M, Piątek R, Brillowska-Dąbrowska A, Konopa G, Kur J. Identification and characterization of single-stranded-DNA-binding proteins from Thermus thermophilus and Thermus aquaticus - new arrangement of binding domains. Microbiology (Reading) 2002; 148:3307-3315. [PMID: 12368464 DOI: 10.1099/00221287-148-10-3307] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Single-stranded-DNA-binding proteins (SSBs) play essential roles in DNA replication, recombination and repair in bacteria, archaea and eukarya. This paper reports the identification and characterization of the SSB-like proteins of the thermophilic bacteria Thermus thermophilus and Thermus aquaticus. These proteins (TthSSB and TaqSSB), in contrast to their known counterparts from mesophilic bacteria, archaea and eukarya, are homodimers, and each monomer contains two ssDNA-binding domains with a conserved OB (oligonucleotide/oligosaccharide-binding) fold, as deduced from the sequence analysis. The N-terminal domain is located in the region from amino acid 1 to 123 and the C-terminal domain is located between amino acids 124 and 264 or 266 in TthSSB and TaqSSB, respectively. Purified TthSSB or TaqSSB binds only to ssDNA and with high affinity. The binding site size for TaqSSB and TthSSB protein corresponds to 30-35 nucleotides. It is concluded that the SSBs of thermophilic and mesophilic bacteria, archaea and eukarya share a common core ssDNA-binding domain. This ssDNA-binding domain was presumably present in the common ancestor to all three major branches of life.
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Affiliation(s)
- Sławomir Dąbrowski
- Technical University of Gdansk, Department of Microbiology, ul. G. Narutowicza 11/12, 80-952 Gdansk, Poland1
| | - Marcin Olszewski
- Technical University of Gdansk, Department of Microbiology, ul. G. Narutowicza 11/12, 80-952 Gdansk, Poland1
| | - Rafał Piątek
- Technical University of Gdansk, Department of Microbiology, ul. G. Narutowicza 11/12, 80-952 Gdansk, Poland1
| | - Anna Brillowska-Dąbrowska
- Technical University of Gdansk, Department of Microbiology, ul. G. Narutowicza 11/12, 80-952 Gdansk, Poland1
| | - Grażyna Konopa
- Department of Molecular Biology, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland2
| | - Jozef Kur
- Technical University of Gdansk, Department of Microbiology, ul. G. Narutowicza 11/12, 80-952 Gdansk, Poland1
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