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Concha-Eloko R, Stock M, De Baets B, Briers Y, Sanjuan R, Domingo-Calap P, Boeckaerts D. DepoScope: Accurate phage depolymerase annotation and domain delineation using large language models. PLoS Comput Biol 2024; 20:e1011831. [PMID: 39102416 DOI: 10.1371/journal.pcbi.1011831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 07/20/2024] [Indexed: 08/07/2024] Open
Abstract
Bacteriophages (phages) are viruses that infect bacteria. Many of them produce specific enzymes called depolymerases to break down external polysaccharide structures. Accurate annotation and domain identification of these depolymerases are challenging due to their inherent sequence diversity. Hence, we present DepoScope, a machine learning tool that combines a fine-tuned ESM-2 model with a convolutional neural network to identify depolymerase sequences and their enzymatic domains precisely. To accomplish this, we curated a dataset from the INPHARED phage genome database, created a polysaccharide-degrading domain database, and applied sequential filters to construct a high-quality dataset, which is subsequently used to train DepoScope. Our work is the first approach that combines sequence-level predictions with amino-acid-level predictions for accurate depolymerase detection and functional domain identification. In that way, we believe that DepoScope can greatly enhance our understanding of phage-host interactions at the level of depolymerases.
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Affiliation(s)
- Robby Concha-Eloko
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, Spain
| | - Michiel Stock
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Bernard De Baets
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Rafael Sanjuan
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, Spain
| | - Pilar Domingo-Calap
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, Spain
| | - Dimitri Boeckaerts
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
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2
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Klejch T, Buffa R, Šimek M, Nešporová K, Exnerová A, Bednařík J, Brandejsová M, Vágnerová H, Fiala F, Velebný V. Enzymatically stable unsaturated hyaluronan-derived oligosaccharides with selective cytostatic properties. Carbohydr Polym 2024; 336:122129. [PMID: 38670770 DOI: 10.1016/j.carbpol.2024.122129] [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: 02/23/2024] [Revised: 03/19/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
Hyaluronan, a linear glycosaminoglycan comprising D-N-acetylglucosamine and D-glucuronic acid, is the main component of the extracellular matrix. Its influence on cell proliferation, migration, inflammation, signalling, and other functions, depends heavily on its molecular weight and chemical modification. Unsaturated HA oligosaccharides are available in defined length and purity. Their potential therapeutic utility can be further improved by chemical modification, e. g., reduction. No synthesis of such modified oligosaccharides, either stepwise or by hyaluronan cleavage, has been reported yet. Here we show a three-step synthesis (esterification, depolymerization and reduction) of unsaturated even numbered hyaluronan oligosaccharides with carboxylates and the reducing terminus reduced to an alcohol. Particular oligosaccharides were synthesised. The modified oligosaccharides are not cleaved by mammalian or bacterial hyaluronidase and do not affect the growth of mouse and human fibroblasts. Further, MTT and NRU viability tests showed that they inhibit the growth of human colon carcinoma cells HT-29 by 20-50 % in concentrations 500-1000 μg/mL. Interestingly, this effect takes place regardless of CD44 receptor expression and was not observed with unmodified HA oligosaccharides. These compounds could serve as enzymatically stable building blocks for biologically active substances.
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Affiliation(s)
- Tomáš Klejch
- Contipro a. s., Dolní Dobrouč 401, 56102, Czech Republic.
| | - Radovan Buffa
- Contipro a. s., Dolní Dobrouč 401, 56102, Czech Republic
| | - Matěj Šimek
- Contipro a. s., Dolní Dobrouč 401, 56102, Czech Republic
| | | | | | - Jiří Bednařík
- Contipro a. s., Dolní Dobrouč 401, 56102, Czech Republic
| | | | - Hana Vágnerová
- Contipro a. s., Dolní Dobrouč 401, 56102, Czech Republic
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3
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Guo Z, Liu M, Zhang D. Potential of phage depolymerase for the treatment of bacterial biofilms. Virulence 2023; 14:2273567. [PMID: 37872768 PMCID: PMC10621286 DOI: 10.1080/21505594.2023.2273567] [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: 03/07/2023] [Accepted: 08/30/2023] [Indexed: 10/25/2023] Open
Abstract
Resistance of bacteria to antibiotics is a major concern in medicine and veterinary science. The bacterial biofilm structures not only prevent the penetration of drugs into cells within the biofilm's interior but also aid in evasion of the host immune system. Hence, there is an urgent need to develop novel therapeutic approaches against bacterial biofilms. One potential strategy to counter biofilms is to use phage depolymerases that degrade the matrix structure of the bacteria and enable access to bacterial cells. This review mainly discusses the methods by which phage depolymerases enhance the efficacy of the human immune system and the therapeutic applications of some phage depolymerases, such as single phage depolymerase application, combined therapy with phage depolymerase and antibiotics, and phage depolymerase cocktails, for treating bacterial biofilms. This review also summarizes the relationship between bacterial biofilms and antibiotic resistance.
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Affiliation(s)
- Zhimin Guo
- Department of Laboratory Medicine, Infectious Diseases and Pathogen Biology Center, The First Hospital of Jilin University, Changchun, China
| | - Mengmeng Liu
- Department of Laboratory Medicine, The First Hospital of Jilin University, Changchun, China
| | - Dan Zhang
- Department of Hepatological Surgery, The First Hospital of Jilin University, Changchun, China
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4
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Zhang Y, Lv F, Su Y, Zhang H, Zhang B. Complete genome sequencing and comparative genomic analysis of three donkey Streptococcus equi subsp. equi isolates. Front Microbiol 2023; 14:1285027. [PMID: 38029076 PMCID: PMC10646407 DOI: 10.3389/fmicb.2023.1285027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Streptococcus equi subspecies equi (S. equi) is the causative agent of strangles, which is one of the most common and highly contagious respiratory infectious illnesses in horses. Streptococcus equi (S. equi) is a horse-specific pathogen that originated from the closely related zoonotic pathogen Streptococcus equi subspecies zooepidemicus (S. zooepidemicus). Despite decades of research, the movement of genetic material across host-restricted diseases remains a mystery. Methods Three S. equi donkey isolates (HTP133, HTP232, and HT1112) were recently isolated from a strangles epidemic on donkey farms in China's Xinjiang Province. In this study, we performed a comprehensive comparative analysis of these isolates using whole genome sequencing and compared them to the published genomic sequences of equine strain S. equi 4047 to uncover evidence of genetic events that shaped the evolution of these donkey S. equi isolates' genomes. Results Whole genome sequencing indicated that both strains were closely related, with comparable gene compositions and a high rate of shared core genomes (1788-2004). Our comparative genomic study indicated that the genome structure is substantially conserved across three donkey strains; however, there are several rearrangements and inversions when compared to the horse isolate S. equi 4047. The virulence factors conveyed by genomic islands and prophages, in particular, played a key role in shaping the pathogenic capacity and genetic diversity of these S. equi strains. Furthermore, we discovered that the HT133 isolate had a strong colonization ability and increased motility; the HT1112 isolates had a significantly higher ability for antimicrobial resistance and biofilm formation, and the HT232 isolate gained pathogenic specialization by acquiring a bacteriophage encoding hyaluronate lyase. Discussion In summary, our findings show that genetic exchange across S. equi strains influences the development of the donkey S. equi genome, offering important genetic insights for future epidemiological studies of S. equi infection.
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Affiliation(s)
| | | | - Yan Su
- Department of Microbiology and Immunology, College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, Xinjiang, China
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Karczewska M, Strzelecki P, Szalewska-Pałasz A, Nowicki D. How to Tackle Bacteriophages: The Review of Approaches with Mechanistic Insight. Int J Mol Sci 2023; 24:ijms24054447. [PMID: 36901878 PMCID: PMC10003480 DOI: 10.3390/ijms24054447] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
Bacteriophage-based applications have a renaissance today, increasingly marking their use in industry, medicine, food processing, biotechnology, and more. However, phages are considered resistant to various harsh environmental conditions; besides, they are characterized by high intra-group variability. Phage-related contaminations may therefore pose new challenges in the future due to the wider use of phages in industry and health care. Therefore, in this review, we summarize the current knowledge of bacteriophage disinfection methods, as well as highlight new technologies and approaches. We discuss the need for systematic solutions to improve bacteriophage control, taking into account their structural and environmental diversity.
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Affiliation(s)
- Monika Karczewska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Patryk Strzelecki
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
- Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg, CNRS, UMR7504, 23 rue du Loess, CEDEX 2, F-67034 Strasbourg, France
| | - Agnieszka Szalewska-Pałasz
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Dariusz Nowicki
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
- Correspondence: ; Tel.: +48-58-523-6065
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Evseev P, Lukianova A, Tarakanov R, Tokmakova A, Popova A, Kulikov E, Shneider M, Ignatov A, Miroshnikov K. Prophage-Derived Regions in Curtobacterium Genomes: Good Things, Small Packages. Int J Mol Sci 2023; 24:ijms24021586. [PMID: 36675099 PMCID: PMC9862828 DOI: 10.3390/ijms24021586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Curtobacterium is a genus of Gram-positive bacteria within the order Actinomycetales. Some Curtobacterium species (C. flaccumfaciens, C. plantarum) are harmful pathogens of agricultural crops such as soybean, dry beans, peas, sugar beet and beetroot, which occur throughout the world. Bacteriophages (bacterial viruses) are considered to be potential curative agents to control the spread of harmful bacteria. Temperate bacteriophages integrate their genomes into bacterial chromosomes (prophages), sometimes substantially influencing bacterial lifestyle and pathogenicity. About 200 publicly available genomes of Curtobacterium species, including environmental metagenomic sequences, were inspected for the presence of sequences of possible prophage origin using bioinformatic methods. The comparison of the search results with several ubiquitous bacterial groups showed the relatively low level of the presence of prophage traces in Curtobacterium genomes. Genomic and phylogenetic analyses were undertaken for the evaluation of the evolutionary and taxonomic positioning of predicted prophages. The analyses indicated the relatedness of Curtobacterium prophage-derived sequences with temperate actinophages of siphoviral morphology. In most cases, the predicted prophages can represent novel phage taxa not described previously. One of the predicted temperate phages was induced from the Curtobacterium genome. Bioinformatic analysis of the modelled proteins encoded in prophage-derived regions led to the discovery of some 100 putative glycopolymer-degrading enzymes that contained enzymatic domains with predicted cell-wall- and cell-envelope-degrading activity; these included glycosidases and peptidases. These proteins can be considered for the experimental design of new antibacterials against Curtobacterium phytopathogens.
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Affiliation(s)
- Peter Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
- Correspondence: (P.E.); (K.M.)
| | - Anna Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
| | - Rashit Tarakanov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia
| | - Anna Tokmakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology National Research University, Institutskiy Per, 9, 141701 Dolgoprudny, Russia
| | - Anastasia Popova
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - Eugene Kulikov
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology National Research University, Institutskiy Per, 9, 141701 Dolgoprudny, Russia
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prosp. 60-letia Oktyabrya, 7-2, 117312 Moscow, Russia
| | - Mikhail Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
| | - Alexander Ignatov
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str. 6, 117198 Moscow, Russia
| | - Konstantin Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
- Correspondence: (P.E.); (K.M.)
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Zhang YS, Gong JS, Yao ZY, Jiang JY, Su C, Li H, Kang CL, Liu L, Xu ZH, Shi JS. Insights into the source, mechanism and biotechnological applications of hyaluronidases. Biotechnol Adv 2022; 60:108018. [PMID: 35853550 DOI: 10.1016/j.biotechadv.2022.108018] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 01/10/2023]
Abstract
It has long been found that hyaluronidases exist in a variety of organisms, playing their roles in various biological processes including infection, envenomation and metabolic regulation through degrading hyaluronan. However, exploiting them as a bioresource for specific applications had not been extensively studied until the latest decades. In recent years, new application scenarios have been developed, which extended the field of application, and emphasized the research value of hyaluronidase. This critical review comprehensively summarizes existing studies on hyaluronidase from different source, particularly in their structures, action patterns, and biological functions in human and mammals. Furthermore, we give in-depth insight into the resource mining and protein engineering process of hyaluronidase, as well as strategies for their high-level production, indicating that mixed strategies should be adopted to obtain well-performing hyaluronidase with efficiency. In addition, advances in application of hyaluronidase were summarized and discussed. Finally, prospects for future researches are proposed, highlighting the importance of further investigation into the characteristics of hyaluronidases, and the necessity of investigating their products for the development of their application value.
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Affiliation(s)
- Yue-Sheng Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, PR China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - Jin-Song Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, PR China.
| | - Zhi-Yuan Yao
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, PR China
| | - Jia-Yu Jiang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, PR China
| | - Chang Su
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, PR China
| | - Heng Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, PR China
| | - Chuan-Li Kang
- Shandong Engineering Laboratory of Sodium Hyaluronate and its Derivatives, Shandong Focusfreda Biotech Co., Ltd, Qufu 273165, PR China
| | - Lei Liu
- Shandong Engineering Laboratory of Sodium Hyaluronate and its Derivatives, Shandong Focusfreda Biotech Co., Ltd, Qufu 273165, PR China
| | - Zheng-Hong Xu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, PR China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, PR China
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Biochemical and Molecular Characteristics of a Novel Hyaluronic Acid Lyase from Citrobacter freundii. Foods 2022; 11:foods11131989. [PMID: 35804804 PMCID: PMC9265501 DOI: 10.3390/foods11131989] [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: 05/06/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022] Open
Abstract
The Gram-negative strain of Citrobacter freundii, YNLX, has the ability to degrade hyaluronic acid. In this study, we expressed a C. freundii hyaluronic acid lyase, from polysaccharide lyase family 8, in Escherichia coli. The purified recombinant enzyme (rHynACF8) showed a substantially higher cleavage activity of hyaluronic acid than chondroitin sulfate. We found that its optimal pH and temperature are 5.5 and 35 °C, respectively. In addition, the enzyme activity was not notably affected by most metal ions. Km and kcat of rHynACF8 towards HA were 1.5 ± 0.01 mg/mL and 30.9 ± 0.5 /s, respectively. rHynACF8 is an endo-acting enzyme. Its cleavage products had dramatically increased antioxidant activity than hyaluronic acid in vitro (p < 0.001). As the molecular weight of hyaluronic acid decreased, the intramolecular interactions among antioxidant functional groups were removed; in the process of the cracking reaction, new double bonds formed and conjugated with the carbonyl group. We presumed that the structural change is the critical factor influencing antioxidant capacity. Overall, we found that rHynACF8 from Gram-negative bacteria with metal ion resistance, indicated the relationship between the function and structure of its antioxidant cleavage product.
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Sindelar M, Jilkova J, Kubala L, Velebny V, Turkova K. Hyaluronidases and hyaluronate lyases: From humans to bacteriophages. Colloids Surf B Biointerfaces 2021; 208:112095. [PMID: 34507069 DOI: 10.1016/j.colsurfb.2021.112095] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 08/05/2021] [Accepted: 09/01/2021] [Indexed: 12/26/2022]
Abstract
Hyaluronan is a non-sulfated negatively-charged linear polymer distributed in most parts of the human body, where it is located around cells in the extracellular matrix of connective tissues and plays an essential role in the organization of tissue architecture. Moreover, hyaluronan is involved in many biological processes and used in many clinical, cosmetic, pharmaceutic, and biotechnological applications worldwide. As interest in hyaluronan applications increases, so does interest in hyaluronidases and hyaluronate lyases, as these enzymes play a major part in hyaluronan degradation. Many hyaluronidases and hyaluronate lyases produced by eukaryotic cells, bacteria, and bacteriophages have so far been described and annotated, and their ability to cleave hyaluronan has been experimentally proven. These enzymes belong to several carbohydrate-active enzyme families, share very low sequence identity, and differ in their cleaving mechanisms and in their structural and functional properties. This review presents a summary of annotated and characterized hyaluronidases and hyaluronate lyases isolated from different sources belonging to distinct protein families, with a main focus on the binding and catalytic residues of the discussed enzymes in the context of their biochemical properties. In addition, the application potential of individual groups of hyaluronidases and hyaluronate lyases is evaluated.
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Affiliation(s)
- Martin Sindelar
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic; Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Jana Jilkova
- Contipro a.s., Dolní Dobrouč 401, 56102, Dolní Dobrouč, Czech Republic; Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Lukas Kubala
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic; Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 65691, Brno, Czech Republic
| | - Vladimir Velebny
- Contipro a.s., Dolní Dobrouč 401, 56102, Dolní Dobrouč, Czech Republic
| | - Kristyna Turkova
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 65691, Brno, Czech Republic.
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Di Lallo G, Falconi M, Iacovelli F, Frezza D, D'Addabbo P. Analysis of Four New Enterococcus faecalis Phages and Modeling of a Hyaluronidase Catalytic Domain from Saphexavirus. PHAGE (NEW ROCHELLE, N.Y.) 2021; 2:131-141. [PMID: 36161247 PMCID: PMC9041502 DOI: 10.1089/phage.2021.0003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Background: Phage therapy (PT), as a method to treat bacterial infections, needs identification of bacteriophages targeting specific pathogenic host. Enterococcus faecalis, a Gram-positive coccus resident in the human gastrointestinal tract, may become pathogenic in hospitalized patients showing acquired resistance to vancomycin and thus representing a possible target for PT. Materials and Methods: We isolated four phages that infect E. faecalis and characterized them by host range screening, transmission electron microscopy, and genome sequencing. We also identified and three-dimensional modeled a new hyaluronidase enzyme. Results: The four phages belong to Siphoviridae family: three Efquatrovirus (namely vB_EfaS_TV51, vB_EfaS_TV54, and vB_EfaS_TV217) and one Saphexavirus (vB_EfaS_TV16). All of them are compatible with lytic cycle. vB_EfaS_TV16 moreover presents a gene encoding for a hyaluronidase enzyme. Conclusions: The identified phages show features suggesting their useful application in PT, particularly the Saphexavirus that may be of enhanced relevance in PT because of its potential biofilm-digestion capability.
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Affiliation(s)
- Gustavo Di Lallo
- Laboratory of Microbiology, Department of Biology, University of Roma Tor Vergata, Roma, Italy
| | - Mattia Falconi
- Structural Bioinformatics Group, Department of Biology, University of Roma Tor Vergata, Roma, Italy
| | - Federico Iacovelli
- Structural Bioinformatics Group, Department of Biology, University of Roma Tor Vergata, Roma, Italy
| | - Domenico Frezza
- Laboratory of Microbiology, Department of Biology, University of Roma Tor Vergata, Roma, Italy
| | - Pietro D'Addabbo
- Computational Biology Unit, Department of Biology, University of Bari, Bari, Italy
- Address correspondence to: Pietro D'Addabbo, PhD, Computational Biology Unit, Department of Biology, University of Bari, Via E. Orabona 4, Bari 70125, Italy
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11
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Azeredo J, García P, Drulis-Kawa Z. Targeting biofilms using phages and their enzymes. Curr Opin Biotechnol 2021; 68:251-261. [PMID: 33714050 DOI: 10.1016/j.copbio.2021.02.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 02/08/2023]
Abstract
The complex biofilm architecture composed of extracellular polymeric structures (EPS) provides a protective shield to physiologically diverse bacterial cells immersed in its structure. The evolutionary interplay between bacteria and their viruses (phages) forced the latter ones to develop specific strategies to overcome the biofilm defensive barriers and kill sessile cells. Phages are equipped with a wide panel of enzyme-degrading EPS macromolecules which together are powerful weapons to combat biofilms. Antibiofilm performance can be achieved by combining phages or phage-borne enzymes with other antimicrobials such as antibiotics. Nevertheless, a variety of enzymes encoded in phage genomes still need to be explored. To advance in biofilm control strategies we must deepen the understanding of the biofilm biology itself, as well as discover and better exploit the unlimited antibacterial potential of phages.
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Affiliation(s)
- Joana Azeredo
- Centro de Engenharia Biológica, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Pilar García
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares sn. 33300, Villaviciosa, Asturias, Spain.
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
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Hirose Y, Yamaguchi M, Takemoto N, Miyoshi-Akiyama T, Sumitomo T, Nakata M, Ikebe T, Hanada T, Yamaguchi T, Kawahara R, Okuno R, Otsuka H, Matsumoto Y, Terashima Y, Kazawa Y, Nakanishi N, Uchida K, Akiyama Y, Iwabuchi K, Nakagawa C, Yamamoto K, Nizet V, Kawabata S. Genetic Characterization of Streptococcus pyogenes emm89 Strains Isolated in Japan From 2011 to 2019. INFECTIOUS MICROBES & DISEASES 2020; 2:160-166. [PMID: 38630060 PMCID: PMC7769053 DOI: 10.1097/im9.0000000000000038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 04/19/2024]
Abstract
Invasive infection caused by Streptococcus pyogenes emm89 strains has been increasing in several countries linked to a recently emergent clade of emm89 strains, designated clade 3. In Japan, the features of emm89 S. pyogenes strains, such as clade classification, remains unknown. In this study, we collected emm89 strains isolated from both streptococcal toxic shock syndrome (STSS) (89 STSS isolates) and noninvasive infections (72 non-STSS isolates) in Japan from 2011 to 2019, and conducted whole-genome sequencing and comparative analysis, which resulted in classification of a large majority into clade 3 regardless of disease severity. In addition, invasive disease-associated factors were found among emm89 strains, including mutations of control of virulence sensor, and absence of the hylP1 gene encoding hyaluronidase. These findings provide new insights into genetic features of emm89 strains.
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Affiliation(s)
- Yujiro Hirose
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
- Department of Pediatrics, University of California at San Diego School of Medicine, La Jolla, CA, USA
| | - Masaya Yamaguchi
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | - Norihiko Takemoto
- Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Tohru Miyoshi-Akiyama
- Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Tomoko Sumitomo
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | - Masanobu Nakata
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Tadayoshi Ikebe
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomoki Hanada
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | - Takahiro Yamaguchi
- Division of Microbiology, Osaka Institute of Public Health, Osaka City, Osaka, Japan
| | - Ryuji Kawahara
- Division of Microbiology, Osaka Institute of Public Health, Osaka City, Osaka, Japan
| | - Rumi Okuno
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Hitoshi Otsuka
- Department of Public Health Sciences, Yamaguchi Prefectural Institute of Public Health and Environment Yamaguchi City, Yamaguchi, Japan
| | - Yuko Matsumoto
- Microbiological Testing and Research Division, Yokohama City Institute of Public Health, Yokohama, Kanagawa, Japan
| | - Yuji Terashima
- Department of Microbiology, Fukushima Prefectural Institute of Public Health, Fukushima City, Fukushima, Japan
| | - Yu Kazawa
- Department of Microbiology, Fukushima Prefectural Institute of Public Health, Fukushima City, Fukushima, Japan
| | - Noriko Nakanishi
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan
| | - Kaoru Uchida
- Department of Bacteriology, Toyama Institute of Health, Imizu, Toyama, Japan
| | - Yumi Akiyama
- Infectious Disease Research Division, Hyogo Prefectural Institute of Public Health Science, Kakogawa, Hyogo, Japan
| | - Kaori Iwabuchi
- Department of Health Science, Iwate Prefectural Research Institute for Environmental Sciences and Public Health, Morioka, Iwate, Japan
| | - Chikara Nakagawa
- Division of Microbiology, Kyoto City Institute of Health and Environmental Sciences, Kyoto City, Kyoto, Japan
| | - Kazunari Yamamoto
- Niigata City Institute of Public Health and the Environment, Niigata City, Niigata, Japan
| | - Victor Nizet
- Department of Pediatrics, University of California at San Diego School of Medicine, La Jolla, CA, USA
- Skaggs School of Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA
| | - Shigetada Kawabata
- Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
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13
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Salvà-Serra F, Jaén-Luchoro D, Jakobsson HE, Gonzales-Siles L, Karlsson R, Busquets A, Gomila M, Bennasar-Figueras A, Russell JE, Fazal MA, Alexander S, Moore ERB. Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies. Sci Rep 2020; 10:11656. [PMID: 32669560 PMCID: PMC7363880 DOI: 10.1038/s41598-020-68249-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/16/2020] [Indexed: 01/23/2023] Open
Abstract
We present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus and an important human pathogen that causes a wide range of infectious diseases. S. pyogenes NCTC 8198T and CCUG 4207T are derived from deposit of the same strain at two different culture collections. NCTC 8198T was sequenced, using a PacBio platform; the genome sequence was assembled de novo, using HGAP. CCUG 4207T was sequenced and a de novo hybrid assembly was generated, using SPAdes, combining Illumina and Oxford Nanopore sequence reads. Both strategies yielded closed genome sequences of 1,914,862 bp, identical in length and sequence identity. Combining short-read Illumina and long-read Oxford Nanopore sequence data circumvented the expected error rate of the nanopore sequencing technology, producing a genome sequence indistinguishable to the one determined with PacBio. Sequence analyses revealed five prophage regions, a CRISPR-Cas system, numerous virulence factors and no relevant antibiotic resistance genes. These two complete genome sequences of the type strain of S. pyogenes will effectively serve as valuable taxonomic and genomic references for infectious disease diagnostics, as well as references for future studies and applications within the genus Streptococcus.
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Affiliation(s)
- Francisco Salvà-Serra
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden.
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden.
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, 413 46, Gothenburg, Sweden.
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 413 46, Gothenburg, Sweden.
- Microbiology, Department of Biology, University of the Balearic Islands, 07122, Palma, Spain.
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 413 46, Gothenburg, Sweden
| | - Hedvig E Jakobsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 413 46, Gothenburg, Sweden
| | - Lucia Gonzales-Siles
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 413 46, Gothenburg, Sweden
| | - Roger Karlsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 413 46, Gothenburg, Sweden
- Nanoxis Consulting AB, 400 16, Gothenburg, Sweden
| | - Antonio Busquets
- Microbiology, Department of Biology, University of the Balearic Islands, 07122, Palma, Spain
| | - Margarita Gomila
- Microbiology, Department of Biology, University of the Balearic Islands, 07122, Palma, Spain
| | | | - Julie E Russell
- National Collection of Type Cultures (NCTC), Public Health England, London, NW9 5EQ, UK
| | - Mohammed Abbas Fazal
- National Collection of Type Cultures (NCTC), Public Health England, London, NW9 5EQ, UK
| | - Sarah Alexander
- National Collection of Type Cultures (NCTC), Public Health England, London, NW9 5EQ, UK
| | - Edward R B Moore
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, 413 46, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 413 46, Gothenburg, Sweden
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14
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Abstract
SAR11 clade members are among the most abundant bacteria on Earth. Their study is complicated by their great diversity and difficulties in being grown and manipulated in the laboratory. On the other hand, and due to their extraordinary abundance, metagenomic data sets provide enormous richness of information about these microbes. Given the major role played by phages in the lifestyle and evolution of prokaryotic cells, the contribution of several new bacteriophage genomes preying on this clade opens windows into the infection strategies and life cycle of its viruses. Such strategies could provide models of attack of large-genome phages preying on streamlined aquatic microbes. The SAR11 clade is one of the most abundant bacterioplankton groups in surface waters of most of the oceans and lakes. However, only 15 SAR11 phages have been isolated thus far, and only one of them belongs to the Myoviridae family (pelagimyophages). Here, we have analyzed 26 sequences of myophages that putatively infect the SAR11 clade. They have been retrieved by mining ca. 45 Gbp aquatic assembled cellular metagenomes and viromes. Most of the myophages were obtained from the cellular fraction (0.2 μm), indicating a bias against this type of virus in viromes. We have found the first myophages that putatively infect Candidatus Fonsibacter (freshwater SAR11) and another group putatively infecting bathypelagic SAR11 phylogroup Ic. The genomes have similar sizes and maintain overall synteny in spite of low average nucleotide identity values, revealing high similarity to marine cyanomyophages. Pelagimyophages recruited metagenomic reads widely from several locations but always much more from cellular metagenomes than from viromes, opposite to what happens with pelagipodophages. Comparing the genomes resulted in the identification of a hypervariable island that is related to host recognition. Interestingly, some genes in these islands could be related to host cell wall synthesis and coinfection avoidance. A cluster of curli-related proteins was widespread among the genomes, although its function is unclear. IMPORTANCE SAR11 clade members are among the most abundant bacteria on Earth. Their study is complicated by their great diversity and difficulties in being grown and manipulated in the laboratory. On the other hand, and due to their extraordinary abundance, metagenomic data sets provide enormous richness of information about these microbes. Given the major role played by phages in the lifestyle and evolution of prokaryotic cells, the contribution of several new bacteriophage genomes preying on this clade opens windows into the infection strategies and life cycle of its viruses. Such strategies could provide models of attack of large-genome phages preying on streamlined aquatic microbes.
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15
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Abstract
The bacteriophages of Streptococcus pyogenes (group A streptococcus) play a key role in population shaping, genetic transfer, and virulence of this bacterial pathogen. Lytic phages like A25 can alter population distributions through elimination of susceptible serotypes but also serve as key mediators for genetic transfer of virulence genes and antibiotic resistance via generalized transduction. The sequencing of multiple S. pyogenes genomes has uncovered a large and diverse population of endogenous prophages that are vectors for toxins and other virulence factors and occupy multiple attachment sites in the bacterial genomes. Some of these sites for integration appear to have the potential to alter the bacterial phenotype through gene disruption. Remarkably, the phage-like chromosomal islands (SpyCI), which share many characteristics with endogenous prophages, have evolved to mediate a growth-dependent mutator phenotype while acting as global transcriptional regulators. The diverse population of prophages appears to share a large pool of genetic modules that promotes novel combinations that may help disseminate virulence factors to different subpopulations of S. pyogenes. The study of the bacteriophages of this pathogen, both lytic and lysogenic, will continue to be an important endeavor for our understanding of how S. pyogenes continues to be a significant cause of human disease.
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Affiliation(s)
- W Michael McShan
- Department of Pharmaceutical Sciences, College of Pharmacy, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73117
| | - Kimberly A McCullor
- Department of Pharmaceutical Sciences, College of Pharmacy, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73117
| | - Scott V Nguyen
- Department of Pharmaceutical Sciences, College of Pharmacy, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73117
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16
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Latka A, Maciejewska B, Majkowska-Skrobek G, Briers Y, Drulis-Kawa Z. Bacteriophage-encoded virion-associated enzymes to overcome the carbohydrate barriers during the infection process. Appl Microbiol Biotechnol 2017; 101:3103-3119. [PMID: 28337580 PMCID: PMC5380687 DOI: 10.1007/s00253-017-8224-6] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/23/2017] [Accepted: 03/04/2017] [Indexed: 11/24/2022]
Abstract
Bacteriophages are bacterial viruses that infect the host after successful receptor recognition and adsorption to the cell surface. The irreversible adherence followed by genome material ejection into host cell cytoplasm must be preceded by the passage of diverse carbohydrate barriers such as capsule polysaccharides (CPSs), O-polysaccharide chains of lipopolysaccharide (LPS) molecules, extracellular polysaccharides (EPSs) forming biofilm matrix, and peptidoglycan (PG) layers. For that purpose, bacteriophages are equipped with various virion-associated carbohydrate active enzymes, termed polysaccharide depolymerases and lysins, that recognize, bind, and degrade the polysaccharide compounds. We discuss the existing diversity in structural locations, variable architectures, enzymatic specificities, and evolutionary aspects of polysaccharide depolymerases and virion-associated lysins (VALs) and illustrate how these aspects can correlate with the host spectrum. In addition, we present methods that can be used for activity determination and the application potential of these enzymes as antibacterials, antivirulence agents, and diagnostic tools.
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Affiliation(s)
- Agnieszka Latka
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland.,Laboratory of Applied Biotechnology, Department of Applied Biosciences, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Barbara Maciejewska
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Grazyna Majkowska-Skrobek
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Applied Biosciences, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland.
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17
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Messina L, Gavira JA, Pernagallo S, Unciti-Broceta JD, Sanchez Martin RM, Diaz-Mochon JJ, Vaccaro S, Conejero-Muriel M, Pineda-Molina E, Caruso S, Musumeci L, Di Pasquale R, Pontillo A, Sincinelli F, Pavan M, Secchieri C. Identification and characterization of a bacterial hyaluronidase and its production in recombinant form. FEBS Lett 2016; 590:2180-9. [PMID: 27311405 DOI: 10.1002/1873-3468.12258] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/12/2016] [Accepted: 06/13/2016] [Indexed: 11/11/2022]
Abstract
Hyaluronidases (Hyals) are broadly used in medical applications to facilitate the dispersion and/or absorption of fluids or medications. This study reports the isolation, cloning, and industrial-scale recombinant production, purification and full characterization, including X-ray structure determination at 1.45 Å, of an extracellular Hyal from the nonpathogenic bacterium Streptomyces koganeiensis. The recombinant S. koganeiensis Hyal (rHyal_Sk) has a novel bacterial catalytic domain with high enzymatic activity, compared with commercially available Hyals, and is more thermostable and presents higher proteolytic resistance, with activity over a broad pH range. Moreover, rHyal_Sk exhibits remarkable substrate specificity for hyaluronic acid (HA) and poses no risk of animal cross-infection.
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Affiliation(s)
- Luciano Messina
- Local Unit Fidia Research Sud, Fidia Farmaceutici S.p.A., Noto, Italy
| | - Jose A Gavira
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones Científicas-Universidad de Granada), Armilla, Spain
| | - Salvatore Pernagallo
- GENYO - Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Spain
| | | | - Rosario M Sanchez Martin
- GENYO - Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Spain.,NanoGetic S.L., PTS Granada, Armilla, Spain.,Facultad de Farmacia, Universidad de Granada, Spain
| | - Juan J Diaz-Mochon
- GENYO - Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Spain.,Facultad de Farmacia, Universidad de Granada, Spain
| | - Susanna Vaccaro
- Local Unit Fidia Research Sud, Fidia Farmaceutici S.p.A., Noto, Italy
| | - Mayte Conejero-Muriel
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones Científicas-Universidad de Granada), Armilla, Spain
| | - Estela Pineda-Molina
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones Científicas-Universidad de Granada), Armilla, Spain
| | - Salvatore Caruso
- Local Unit Fidia Research Sud, Fidia Farmaceutici S.p.A., Noto, Italy
| | - Luca Musumeci
- Local Unit Fidia Research Sud, Fidia Farmaceutici S.p.A., Noto, Italy
| | | | | | | | - Mauro Pavan
- Fidia Farmaceutici S.p.A., Abano Terme, Italy
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18
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Drulis-Kawa Z, Majkowska-Skrobek G, Maciejewska B. Bacteriophages and phage-derived proteins--application approaches. Curr Med Chem 2016; 22:1757-73. [PMID: 25666799 PMCID: PMC4468916 DOI: 10.2174/0929867322666150209152851] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 11/29/2014] [Accepted: 02/02/2015] [Indexed: 12/17/2022]
Abstract
Currently, the bacterial resistance, especially to most commonly used antibiotics has proved to be a severe therapeutic problem. Nosocomial and community-acquired infections are usually caused by multidrug resistant strains. Therefore, we are forced to develop an alternative or supportive treatment for successful cure of life-threatening infections. The idea of using natural bacterial pathogens such as bacteriophages is already well known. Many papers have been published proving the high antibacterial efficacy of lytic phages tested in animal models as well as in the clinic. Researchers have also investigated the application of non-lytic phages and temperate phages, with promising results. Moreover, the development of molecular biology and novel generation methods of sequencing has opened up new possibilities in the design of engineered phages and recombinant phage-derived proteins. Encouraging performances were noted especially for phage enzymes involved in the first step of viral infection responsible for bacterial envelope degradation, named depolymerases. There are at least five major groups of such enzymes – peptidoglycan hydrolases, endosialidases, endorhamnosidases, alginate lyases and hyaluronate lyases – that have application potential. There is also much interest in proteins encoded by lysis cassette genes (holins, endolysins, spanins) responsible for progeny release during the phage lytic cycle. In this review, we discuss several issues of phage and phage-derived protein application approaches in therapy, diagnostics and biotechnology in general.
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Affiliation(s)
- Zuzanna Drulis-Kawa
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
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19
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Lai MJ, Chang KC, Huang SW, Luo CH, Chiou PY, Wu CC, Lin NT. The Tail Associated Protein of Acinetobacter baumannii Phage ΦAB6 Is the Host Specificity Determinant Possessing Exopolysaccharide Depolymerase Activity. PLoS One 2016; 11:e0153361. [PMID: 27077375 PMCID: PMC4831824 DOI: 10.1371/journal.pone.0153361] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 03/29/2016] [Indexed: 12/31/2022] Open
Abstract
Acinetobacter baumannii is a non-fermenting, gram-negative bacterium. In recent years, the frequency of A. baumannii infections has continued to increase, and multidrug-resistant strains are emerging in hospitalized patients. Therefore, as therapeutic options become limited, the potential of phages as natural antimicrobial agents to control infections is worth reconsidering. In our previous study, we isolated ten virulent double-stranded DNA A. baumannii phages, ϕAB1-9 and ϕAB11, and found that each has a narrow host range. Many reports indicate that receptor-binding protein of phage mediates host recognition; however, understanding of the specific interactions between A. baumannii and phages remains very limited. In this study, host determinants of A. baumannii phages were investigated. Sequence comparison of ϕAB6 and ϕAB1 revealed high degrees of conservation among their genes except the tail fiber protein (ORF41 in ϕAB1 and ORF40 in ϕAB6). Furthermore, we found that ORF40ϕAB6 has polysaccharide depolymerase activity capable of hydrolyzing the A. baumannii exopolysaccharide and is a component of the phage tail apparatus determining host specificity. Thus, the lytic phages and their associated depolymerase not only have potential as alternative therapeutic agents for treating A. baumannii infections but also provide useful and highly specific tools for studying host strain exopolysaccharides and producing glycoconjugate vaccines.
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Affiliation(s)
- Meng-Jiun Lai
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Kai-Chih Chang
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Shiuan-Wen Huang
- Master Program in Microbiology and Immunology, School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Cheng-Hung Luo
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan
| | - Pei-Yu Chiou
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan
| | - Chao-Chuan Wu
- Department of Surgery, Buddhist Tzu Chi General Hospital, Taipei, Taiwan
| | - Nien-Tsung Lin
- Master Program in Microbiology and Immunology, School of Medicine, Tzu Chi University, Hualien, Taiwan
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan
- * E-mail:
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20
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Simpson DJ, Sacher JC, Szymanski CM. Development of an Assay for the Identification of Receptor Binding Proteins from Bacteriophages. Viruses 2016; 8:v8010017. [PMID: 26761028 PMCID: PMC4728577 DOI: 10.3390/v8010017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/11/2015] [Accepted: 12/18/2015] [Indexed: 12/13/2022] Open
Abstract
Recently, a large number of new technologies have been developed that exploit the unique properties of bacteriophage receptor binding proteins (RBPs). These include their use in diagnostic applications that selectively capture bacteria and as therapeutics that reduce bacterial colonization in vivo. RBPs exhibit comparable, and in many cases superior, stability, receptor specificity, and affinity to other carbohydrate binding proteins such as antibodies or lectins. In order to further exploit the use of RBPs, we have developed an assay for discovering RBPs using phage genome expression libraries and protein screens to identify binding partners that recognize the host bacterium. When phage P22 was screened using this assay, Gp9 was the only RBP discovered, confirming previous predictions that this is the sole RBP encoded by this phage. We then examined the Escherichia coli O157:H7 typing phage 1 in our assay and identified a previously undescribed RBP. This general approach has the potential to assist in the identification of RBPs from other bacteriophages.
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Affiliation(s)
- David J Simpson
- Alberta Glycomics Centre and Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Jessica C Sacher
- Alberta Glycomics Centre and Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Christine M Szymanski
- Alberta Glycomics Centre and Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
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21
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Gutiérrez D, Briers Y, Rodríguez-Rubio L, Martínez B, Rodríguez A, Lavigne R, García P. Role of the Pre-neck Appendage Protein (Dpo7) from Phage vB_SepiS-phiIPLA7 as an Anti-biofilm Agent in Staphylococcal Species. Front Microbiol 2015; 6:1315. [PMID: 26635776 PMCID: PMC4658415 DOI: 10.3389/fmicb.2015.01315] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/09/2015] [Indexed: 01/10/2023] Open
Abstract
Staphylococcus epidermidis and Staphylococcus aureus are important causative agents of hospital-acquired infections and bacteremia, likely due to their ability to form biofilms. The production of a dense exopolysaccharide (EPS) matrix enclosing the cells slows the penetration of antibiotic down, resulting in therapy failure. The EPS depolymerase (Dpo7) derived from bacteriophage vB_SepiS-phiIPLA7, was overexpressed in Escherichia coli and characterized. A dose dependent but time independent response was observed after treatment of staphylococcal 24 h-biofilms with Dpo7. Maximum removal (>90%) of biofilm-attached cells was obtained with 0.15 μM of Dpo7 in all polysaccharide producer strains but Dpo7 failed to eliminate polysaccharide-independent biofilm formed by S. aureus V329. Moreover, the pre-treatment of polystyrene surfaces with Dpo7 reduced the biofilm biomass by 53–85% in the 67% of the tested strains. This study supports the use of phage-encoded EPS depolymerases to prevent and disperse staphylococcal biofilms, thereby making bacteria more susceptible to the action of antimicrobials.
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Affiliation(s)
- Diana Gutiérrez
- Consejo Superior de Investigaciones Científicas - Instituto de Productos Lácteos de Asturias Villaviciosa, Spain
| | - Yves Briers
- Laboratory of Gene Technology, KU Leuven Heverlee, Belgium ; Laboratory of Applied Biotechnology, Ghent University Ghent, Belgium
| | - Lorena Rodríguez-Rubio
- Consejo Superior de Investigaciones Científicas - Instituto de Productos Lácteos de Asturias Villaviciosa, Spain ; Laboratory of Gene Technology, KU Leuven Heverlee, Belgium
| | - Beatriz Martínez
- Consejo Superior de Investigaciones Científicas - Instituto de Productos Lácteos de Asturias Villaviciosa, Spain
| | - Ana Rodríguez
- Consejo Superior de Investigaciones Científicas - Instituto de Productos Lácteos de Asturias Villaviciosa, Spain
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven Heverlee, Belgium
| | - Pilar García
- Consejo Superior de Investigaciones Científicas - Instituto de Productos Lácteos de Asturias Villaviciosa, Spain
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22
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Genome Sequence of Streptococcus phocae subsp. phocae Strain ATCC 51973T Isolated from a Harbor Seal (Phoca vitulina). GENOME ANNOUNCEMENTS 2015; 3:3/6/e01307-15. [PMID: 26586875 PMCID: PMC4653777 DOI: 10.1128/genomea.01307-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Streptococcus phocae subsp. phocae is a pathogen that affects different pinniped and mammalian species. This announcement reports the genome sequence of the type strain ATCC 51973 isolated in Norway from clinical specimens of harbor seal (Phoca vitulina), revealing interesting genes related to possible virulence factors.
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Buth SA, Menin L, Shneider MM, Engel J, Boudko SP, Leiman PG. Structure and Biophysical Properties of a Triple-Stranded Beta-Helix Comprising the Central Spike of Bacteriophage T4. Viruses 2015; 7:4676-706. [PMID: 26295253 PMCID: PMC4576200 DOI: 10.3390/v7082839] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/10/2015] [Accepted: 08/13/2015] [Indexed: 12/22/2022] Open
Abstract
Gene product 5 (gp5) of bacteriophage T4 is a spike-shaped protein that functions to disrupt the membrane of the target cell during phage infection. Its C-terminal domain is a long and slender β-helix that is formed by three polypeptide chains wrapped around a common symmetry axis akin to three interdigitated corkscrews. The folding and biophysical properties of such triple-stranded β-helices, which are topologically related to amyloid fibers, represent an unsolved biophysical problem. Here, we report structural and biophysical characterization of T4 gp5 β-helix and its truncated mutants of different lengths. A soluble fragment that forms a dimer of trimers and that could comprise a minimal self-folding unit has been identified. Surprisingly, the hydrophobic core of the β-helix is small. It is located near the C-terminal end of the β-helix and contains a centrally positioned and hydrated magnesium ion. A large part of the β-helix interior comprises a large elongated cavity that binds palmitic, stearic, and oleic acids in an extended conformation suggesting that these molecules might participate in the folding of the complete β-helix.
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Affiliation(s)
- Sergey A Buth
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), BSP 415, 1015 Lausanne, Switzerland.
| | - Laure Menin
- Service de Spectrométrie de Masse, ISIC, EPFL, BCH 1520, 1015 Lausanne, Switzerland.
| | - Mikhail M Shneider
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), BSP 415, 1015 Lausanne, Switzerland.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Molecular Bioengineering, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia.
| | - Jürgen Engel
- Department of Biophysical Chemistry, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.
| | - Sergei P Boudko
- Department of Biophysical Chemistry, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA.
- The Research Department, Shriner's Hospital for Children, 3101 Sam Jackson Park Road, Portland, OR 97239, USA.
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, 3181 Sam Jackson Park Road, Portland, OR 97239, USA.
| | - Petr G Leiman
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), BSP 415, 1015 Lausanne, Switzerland.
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA.
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24
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Singh SK, Bharati AP, Singh N, Pandey P, Joshi P, Singh K, Mitra K, Gayen JR, Sarkar J, Akhtar MS. The prophage-encoded hyaluronate lyase has broad substrate specificity and is regulated by the N-terminal domain. J Biol Chem 2014; 289:35225-36. [PMID: 25378402 DOI: 10.1074/jbc.m113.507673] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Streptococcus equi is the causative agent of the highly contagious disease "strangles" in equines and zoonotic meningitis in human. Spreading of infection in host tissues is thought to be facilitated by the bacterial gene encoded extracellular hyaluronate lyase (HL), which degrades hyaluronan (HA), chondroitin 6-sulfate, and dermatan sulfate of the extracellular matrix). The clinical strain S. equi 4047 however, lacks a functional extracellular HL. The prophages of S. equi and other streptococci encode intracellular HLs which are reported to partially degrade HA and do not cleave any other glycosaminoglycans. The phage HLs are thus thought to play a role limited to the penetration of streptococcal HA capsules, facilitating bacterial lysogenization and not in the bacterial pathogenesis. Here we systematically looked into the structure-function relationship of S. equi 4047 phage HL. Although HA is the preferred substrate, this HL has weak activity toward chondroitin 6-sulfate and dermatan sulfate and can completely degrade all of them. Even though the catalytic triple-stranded β-helix domain of phage HL is functionally independent, its catalytic efficiency and specificity is influenced by the N-terminal domain. The phage HL also interacts with human transmembrane glycoprotein CD44. The above results suggest that the streptococci can use phage HLs to degrade glycosaminoglycans of the extracellular matrix for spreading virulence factors and toxins while utilizing the disaccharides as a nutrient source for proliferation at the site of infection.
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Affiliation(s)
| | | | - Neha Singh
- From the Molecular and Structural Biology Division
| | | | | | - Kavita Singh
- Sophisticated Analytical Instrument Facility, Council of Scientific and Industrial Research-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India, PIN 226 031 and
| | - Kalyan Mitra
- Sophisticated Analytical Instrument Facility, Council of Scientific and Industrial Research-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow, India, PIN 226 031 and Academy of Scientific and Innovative Research, Chennai, India, PIN 600 113
| | - Jiaur R Gayen
- Pharmacokinetics and Metabolism Division, and Academy of Scientific and Innovative Research, Chennai, India, PIN 600 113
| | - Jayanta Sarkar
- Biochemistry Division, Academy of Scientific and Innovative Research, Chennai, India, PIN 600 113
| | - Md Sohail Akhtar
- From the Molecular and Structural Biology Division, Academy of Scientific and Innovative Research, Chennai, India, PIN 600 113
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25
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Streptococcus zooepidemicus and Streptococcus equi evolution: the role of CRISPRs. Biochem Soc Trans 2014; 41:1437-43. [PMID: 24256234 DOI: 10.1042/bst20130165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The host-restricted bacterium Streptococcus equi is the causative agent of equine strangles, the most frequently diagnosed infectious disease of horses worldwide. The disease is characterized by abscessation of the lymph nodes of the head and neck, leading to significant welfare and economic cost. S. equi is believed to have evolved from an ancestral strain of Streptococcus zooepidemicus, an opportunistic pathogen of horses and other animals. Comparison of the genome of S. equi strain 4047 with those of S. zooepidemicus identified examples of gene loss due to mutation and deletion, and gene gain through the acquisition of mobile genetic elements that have probably shaped the pathogenic specialization of S. equi. In particular, deletion of the CRISPR (clustered regularly interspaced short palindromic repeats) locus in the ancestor of S. equi may have predisposed the bacterium to acquire and incorporate new genetic material into its genome. These include four prophages and a novel integrative conjugative element. The virulence cargo carried by these mobile genetic elements is believed to have shaped the ability of S. equi to cause strangles. Further sequencing of S. zooepidemicus has highlighted the diversity of this opportunistic pathogen. Again, CRISPRs are postulated to influence evolution, balancing the need for gene gain over genome stability. Analysis of spacer sequences suggest that these pathogens may be susceptible to a limited range of phages and provide further evidence of cross-species exchange of genetic material among Streptococcus pyogenes, Streptococcus agalactiae and Streptococcus dysgalactiae.
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26
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Garron ML, Cygler M. Uronic polysaccharide degrading enzymes. Curr Opin Struct Biol 2014; 28:87-95. [PMID: 25156747 DOI: 10.1016/j.sbi.2014.07.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/24/2014] [Accepted: 07/30/2014] [Indexed: 12/13/2022]
Abstract
In the past several years progress has been made in the field of structure and function of polysaccharide lyases (PLs). The number of classified polysaccharide lyase families has increased to 23 and more detailed analysis has allowed the identification of more closely related subfamilies, leading to stronger correlation between each subfamily and a unique substrate. The number of as yet unclassified polysaccharide lyases has also increased and we expect that sequencing projects will allow many of these unclassified sequences to emerge as new families. The progress in structural analysis of PLs has led to having at least one representative structure for each of the families and for two unclassified enzymes. The newly determined structures have folds observed previously in other PL families and their catalytic mechanisms follow either metal-assisted or Tyr/His mechanisms characteristic for other PL enzymes. Comparison of PLs with glycoside hydrolases (GHs) shows several folds common to both classes but only for the β-helix fold is there strong indication of divergent evolution from a common ancestor. Analysis of bacterial genomes identified gene clusters containing multiple polysaccharide cleaving enzymes, the Polysaccharides Utilization Loci (PULs), and their gene complement suggests that they are organized to process completely a specific polysaccharide.
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Affiliation(s)
- Marie-Line Garron
- Aix-Marseille University, AFMB UMR7257, 163 Avenue de Luminy, 13288 Marseille, France; CNRS, AFMB UMR7257, 163 Avenue de Luminy, 13288 Marseille, France
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada.
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27
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Singh SK, Malhotra S, Akhtar MS. Characterization of hyaluronic acid specific hyaluronate lyase (HylP) from Streptococcus pyogenes. Biochimie 2014; 102:203-10. [DOI: 10.1016/j.biochi.2014.03.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 03/25/2014] [Indexed: 11/30/2022]
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28
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Spinelli S, Veesler D, Bebeacua C, Cambillau C. Structures and host-adhesion mechanisms of lactococcal siphophages. Front Microbiol 2014; 5:3. [PMID: 24474948 PMCID: PMC3893620 DOI: 10.3389/fmicb.2014.00003] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 01/04/2014] [Indexed: 12/29/2022] Open
Abstract
The Siphoviridae family of bacteriophages is the largest viral family on earth and comprises members infecting both bacteria and archaea. Lactococcal siphophages infect the Gram-positive bacterium Lactococcus lactis, which is widely used for industrial milk fermentation processes (e.g., cheese production). As a result, lactococcal phages have become one of the most thoroughly characterized class of phages from a genomic standpoint. They exhibit amazing and intriguing characteristics. First, each phage has a strict specificity toward a unique or a handful of L. lactis host strains. Second, most lactococcal phages possess a large organelle at their tail tip (termed the baseplate), bearing the receptor binding proteins (RBPs) and mediating host adsorption. The recent accumulation of structural and functional data revealed the modular structure of their building blocks, their different mechanisms of activation and the fine specificity of their RBPs. These results also illustrate similarities and differences between lactococcal Siphoviridae and Gram-negative infecting Myoviridae.
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Affiliation(s)
- Silvia Spinelli
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Aix-Marseille Université Marseille, France ; Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Centre National de la Recherche Scientifique Marseille, France
| | - David Veesler
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Aix-Marseille Université Marseille, France ; Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Centre National de la Recherche Scientifique Marseille, France
| | - Cecilia Bebeacua
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Aix-Marseille Université Marseille, France ; Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Centre National de la Recherche Scientifique Marseille, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Aix-Marseille Université Marseille, France ; Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Centre National de la Recherche Scientifique Marseille, France
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29
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Yan J, Mao J, Xie J. Bacteriophage Polysaccharide Depolymerases and Biomedical Applications. BioDrugs 2013; 28:265-74. [DOI: 10.1007/s40259-013-0081-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Singh A, Arutyunov D, Szymanski CM, Evoy S. Bacteriophage based probes for pathogen detection. Analyst 2012; 137:3405-21. [PMID: 22724121 DOI: 10.1039/c2an35371g] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Rapid and specific detection of pathogenic bacteria is important for the proper treatment, containment and prevention of human, animal and plant diseases. Identifying unique biological probes to achieve a high degree of specificity and minimize false positives has therefore garnered much interest in recent years. Bacteriophages are obligate intracellular parasites that subvert bacterial cell resources for their own multiplication and production of disseminative new virions, which repeat the cycle by binding specifically to the host surface receptors and injecting genetic material into the bacterial cells. The precision of host recognition in phages is imparted by the receptor binding proteins (RBPs) that are often located in the tail-spike or tail fiber protein assemblies of the virions. Phage host recognition specificity has been traditionally exploited for bacterial typing using laborious and time consuming bacterial growth assays. At the same time this feature makes phage virions or RBPs an excellent choice for the development of probes capable of selectively capturing bacteria on solid surfaces with subsequent quick and automatic detection of the binding event. This review focuses on the description of pathogen detection approaches based on immobilized phage virions as well as pure recombinant RBPs. Specific advantages of RBP-based molecular probes are also discussed.
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Affiliation(s)
- Amit Singh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2V4, Canada.
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31
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Park JK, Choi DJ, Kim SM, Choi HN, Park JW, Jang SJ, Choo YK, Lee CG, Park YI. Purification and characterization of a polysialic acid-specific sialidase from Pseudomonas fluorescens JK-0412. BIOTECHNOL BIOPROC E 2012. [DOI: 10.1007/s12257-011-0495-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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32
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Structure of the receptor-binding carboxy-terminal domain of bacteriophage T7 tail fibers. Proc Natl Acad Sci U S A 2012; 109:9390-5. [PMID: 22645347 DOI: 10.1073/pnas.1119719109] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The six bacteriophage T7 tail fibers, homo-trimers of gene product 17, are thought to be responsible for the first specific, albeit reversible, attachment to Escherichia coli lipopolysaccharide. The protein trimer forms kinked fibers comprised of an amino-terminal tail-attachment domain, a slender shaft, and a carboxyl-terminal domain composed of several nodules. Previously, we expressed, purified, and crystallized a carboxyl-terminal fragment comprising residues 371-553. Here, we report the structure of this protein trimer, solved using anomalous diffraction and refined at 2 Å resolution. Amino acids 371-447 form a tapered pyramid with a triangular cross-section composed of interlocked β-sheets from each of the three chains. The triangular pyramid domain has three α-helices at its narrow end, which are connected to a carboxyl-terminal three-blade β-propeller tip domain by flexible loops. The monomers of this tip domain each contain an eight-stranded β-sandwich. The exact topology of the β-sandwich fold is novel, but similar to that of knob domains of other viral fibers and the phage Sf6 needle. Several host-range change mutants have been mapped to loops located on the top of this tip domain, suggesting that this surface of the tip domain interacts with receptors on the cell surface.
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33
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Casjens SR, Molineux IJ. Short noncontractile tail machines: adsorption and DNA delivery by podoviruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:143-79. [PMID: 22297513 DOI: 10.1007/978-1-4614-0980-9_7] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Tailed dsDNA bacteriophage virions bind to susceptible cells with the tips of their tails and then deliver their DNA through the tail into the cells to initiate infection. This chapter discusses what is known about this process in the short-tailed phages (Podoviridae). Their short tails require that many of these virions adsorb to the outer layers of the cell and work their way down to the outer membrane surface before releasing their DNA. Interestingly, the receptor-binding protein of many short-tailed phages (and some with long tails) has an enzymatic activity that cleaves their polysaccharide receptors. Reversible adsorption and irreversible adsorption to primary and secondary receptors are discussed, including how sequence divergence in tail fiber and tailspike proteins leads to different host specificities. Upon reaching the outer membrane of Gram-negative cells, some podoviral tail machines release virion proteins into the cell that help the DNA efficiently traverse the outer layers of the cell and/or prepare the cell cytoplasm for phage genome arrival. Podoviruses utilize several rather different variations on this theme. The virion DNA is then released into the cell; the energetics of this process is discussed. Phages like T7 and N4 deliver their DNA relatively slowly, using enzymes to pull the genome into the cell. At least in part this mechanism ensures that genes in late-entering DNA are not expressed at early times. On the other hand, phages like P22 probably deliver their DNA more rapidly so that it can be circularized before the cascade of gene expression begins.
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Affiliation(s)
- Sherwood R Casjens
- Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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34
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35
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Schulz EC, Ficner R. Knitting and snipping: chaperones in β-helix folding. Curr Opin Struct Biol 2011; 21:232-9. [PMID: 21330133 DOI: 10.1016/j.sbi.2011.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 01/20/2011] [Accepted: 01/20/2011] [Indexed: 01/01/2023]
Abstract
Hallmarks of proteins containing β-helices are their increased stability and rigidity and their aggregation prone folding pathways. While parallel β-helices fold independently, the folding and assembly of many triple β-helices depends on a registration signal in order to adopt the correct three-dimensional structure. In some cases this is a mere trimerization domain, in others specialized chaperones are required. Recently, the crystal structures of two classes of intramolecular chaperones of β-helical proteins have been determined. Both mediate the assembly of large tailspike proteins and release themselves after maturation; however, they differ substantially in their structure and autoproteolytic release mechanisms.
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Affiliation(s)
- Eike C Schulz
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
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36
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Elmabrouk ZH, Vincent F, Zhang M, Smith NL, Turkenburg JP, Charnock SJ, Black GW, Taylor EJ. Crystal structures of a family 8 polysaccharide lyase reveal open and highly occluded substrate-binding cleft conformations. Proteins 2010; 79:965-74. [PMID: 21287626 DOI: 10.1002/prot.22938] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 10/22/2010] [Accepted: 10/29/2010] [Indexed: 11/06/2022]
Abstract
Bacterial enzymatic degradation of glycosaminoglycans such as hyaluronan and chondroitin is facilitated by polysaccharide lyases. Family 8 polysaccharide lyase (PL8) enzymes contain at least two domains: one predominantly composed of α-helices, the α-domain, and another predominantly composed of β-sheets, the β-domain. Simulation flexibility analyses indicate that processive exolytic cleavage of hyaluronan, by PL8 hyaluronate lyases, is likely to involve an interdomain shift, resulting in the opening/closing of the substrate-binding cleft between the α- and β-domains, facilitating substrate translocation. Here, the Streptomyces coelicolor A3(2) PL8 enzyme was recombinantly expressed in and purified from Escherichia coli and biochemically characterized as a hyaluronate lyase. By using X-ray crystallography its structure was solved in complex with hyaluronan and chondroitin disaccharides. These findings show key catalytic interactions made by the different substrates, and on comparison with all other PL8 structures reveals that the substrate-binding cleft of the S. coelicolor enzyme is highly occluded. A third structure of the enzyme, harboring a mutation of the catalytic tyrosine, created via site-directed mutagenesis, interestingly revealed an interdomain shift that resulted in the opening of the substrate-binding cleft. These results add further support to the proposed processive mechanism of action of PL8 hyaluronate lyases and may indicate that the mechanism of action is likely to be universally used by PL8 hyaluronate lyases.
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Affiliation(s)
- Zainab H Elmabrouk
- Department of Biomedical Sciences, School of Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, United Kingdom
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37
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Leiman PG, Arisaka F, van Raaij MJ, Kostyuchenko VA, Aksyuk AA, Kanamaru S, Rossmann MG. Morphogenesis of the T4 tail and tail fibers. Virol J 2010; 7:355. [PMID: 21129200 PMCID: PMC3004832 DOI: 10.1186/1743-422x-7-355] [Citation(s) in RCA: 178] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 12/03/2010] [Indexed: 01/07/2023] Open
Abstract
Remarkable progress has been made during the past ten years in elucidating the structure of the bacteriophage T4 tail by a combination of three-dimensional image reconstruction from electron micrographs and X-ray crystallography of the components. Partial and complete structures of nine out of twenty tail structural proteins have been determined by X-ray crystallography and have been fitted into the 3D-reconstituted structure of the "extended" tail. The 3D structure of the "contracted" tail was also determined and interpreted in terms of component proteins. Given the pseudo-atomic tail structures both before and after contraction, it is now possible to understand the gross conformational change of the baseplate in terms of the change in the relative positions of the subunit proteins. These studies have explained how the conformational change of the baseplate and contraction of the tail are related to the tail's host cell recognition and membrane penetration function. On the other hand, the baseplate assembly process has been recently reexamined in detail in a precise system involving recombinant proteins (unlike the earlier studies with phage mutants). These experiments showed that the sequential association of the subunits of the baseplate wedge is based on the induced-fit upon association of each subunit. It was also found that, upon association of gp53 (gene product 53), the penultimate subunit of the wedge, six of the wedge intermediates spontaneously associate to form a baseplate-like structure in the absence of the central hub. Structure determination of the rest of the subunits and intermediate complexes and the assembly of the hub still require further study.
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Affiliation(s)
- Petr G Leiman
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut de Physique des Systèmes Biologiques, BSP-415, CH-1015 Lausanne, Switzerland.
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38
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Vuong TV, Wilson DB. Glycoside hydrolases: catalytic base/nucleophile diversity. Biotechnol Bioeng 2010; 107:195-205. [PMID: 20552664 DOI: 10.1002/bit.22838] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recent studies have shown that a number of glycoside hydrolase families do not follow the classical catalytic mechanisms, as they lack a typical catalytic base/nucleophile. A variety of mechanisms are used to replace this function, including substrate-assisted catalysis, a network of several residues, and the use of non-carboxylate residues or exogenous nucleophiles. Removal of the catalytic base/nucleophile by mutation can have a profound impact on substrate specificity, producing enzymes with completely new functions.
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Affiliation(s)
- Thu V Vuong
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
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39
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Garron ML, Cygler M. Structural and mechanistic classification of uronic acid-containing polysaccharide lyases. Glycobiology 2010; 20:1547-73. [PMID: 20805221 DOI: 10.1093/glycob/cwq122] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Polysaccharide lyases (PLs) have been assigned to 21 families based on their sequences, with ~ 50 singletons awaiting further classification. For 19 of these families, the structure of at least one protein is known. In this review, we have analyzed the available structural information and show that presently known PL families belong to six general folds. Only two general catalytic mechanisms have been observed among these PLs: (1) metal-assisted neutralization of the acidic group of the sugar next to the cleaved bond, with, rather unusually, arginine or lysine playing the role of Brønsted base and (2) neutralization of the acidic group on the sugar by a close approach of an amino or acidic group forcing its protonation and Tyr or Tyr-His acting as the Brønsted base and acid.
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Affiliation(s)
- Marie-Line Garron
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 1Y6
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40
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Lee JH, Moore LD, Kumar S, Pritchard DG, Ponnazhagan S, Deivanayagam C. Bacteriophage hyaluronidase effectively inhibits growth, migration and invasion by disrupting hyaluronan-mediated Erk1/2 activation and RhoA expression in human breast carcinoma cells. Cancer Lett 2010; 298:238-49. [PMID: 20688428 DOI: 10.1016/j.canlet.2010.07.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 07/08/2010] [Accepted: 07/12/2010] [Indexed: 10/19/2022]
Abstract
Aberrant hyaluronan production has been implicated in many types of tumor. In this context, hyaluronidase has been explored as a viable therapeutic approach to reduce tumoral hyaluronan. However, elevated levels of hyaluronan in tumors are often associated with high expression levels of cellular hyaluronidases, which consequently produce various sizes of saturated hyaluronan fragments with divergent pro-tumoral activities. The current study shows that different hyaluronan metabolisms of mammalian and microbial hyaluronidases could elicit distinct alterations in cancer cell behavior. Unlike saturated hyaluronan metabolites, unsaturated hyaluronan oligosaccharides produced by bacteriophage hyaluronidase, HylP, had no biological effect on growth of breast carcinoma cells. More importantly, HylP's metabolic process of hyaluronan into non-detrimental oligosaccharides significantly decreased breast cancer cell proliferation, migration and invasion by disrupting Erk1/2 activation and RhoA expression. Our results suggest that it may be possible to exploit HylP's unique enzymatic activity in suppressing hyaluronan-mediated tumor growth and progression.
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Affiliation(s)
- Joo Hyoung Lee
- Department of Physiology and Biophysics, University of Alabama, Birmingham, AL 35294-4400, USA
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41
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Thompson JE, Pourhossein M, Waterhouse A, Hudson T, Goldrick M, Derrick JP, Roberts IS. The K5 lyase KflA combines a viral tail spike structure with a bacterial polysaccharide lyase mechanism. J Biol Chem 2010; 285:23963-9. [PMID: 20519506 DOI: 10.1074/jbc.m110.127571] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
K5 lyase A (KflA) is a tail spike protein (TSP) encoded by a K5A coliphage, which cleaves K5 capsular polysaccharide, a glycosaminoglycan with the repeat unit [-4)-betaGlcA-(1,4)- alphaGlcNAc(1-], displayed on the surface of Escherichia coli K5 strains. The crystal structure of KflA reveals a trimeric arrangement, with each monomer containing a right-handed, single-stranded parallel beta-helix domain. Stable trimer formation by the intertwining of strands in the C-terminal domain, followed by proteolytic maturation, is likely to be catalyzed by an autochaperone as described for K1F endosialidase. The structure of KflA represents the first bacteriophage tail spike protein combining polysaccharide lyase activity with a single-stranded parallel beta-helix fold. We propose a catalytic site and mechanism representing convergence with the syn-beta-elimination site of heparinase II from Pedobacter heparinus.
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Affiliation(s)
- James E Thompson
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
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Martinez-Fleites C, Smith NL, Turkenburg JP, Black GW, Taylor EJ. Structures of two truncated phage-tail hyaluronate lyases from Streptococcus pyogenes serotype M1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:963-6. [PMID: 19850999 PMCID: PMC2765878 DOI: 10.1107/s1744309109032813] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 08/19/2009] [Indexed: 01/13/2023]
Abstract
The crystal structures of truncated forms of the Streptococcus pyogenes phage-encoded hyaluronate lyases HylP2 and HylP3 were determined by molecular replacement to 1.6 and 1.9 A resolution, respectively. The truncated forms crystallized in a hexagonal space group, forming a trimer around the threefold crystallographic axis. The arrangement of the fold is very similar to that observed in the structure of the related hyaluronate lyase HylP1. The structural elements putatively involved in substrate recognition are found to be conserved in both the HylP2 and HylP3 fragments.
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Affiliation(s)
- Carlos Martinez-Fleites
- Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5YW, England
| | - Nicola L. Smith
- School of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, England
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, England
| | - Johan P. Turkenburg
- Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5YW, England
| | - Gary W. Black
- School of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, England
| | - Edward J. Taylor
- Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5YW, England
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Polysaccharide binding sites in hyaluronate lyase - crystal structures of native phage-encoded hyaluronate lyase and its complexes with ascorbic acid and lactose. FEBS J 2009; 276:3392-402. [DOI: 10.1111/j.1742-4658.2009.07065.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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44
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Lindsay AM, Zhang M, Mitchell Z, Holden MTG, Waller AS, Sutcliffe IC, Black GW. The Streptococcus equi prophage-encoded protein SEQ2045 is a hyaluronan-specific hyaluronate lyase that is produced during equine infection. MICROBIOLOGY-SGM 2009; 155:443-449. [PMID: 19202092 DOI: 10.1099/mic.0.020826-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Streptococcus equi causes equine 'strangles'. Hyaluronate lyases, which degrade connective tissue hyaluronan and chondroitins, are thought to facilitate streptococcal invasion of the host. However, prophage-encoded hyaluronate lyases are hyaluronan-specific and are thought to be primarily involved in the degradation of the hyaluronan capsule of streptococci during bacteriophage infection. To understand the role of prophage-encoded hyaluronate lyases further, we have biochemically characterized such a hyaluronate lyase, SEQ2045 from S. equi, and have shown that it is produced during equine infection. Prophage-encoded hyaluronan-specific hyaluronate lyases may therefore play a more direct role in disease pathogenesis than previously thought.
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Affiliation(s)
- Anna-Marie Lindsay
- School of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Meng Zhang
- School of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Zoe Mitchell
- Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK
| | | | - Andrew S Waller
- Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK
| | - Iain C Sutcliffe
- School of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Gary W Black
- School of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
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Mishra P, Bhakuni V. Self-assembly of bacteriophage-associated hyaluronate lyase (HYLP2) into an enzymatically active fibrillar film. J Biol Chem 2009; 284:5240-9. [PMID: 18849564 DOI: 10.1074/jbc.m806730200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The in vitro assembly of a soluble protein into its mature fibrillar form is usually accompanied by loss of its functional activity. Our study is the first demonstration of a natural enzyme (HylP2) retaining its enzymatic activity on conversion from pre-fibril to mature fibril and supports the contention that minor conformational changes in the native folded form of a protein can lead to the formation of a functional fibril. Hyaluronate lyase (HylP2) is a natural enzyme of bacteriophage 10403 of Streptococcus pyogenes. At pH 5.0, the enzyme undergoes partial unfolding localized in its N-terminal domain while the C-terminal domain maintains its folded trimeric conformation. This structural variant of HylP2 retains about 70% enzymatic activity with hyaluronan. It further self-assembles into a fibrillar film in vitro through solvent-exposed nonpolar surfaces and intermolecular beta-sheet formation by the beta-strands in the protein. Interestingly, the mature fibrillar film of HylP2 also retains about 60 and 20% enzymatic activity for hyaluronic acid and chondroitin sulfate, respectively. The possession of broad substrate specificity by the fibrillar form of HylP2 indicates that fluctuations in pH, which do not lead to loss of functionality of HylP2, might assist in bacterial pathogenesis. The formation of fibrillar film-like structure has been observed for the first time among the hyaluronidase enzymes. After acquiring this film-like structure in bacteriophage, HylP2 still retains its enzymatic activity, which establishes that these fibrils are a genuinely acquired protein fold/structure.
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Affiliation(s)
- Parul Mishra
- Division of Molecular and Structural Biology, Central Drug Research Institute, Lucknow 226001, India
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Barbirz S, Müller JJ, Uetrecht C, Clark AJ, Heinemann U, Seckler R. Crystal structure ofEscherichia coliphage HK620 tailspike: podoviral tailspike endoglycosidase modules are evolutionarily related. Mol Microbiol 2008; 69:303-16. [DOI: 10.1111/j.1365-2958.2008.06311.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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47
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Ochiai A, Itoh T, Maruyama Y, Kawamata A, Mikami B, Hashimoto W, Murata K. A novel structural fold in polysaccharide lyases: Bacillus subtilis family 11 rhamnogalacturonan lyase YesW with an eight-bladed beta-propeller. J Biol Chem 2007; 282:37134-45. [PMID: 17947240 DOI: 10.1074/jbc.m704663200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rhamnogalacturonan (RG) lyase produced by plant pathogenic and saprophytic microbes plays an important role in degrading plant cell walls. An extracellular RG lyase YesW from saprophytic Bacillus subtilis is a member of polysaccharide lyase family 11 and cleaves glycoside bonds in polygalacturonan as well as RG type-I through a beta-elimination reaction. Crystal structures of YesW and its complex with galacturonan disaccharide, a reaction product analogue, were determined at 1.4 and 2.5 A resolutions with final R-factors of 16.4% and 16.6%, respectively. The enzyme is composed of an eight-bladed beta-propeller with a deep cleft in the center as a basic scaffold, and its structural fold has not been seen in polysaccharide lyases analyzed thus far. Structural analysis of the disaccharide-bound YesW and a site-directed mutagenesis study suggested that Arg-452 and Lys-535 stabilize the carboxyl group of the acidic polysaccharide molecule and Tyr-595 makes a stack interaction with the sugar pyranose ring. In addition to amino acid residues binding to the disaccharide, one calcium ion, which is coordinated by Asp-401, Glu-422, His-363, and His-399, may mediate the enzyme activity. This is, to our knowledge, the first report of a new structural category with a beta-propeller fold in polysaccharide lyases and provides structural insights into substrate binding by RG lyase.
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Affiliation(s)
- Akihito Ochiai
- Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Japan
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Zhang M, McDonald FM, Sturrock SS, Charnock SJ, Humphery-Smith I, Black GW. Group A streptococcus cell-associated pathogenic proteins as revealed by growth in hyaluronic acid-enriched media. Proteomics 2007; 7:1379-90. [PMID: 17407184 DOI: 10.1002/pmic.200600578] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Group A streptococcus (GAS), also know as Streptococcus pyogenes, is a human pathogen and can cause several fatal invasive diseases such as necrotising fasciitis, the so-called flesh-eating disease, and toxic shock syndrome. The destruction of connective tissue and the hyaluronic acid (HA) therein, is a key element of GAS pathogenesis. We therefore propagated GAS in HA-enriched growth media in an attempt to create a simple biological system that could reflect some elements of GAS pathogenesis. Our results show that several recognised virulence factors were up-regulated in HA-enriched media, including the M1 protein, a collagen-like surface protein and the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase, which has been shown to play important roles in streptococcal pathogenesis. Interestingly, two hypothetical proteins of unknown function were also up-regulated and detailed bioinformatics analysis showed that at least one of these hypothetical proteins is likely to be involved in pathogenesis. It was therefore concluded that this simple biological system provided a valuable tool for the identification of potential GAS virulence factors.
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Affiliation(s)
- Meng Zhang
- Biomolecular and Biomedical Research Centre, School of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK.
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49
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Abstract
BACKGROUND The genomes of both long-genome (> 200 Kb) bacteriophages and long-genome eukaryotic viruses have cellular gene homologs whose selective advantage is not explained. These homologs add genomic and possibly biochemical complexity. Understanding their significance requires a definition of complexity that is more biochemically oriented than past empirically based definitions. HYPOTHESIS Initially, I propose two biochemistry-oriented definitions of complexity: either decreased randomness or increased encoded information that does not serve immediate needs. Then, I make the assumption that these two definitions are equivalent. This assumption and recent data lead to the following four-part hypothesis that explains the presence of cellular gene homologs in long bacteriophage genomes and also provides a pathway for complexity increases in prokaryotic cells: (1) Prokaryotes underwent evolutionary increases in biochemical complexity after the eukaryote/prokaryote splits. (2) Some of the complexity increases occurred via multi-step, weak selection that was both protected from strong selection and accelerated by embedding evolving cellular genes in the genomes of bacteriophages and, presumably, also archaeal viruses (first tier selection). (3) The mechanisms for retaining cellular genes in viral genomes evolved under additional, longer-term selection that was stronger (second tier selection). (4) The second tier selection was based on increased access by prokaryotic cells to improved biochemical systems. This access was achieved when DNA transfer moved to prokaryotic cells both the more evolved genes and their more competitive and complex biochemical systems. TESTING THE HYPOTHESIS I propose testing this hypothesis by controlled evolution in microbial communities to (1) determine the effects of deleting individual cellular gene homologs on the growth and evolution of long genome bacteriophages and hosts, (2) find the environmental conditions that select for the presence of cellular gene homologs, (3) determine which, if any, bacteriophage genes were selected for maintaining the homologs and (4) determine the dynamics of homolog evolution. IMPLICATIONS OF THE HYPOTHESIS This hypothesis is an explanation of evolutionary leaps in general. If accurate, it will assist both understanding and influencing the evolution of microbes and their communities. Analysis of evolutionary complexity increase for at least prokaryotes should include analysis of genomes of long-genome bacteriophages.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900, USA.
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50
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Fushinobu S, Hidaka M, Miyanaga A, Imamura H. New Structural Insights on Carbohydrate-active Enzymes. J Appl Glycosci (1999) 2007. [DOI: 10.5458/jag.54.95] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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