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Mori T, Masuzawa N, Kondo K, Nakanishi Y, Chida S, Uehara D, Katahira M, Takeda M. A heterodimeric hyaluronate lyase secreted by the activated sludge bacterium Haliscomenobacter hydrossis. Biosci Biotechnol Biochem 2023; 87:256-266. [PMID: 36535637 DOI: 10.1093/bbb/zbac207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
Haliscomenobacter hydrossis is a filamentous bacterium common in activated sludge. The bacterium was found to utilize hyaluronic acid, and hyaluronate lyase activity was detected in its culture. However, no hyaluronate lyase gene was found in the genome, suggesting the bacterium secretes a novel hyaluronate lyase. The purified enzyme exhibited two bands on SDS-PAGE and a single peak on gel filtration chromatography, suggesting a heterodimeric composition. N-terminal amino acid sequence and mass spectrometric analyses suggested that the subunits are molybdopterin-binding and [2Fe-2S]-binding subunits of a xanthine oxidase family protein. The presence of the cofactors was confirmed using spectrometric analysis. Oxidase activity was not detected, revealing that the enzyme is not an oxidase but a hyaluronate lyase. Nuclear magnetic resonance analysis of the enzymatic digest revealed that the enzyme breaks hyaluronic acid to 3-(4-deoxy-β-d-gluc-4-enuronosyl)-N-acetyl-d-glucosamine. As hyaluronate lyases (EC 4.2.2.1) are monomeric or trimeric, the enzyme is the first heterodimeric hyaluronate lyase.
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Affiliation(s)
- Tomomi Mori
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
| | - Nozomi Masuzawa
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
| | - Keiko Kondo
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan.,Biomass Product Tree Industry-Academia Collaborative Research Laboratory, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Yuta Nakanishi
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
| | - Shun Chida
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
| | - Daiki Uehara
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan.,Biomass Product Tree Industry-Academia Collaborative Research Laboratory, Kyoto University, Gokasho, Uji, Kyoto, Japan.,Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Minoru Takeda
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
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2
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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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3
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Tu IF, Lin TL, Yang FL, Lee IM, Tu WL, Liao JH, Ko TP, Wu WJ, Jan JT, Ho MR, Chou CY, Wang AHJ, Wu CY, Wang JT, Huang KF, Wu SH. Structural and biological insights into Klebsiella pneumoniae surface polysaccharide degradation by a bacteriophage K1 lyase: implications for clinical use. J Biomed Sci 2022; 29:9. [PMID: 35130876 PMCID: PMC8822698 DOI: 10.1186/s12929-022-00792-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/24/2022] [Indexed: 11/18/2022] Open
Abstract
Background K1 capsular polysaccharide (CPS)-associated Klebsiella pneumoniae is the primary cause of pyogenic liver abscesses (PLA) in Asia. Patients with PLA often have serious complications, ultimately leading to a mortality of ~ 5%. This K1 CPS has been reported as a promising target for development of glycoconjugate vaccines against K. pneumoniae infection. The pyruvylation and O-acetylation modifications on the K1 CPS are essential to the immune response induced by the CPS. To date, however, obtaining the fragments of K1 CPS that contain the pyruvylation and O-acetylation for generating glycoconjugate vaccines still remains a challenge. Methods We analyzed the digested CPS products with NMR spectroscopy and mass spectrometry to reveal a bacteriophage-derived polysaccharide depolymerase specific to K1 CPS. The biochemical and biophysical properties of the enzyme were characterized and its crystal structures containing bound CPS products were determined. We also performed site-directed mutagenesis, enzyme kinetic analysis, phage absorption and infectivity studies, and treatment of the K. pneumoniae-infected mice with the wild-type and mutant enzymes. Results We found a bacteriophage-derived polysaccharide lyase that depolymerizes the K1 CPS into fragments of 1–3 repeating trisaccharide units with the retention of the pyruvylation and O-acetylation, and thus the important antigenic determinants of intact K1 CPS. We also determined the 1.46-Å-resolution, product-bound crystal structure of the enzyme, revealing two distinct carbohydrate-binding sites in a trimeric β-helix architecture, which provide the first direct evidence for a second, non-catalytic, carbohydrate-binding site in bacteriophage-derived polysaccharide depolymerases. We demonstrate the tight interaction between the pyruvate moiety of K1 CPS and the enzyme in this second carbohydrate-binding site to be crucial to CPS depolymerization of the enzyme as well as phage absorption and infectivity. We also demonstrate that the enzyme is capable of protecting mice from K1 K. pneumoniae infection, even against a high challenge dose. Conclusions Our results provide insights into how the enzyme recognizes and depolymerizes the K1 CPS, and demonstrate the potential use of the protein not only as a therapeutic agent against K. pneumoniae, but also as a tool to prepare structurally-defined oligosaccharides for the generation of glycoconjugate vaccines against infections caused by this organism. Supplementary Information The online version contains supplementary material available at 10.1186/s12929-022-00792-4.
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Affiliation(s)
- I-Fan Tu
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Tzu-Lung Lin
- Department of Microbiology, National Taiwan University Hospital, Taipei, 100, Taiwan
| | - Feng-Ling Yang
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - I-Ming Lee
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Wei-Lin Tu
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Jia-Tsrong Jan
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Ching-Yi Chou
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Chung-Yi Wu
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Jin-Town Wang
- Department of Microbiology, National Taiwan University Hospital, Taipei, 100, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan.
| | - Shih-Hsiung Wu
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan. .,Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan.
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4
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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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5
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Patil SP, Shirsath LP, Chaudhari BL. A halotolerant hyaluronidase from newly isolated Brevibacterium halotolerans DC1: Purification and characterization. Int J Biol Macromol 2020; 166:839-850. [PMID: 33152358 DOI: 10.1016/j.ijbiomac.2020.10.240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/09/2020] [Accepted: 10/30/2020] [Indexed: 11/29/2022]
Abstract
An enzyme hyaluronidase (hyase) producing halotolerant bacterium was isolated from dental caries and identified as Brevibacterium halotolerans DC1. Higher growth and hyase production were observed in nutrient broth fortified with hyaluronic acid at pH 7.0, temperature 37 °C, 120 rpm upon 48 h of incubation. Hyase was purified using salt precipitation, DEAE cellulose ion exchange, and Sephadex G-100 gel filtration chromatography. The enzyme was purified to 13-fold with 67.19% recovery of activity and 26.37 U/mg of specific activity. SDS-PAGE and zymography revealed it to be near to homogeneity showing a relative molecular weight of about 43 kDa that was confirmed by MALDI-TOF MS. This hyase was very active and stable at pH 7.0 and temperature 40 °C. The presence of metal ions Ca2+ and Mg2+ increased its activity while Zn2+ and Cu2+ severely inhibited it. Being stable at 2 M NaCl, hyase exhibited its halotolerant nature. This enzyme showed wide substrate specificity where hyaluronic acid (HA) was the best substrate. The kinetic studies revealed that Km and Vmax were 91.3 μg/mL and 306.2 μg/mL/min respectively. This is the first report of hyaluronidase from a halotolerant Brevibacterium spp. which can find applications under high salinity.
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Affiliation(s)
- Sandip P Patil
- Department of Microbiology and Biotechnology, R. C. Patel Arts, Commerce and Science College, Shirpur 425 405, India
| | - Leena P Shirsath
- Department of Microbiology and Biotechnology, R. C. Patel Arts, Commerce and Science College, Shirpur 425 405, India
| | - Bhushan L Chaudhari
- Department of Microbiology, School of Life Sciences, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon 425 001, India.
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6
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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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7
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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: 123] [Impact Index Per Article: 15.4] [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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8
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The C-terminus hot spot region helps in the fibril formation of bacteriophage-associated hyaluronate lyase (HylP2). Sci Rep 2015; 5:14429. [PMID: 26395159 PMCID: PMC4585773 DOI: 10.1038/srep14429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 08/21/2015] [Indexed: 11/09/2022] Open
Abstract
The bacteriophage encoded hyaluronate lyases (HylP and HylP2) degrade hyaluronan and other glycosaminoglycans. HylP2 forms a functional fibril under acidic conditions in which its N-terminus is proposed to form the fibrillar core, leading to nucleation and acceleration of fibril formation. Here we report the presence of a hot spot region (A144GVVVY149) towards the carboxy terminus of HylP2, essential for the acceleration of fibril formation. The 'hot spot' is observed to be inherently mutated for valines (A178AMVMY183) in case of HylP. The N- terminal swapped chimeras between these phage HLs ((N)HylP2(C)HylP and (N)HylP(C)HylP2) or HylP did not form fibrils at acidic pH. However, seeding of prefibrils of HylP2 recompensed nucleation and led to fibrillation in (N)HylP(C)HylP2. The V147A mutation in the 'hot spot' region abolished fibril formation in HylP2. The M179V and M181V double mutations in the 'hot spot' region of HylP led to fibrillation with the seeding of prefibrils. It appears that fibrillation in HylP2 even though is initiated by the N-terminus, is accelerated by the conserved 'hot spot' region in the C-terminus. A collagenous (Gly-X-Y)10 motif in the N-terminus and a mutated 'hot spot' region in the C-terminus of HylP affect fibrillar nucleation and acceleration respectively.
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9
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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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Pavlov VA, Klabunovskii EI. The origin of homochirality in nature: a possible version. RUSSIAN CHEMICAL REVIEWS 2015. [DOI: 10.1070/rcr4444] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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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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12
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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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13
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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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14
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Boffi JC, Wedemeyer C, Lipovsek M, Katz E, Calvo DJ, Elgoyhen AB. Positive modulation of the α9α10 nicotinic cholinergic receptor by ascorbic acid. Br J Pharmacol 2013; 168:954-65. [PMID: 22994414 DOI: 10.1111/j.1476-5381.2012.02221.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 09/01/2012] [Accepted: 09/07/2012] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND AND PURPOSE The activation of α9α10 nicotinic cholinergic receptors (nAChRs) present at the synapse between efferent olivocochlear fibres and cochlear hair cells can prevent acoustic trauma. Hence, pharmacological potentiators of these receptors could be useful therapeutically. In this work, we characterize ascorbic acid as a positive modulator of recombinant α9α10 nAChRs. EXPERIMENTAL APPROACH ACh-evoked responses were analysed under two-electrode voltage-clamp recordings in Xenopus laevis oocytes injected with α9 and α10 cRNAs. KEY RESULTS Ascorbic acid potentiated ACh responses in X. laevis oocytes expressing α9α10 (but not α4β2 or α7) nAChRs, in a concentration-dependent manner, with an effective concentration range of 1-30 mM. The compound did not affect the receptor's current-voltage profile nor its apparent affinity for ACh, but it significantly enhanced the maximal evoked currents (percentage of ACh maximal response, 240 ± 20%). This effect was specific for the L form of reduced ascorbic acid. Substitution of the extracellular cysteine residues present in loop C of the ACh binding site did not affect the potentiation. Ascorbic acid turned into a partial agonist of α9α10 nAChRs bearing a point mutation at the pore domain of the channel (TM2 V13'T mutant). A positive allosteric mechanism of action rather than an antioxidant effect of ascorbic acid is proposed. CONCLUSIONS AND IMPLICATIONS The present work describes one of the few agents that activates or potentiates α9α10 nAChRs and leads to new avenues for designing drugs with potential therapeutic use in inner ear disorders.
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Affiliation(s)
- J C Boffi
- Instituto de Investigaciones en Ingeniería, Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Buenos Aires, Argentina
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15
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Pozharski E, Weichenberger CX, Rupp B. Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:150-67. [PMID: 23385452 DOI: 10.1107/s0907444912044423] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/26/2012] [Indexed: 11/10/2022]
Abstract
As a result of substantial instrumental automation and the continuing improvement of software, crystallographic studies of biomolecules are conducted by non-experts in increasing numbers. While improved validation almost ensures that major mistakes in the protein part of structure models are exceedingly rare, in ligand-protein complex structures, which in general are most interesting to the scientist, ambiguous ligand electron density is often difficult to interpret and the modelled ligands are generally more difficult to properly validate. Here, (i) the primary technical reasons and potential human factors leading to problems in ligand structure models are presented; (ii) the most common categories of building errors or overinterpretation are classified; (iii) a few instructive and specific examples are discussed in detail, including an electron-density-based analysis of ligand structures that do not contain any ligands; (iv) means of avoiding such mistakes are suggested and the implications for database validity are discussed and (v) a user-friendly software tool that allows non-expert users to conveniently inspect ligand density is provided.
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Affiliation(s)
- Edwin Pozharski
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, USA.
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16
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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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17
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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: 76] [Impact Index Per Article: 6.3] [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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18
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Takata T, Haase-Pettingell C, King J. The C-terminal cysteine annulus participates in auto-chaperone function for Salmonella phage P22 tailspike folding and assembly. BACTERIOPHAGE 2012; 2:36-49. [PMID: 22666655 PMCID: PMC3357383 DOI: 10.4161/bact.19775] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Elongated trimeric adhesins are a distinct class of proteins employed by phages and viruses to recognize and bind to their host cells, and by bacteria to bind to their target cells and tissues. The tailspikes of E. coli phage K1F and Bacillus phage Ø29 exhibit auto-chaperone activity in their trimeric C-terminal domains. The P22 tailspike is structurally homologous to those adhesins. Though there are no disulfide bonds or reactive cysteines in the native P22 tailspikes, a set of C-terminal cysteines are very reactive in partially folded intermediates, implying an unusual local conformation in the domain. This is likely to be involved in the auto-chaperone function. We examined the unusual reactivity of C-terminal tailspike cysteines during folding and assembly as a potential reporter of auto-chaperone function. Reaction with IAA blocked productive refolding in vitro, but not off-pathway aggregation. Two-dimensional PAGE revealed that the predominant intermediate exhibiting reactive cysteine side chains was a partially folded monomer. Treatment with reducing reagent promoted native trimer formation from these species, consistent with transient disulfide bonds in the auto-chaperone domain. Limited enzymatic digestion and mass spectrometry of folding and assembly intermediates indicated that the C-terminal domain was compact in the protrimer species. These results indicate that the C-terminal domain of the P22 tailspike folds itself and associates prior to formation of the protrimer intermediate, and not after, as previously proposed. The C-terminal cysteines and triple β-helix domains apparently provide the staging for the correct auto-chaperone domain formation, needed for alignment of P22 tailspike native trimer.
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Affiliation(s)
- Takumi Takata
- Department of Biology; Massachusetts Institute of Technology; Cambridge, MA USA
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19
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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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20
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21
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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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22
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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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23
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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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24
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Ochiai A, Yamasaki M, Mikami B, Hashimoto W, Murata K. Crystal structure of exotype alginate lyase Atu3025 from Agrobacterium tumefaciens. J Biol Chem 2010; 285:24519-28. [PMID: 20507980 DOI: 10.1074/jbc.m110.125450] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alginate, a major component of the cell wall matrix in brown seaweeds, is degraded by alginate lyases through a beta-elimination reaction. Almost all alginate lyases act endolytically on substrate, thereby yielding unsaturated oligouronic acids having 4-deoxy-l-erythro-hex-4-enepyranosyluronic acid at the nonreducing end. In contrast, Agrobacterium tumefaciens alginate lyase Atu3025, a member of polysaccharide lyase family 15, acts on alginate polysaccharides and oligosaccharides exolytically and releases unsaturated monosaccharides from the substrate terminal. The crystal structures of Atu3025 and its inactive mutant in complex with alginate trisaccharide (H531A/DeltaGGG) were determined at 2.10- and 2.99-A resolutions with final R-factors of 18.3 and 19.9%, respectively, by x-ray crystallography. The enzyme is comprised of an alpha/alpha-barrel + anti-parallel beta-sheet as a basic scaffold, and its structural fold has not been seen in alginate lyases analyzed thus far. The structural analysis of H531A/DeltaGGG and subsequent site-directed mutagenesis studies proposed the enzyme reaction mechanism, with His(311) and Tyr(365) as the catalytic base and acid, respectively. Two structural determinants, i.e. a short alpha-helix in the central alpha/alpha-barrel domain and a conformational change at the interface between the central and C-terminal domains, are essential for the exolytic mode of action. This is, to our knowledge, the first report on the structure of the family 15 enzyme.
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Affiliation(s)
- Akihito Ochiai
- Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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