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Ashy RA, Jalal RS, Sonbol HS, Alqahtani MD, Sefrji FO, Alshareef SA, Alshehrei FM, Abuauf HW, Baz L, Tashkandi MA, Hakeem IJ, Refai MY, Abulfaraj AA. Functional annotation of rhizospheric phageome of the wild plant species Moringa oleifera. Front Microbiol 2023; 14:1166148. [PMID: 37260683 PMCID: PMC10227523 DOI: 10.3389/fmicb.2023.1166148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/10/2023] [Indexed: 06/02/2023] Open
Abstract
Introduction The study aims to describe phageome of soil rhizosphere of M.oleifera in terms of the genes encoding CAZymes and other KEGG enzymes. Methods Genes of the rhizospheric virome of the wild plant species Moringa oleifera were investigated for their ability to encode useful CAZymes and other KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes and to resist antibiotic resistance genes (ARGs) in the soil. Results Abundance of these genes was higher in the rhizospheric microbiome than in the bulk soil. Detected viral families include the plant viral family Potyviridae as well as the tailed bacteriophages of class Caudoviricetes that are mainly associated with bacterial genera Pseudomonas, Streptomyces and Mycobacterium. Viral CAZymes in this soil mainly belong to glycoside hydrolase (GH) families GH43 and GH23. Some of these CAZymes participate in a KEGG pathway with actions included debranching and degradation of hemicellulose. Other actions include biosynthesizing biopolymer of the bacterial cell wall and the layered cell wall structure of peptidoglycan. Other CAZymes promote plant physiological activities such as cell-cell recognition, embryogenesis and programmed cell death (PCD). Enzymes of other pathways help reduce the level of soil H2O2 and participate in the biosynthesis of glycine, malate, isoprenoids, as well as isoprene that protects plant from heat stress. Other enzymes act in promoting both the permeability of bacterial peroxisome membrane and carbon fixation in plants. Some enzymes participate in a balanced supply of dNTPs, successful DNA replication and mismatch repair during bacterial cell division. They also catalyze the release of signal peptides from bacterial membrane prolipoproteins. Phages with the most highly abundant antibiotic resistance genes (ARGs) transduce species of bacterial genera Pseudomonas, Streptomyces, and Mycobacterium. Abundant mechanisms of antibiotic resistance in the rhizosphere include "antibiotic efflux pump" for ARGs soxR, OleC, and MuxB, "antibiotic target alteration" for parY mutant, and "antibiotic inactivation" for arr-1. Discussion These ARGs can act synergistically to inhibit several antibiotics including tetracycline, penam, cephalosporin, rifamycins, aminocoumarin, and oleandomycin. The study highlighted the issue of horizontal transfer of ARGs to clinical isolates and human gut microbiome.
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Affiliation(s)
- Ruba A. Ashy
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Rewaa S. Jalal
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Hana S. Sonbol
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mashael D. Alqahtani
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fatmah O. Sefrji
- Department of Biology, College of Science, Taibah University, Al-Madinah Al-Munawwarah, Saudi Arabia
| | - Sahar A. Alshareef
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah, Saudi Arabia
| | - Fatimah M. Alshehrei
- Department of Biology, Jumum College University, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Haneen W. Abuauf
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Lina Baz
- Department of Biochemistry, Faculty of Science, King AbdulAziz University, Jeddah, Saudi Arabia
| | - Manal A. Tashkandi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Israa J. Hakeem
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Mohammed Y. Refai
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Aala A. Abulfaraj
- Biological Sciences Department, College of Science & Arts, King AbdulAziz University, Rabigh, Saudi Arabia
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Debbarma S, Acharya A, Mangang YA, Monsang SJ, Choudhury TG, Parhi J, Pandey PK. Immune-biochemical response and immune gene expression profiling of Labeo rohita fingerlings fed with ethanolic tea leaf extracts and its survivability against Aeromonas hydrophila infection. FISH & SHELLFISH IMMUNOLOGY 2022; 130:520-529. [PMID: 36167295 DOI: 10.1016/j.fsi.2022.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 08/21/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
The present study was conducted to evaluate the immunostimulatory effect of tea leaf extract (Camellia sinensis) on Labeo rohita and its resistance against Aeromonas hydrophila infection. The ethanolic extract of green tea (GTEE) was found to be the most potent as compared to other solvent extract which was used for further study. It was used to evaluate immune-biochemical response of L. rohita fingerlings, fed with tea leaf extract (control- 0.0%, 0.2% (T1), 0.4% (T2), 0.8% (T3) and 1% (T4) of GTEE kg-1 feed). Different biochemical parameters like glucose, ALP, GPT, GOT, and immunological parameters like lysozyme activity, NBT, anti-protease activity, myeloperoxidase activity, plasma protein, and immune relevant genes (IL-10, C3, Lysozyme G type and iNOS) expressions were carried out. The immunological parameters such as lysozyme activity, NBT and myeloperoxidase activity showed significantly high value once fed with GTEE incorporated diets. Significant up-regulation of immune genes indicated the enhancement of immune response at molecular level. The biochemical parameters were found to be significantly decreasing, indicating that the extract had hepato-protective effect and can help to overcome stress. The fish, fed with GTEE incorporated diets, showed resistance against A. hydrophila when compared with the control group. 0.2% GTEE showed the highest post-challenged survival (76.67%). From the present study, it is concluded that GTEE @ 0.2% can be used as potent immunostimulant as a sustainable alternative prophylactic and therapeutic agent in aquaculture.
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Affiliation(s)
- Sourabh Debbarma
- College of Fisheries, CAU, Lembucherra, Agartala, Tripura, 799210, India
| | - Arpit Acharya
- College of Fisheries, CAU, Lembucherra, Agartala, Tripura, 799210, India
| | | | | | | | - Janmejay Parhi
- College of Fisheries, CAU, Lembucherra, Agartala, Tripura, 799210, India
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González R, González D, Stambuk F, Ramírez F, Guzmán F, Mercado L, Rojas R, Henríquez C, Brokordt K, Schmitt P. A g-type lysozyme from the scallop Argopecten purpuratus participates in the immune response and in the stability of the hemolymph microbiota. FISH & SHELLFISH IMMUNOLOGY 2022; 123:324-334. [PMID: 35314329 DOI: 10.1016/j.fsi.2022.03.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/15/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Lysozymes are antimicrobial acid hydrolases widely distributed in nature. They are located inside the cells in lysosomes, or they are secreted to the extracellular space, where they can lyse the cell wall of certain species of bacteria via hydrolysis of the peptidoglycan. Thus, lysozymes are bacteriolytic enzymes and play a major biological role in biodefense, as these enzymes can act as antibacterial and immune-modulating agents. In this study, we characterized a g-type lysozyme from the scallop Argopecten purpuratus named ApGlys. The cDNA sequence comprises an open reading frame (ORF) of 600 nucleotides, codifying for a putative protein of 200 amino acids with a signal peptide of 18 amino acids. The deduced mature protein sequence displays a molecular weight of 20.07 kDa and an isoelectric point (pI) of 6.49. ApGlys deduced protein sequence exhibits conserved residues associated with catalytic activity and substrate fixation in other g-type lysozymes. The phylogenetic analysis revealed a high degree of identity of ApGlys with other mollusk g-type lysozymes, which form a restricted and separated clade from the vertebrate lysozymes. ApGlys transcripts were constitutively and highly expressed in the digestive gland, and it was induced in hemocytes and gills of scallops after an immune challenge. Furthermore, the ApGlys protein was located inside hemocytes of immunostimulated scallops, determined by immunofluorescence analysis. Finally, the transcript silencing of ApGlys by RNA interference led to an increase of total culturable bacteria from the scallop hemolymph. Furthermore, we detected a higher diversity of the bacterial community in ApGlys-silenced scallops and an imbalance of certain bacterial groups present in the hemolymph by 16S rDNA deep amplicon sequencing. Overall, our results showed that ApGlys is a new member of scallop lysozymes that is implicated in the immune response and in the microbial homeostasis of A. purpuratus hemolymph.
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Affiliation(s)
- Roxana González
- Laboratorio de Fisiología y Genética Marina (FIGEMA), Departamento de Acuicultura, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile; Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Daniel González
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Felipe Stambuk
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Felipe Ramírez
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Fanny Guzmán
- Núcleo Biotecnología Curauma. Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Luis Mercado
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Rodrigo Rojas
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile
| | - Carlos Henríquez
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Larrondo 1281, Coquimbo, Chile
| | - Katherina Brokordt
- Laboratorio de Fisiología y Genética Marina (FIGEMA), Departamento de Acuicultura, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile; Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Larrondo 1281, Coquimbo, Chile; Centro de Innovación Acuícola (AquaPacífico), Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
| | - Paulina Schmitt
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.
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Song Q, Xiao Y, Xiao Z, Liu T, Li J, Li P, Han F. Lysozymes in Fish. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15039-15051. [PMID: 34890178 DOI: 10.1021/acs.jafc.1c06676] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In recent years, the deterioration of the aquaculture ecological environment has led to a high incidence of fish diseases. Lysozymes, important antimicrobial enzymes, play an important role in the innate immune system of fish. The studies of fish lysozymes benefit the control of fish infections caused by pathogens. In this review, we reviewed recent progress in fish lysozymes, including their classification, structural characteristics, biological functions and mechanisms, tissue distributions, and properties of their recombinant proteins, which will help us to systematically understand the fish lysozymes and facilitate their applications in the fields of food and agriculture.
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Affiliation(s)
- Qing Song
- Ningbo Institute of Northwestern Polytechnical University, Frontiers Science Center for Flexible Electronics (FSCFE), Shaanxi Institute of Flexible Electronics (SIFE), Shaanxi Institute of Biomedical Materials and Engineering (SIBME), Northwestern Polytechnical University, Xi'an, Shaanxi 710072, People's Republic of China
| | - Yao Xiao
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, Fujian 361021, People's Republic of China
| | - Zihan Xiao
- Ningbo Institute of Northwestern Polytechnical University, Frontiers Science Center for Flexible Electronics (FSCFE), Shaanxi Institute of Flexible Electronics (SIFE), Shaanxi Institute of Biomedical Materials and Engineering (SIBME), Northwestern Polytechnical University, Xi'an, Shaanxi 710072, People's Republic of China
| | - Tong Liu
- Sichuan Tengli Agri-Tech Company, Limited, Deyang, Sichuan 618200, People's Republic of China
| | - Jiacheng Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, Fujian 361021, People's Republic of China
| | - Peng Li
- Ningbo Institute of Northwestern Polytechnical University, Frontiers Science Center for Flexible Electronics (FSCFE), Shaanxi Institute of Flexible Electronics (SIFE), Shaanxi Institute of Biomedical Materials and Engineering (SIBME), Northwestern Polytechnical University, Xi'an, Shaanxi 710072, People's Republic of China
| | - Fang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen, Fujian 361021, People's Republic of China
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Zhang X, Chi H, Li G, Irwin DM, Zhang S, Rossiter SJ, Liu Y. Parallel Independent Losses of G-Type Lysozyme Genes in Hairless Aquatic Mammals. Genome Biol Evol 2021; 13:6358722. [PMID: 34450623 PMCID: PMC8449827 DOI: 10.1093/gbe/evab201] [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] [Accepted: 08/23/2021] [Indexed: 12/03/2022] Open
Abstract
Lysozyme enzymes provide classic examples of molecular adaptation and parallel evolution, however, nearly all insights to date come from chicken-type (c-type) lysozymes. Goose-type (g-type) lysozymes occur in diverse vertebrates, with multiple independent duplications reported. Most mammals possess two g-type lysozyme genes (Lyg1 and Lyg2), the result of an early duplication, although some lineages are known to have subsequently lost one copy. Here we examine g-type lysozyme evolution across >250 mammals and reveal widespread losses of either Lyg1 or Lyg2 in several divergent taxa across the mammal tree of life. At the same time, we report strong evidence of extensive losses of both gene copies in cetaceans and sirenians, with an additional putative case of parallel loss in the tarsier. To validate these findings, we inspected published short-read data and confirmed the presence of loss of function mutations. Despite these losses, comparisons of selection pressures between intact g- and c-type lysozyme genes showed stronger purifying selection in the former, indicative of conserved function. Although the reasons for the evolutionary loss of g-type lysozymes in fully aquatic mammals are not known, we suggest that this is likely to at least partially relate to their hairlessness. Indeed, although Lyg1 does not show tissue-specific expression, recent studies have linked Lyg2 expression to anagen hair follicle development and hair loss. Such a role for g-type lysozyme would explain why the Lyg2 gene became obsolete when these taxa lost their body hair.
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Affiliation(s)
- Xiaoqing Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Hai Chi
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Zoonosis of Liaoning Province, Shenyang Agricultural University, Shenyang, China
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Moreno-Córdova EN, Islas-Osuna MA, Contreras-Vergara CA, López-Zavala AA, Ruiz-Bustos E, Reséndiz-Sandoval MG, Castillo-Yañez FJ, Criscitiello MF, Arvizu-Flores AA. Molecular characterization and expression analysis of the chicken-type and goose-type lysozymes from totoaba (Totoaba macdonaldi). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 113:103807. [PMID: 32735961 DOI: 10.1016/j.dci.2020.103807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/23/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Lysozymes play a key role in innate immune response to bacterial pathogens, catalyzing the hydrolysis of the peptidoglycan layer of bacterial cell walls. In this study, the genes encoding the c-type (TmLyzc) and g-type (TmLyzg) lysozymes from Totoaba macdonaldi were cloned and characterized. The cDNA sequences of TmLyzg and TmLyzc were 582 and 432 bp, encoding polypeptides of 193 and 143 amino acids, respectively. Amino acid sequences of these lysozymes shared high identity (60-90%) with their counterparts of other teleosts and showed conserved functional-structural signatures of the lysozyme superfamily. Phylogenetic analysis indicated a close relationship with their vertebrate homologues but distinct evolutionary paths for each lysozyme. Expression analysis by qRT-PCR revealed that TmLyzc was expressed in stomach and pyloric caeca, while TmLyzg was highly expressed in stomach and heart. These results suggest that both lysozymes play important roles in defense of totoaba against bacterial infections or as digestive enzyme.
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Affiliation(s)
- Elena N Moreno-Córdova
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora. Blvd. Rosales S/N, Centro. Hermosillo, SON, CP, 83000, Mexico
| | - María A Islas-Osuna
- Departamento de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, Gustavo Enrique Astiazarán Rosas, N0. 46. Hermosillo, SON, CP, 83304, Mexico
| | - Carmen A Contreras-Vergara
- Departamento de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, Gustavo Enrique Astiazarán Rosas, N0. 46. Hermosillo, SON, CP, 83304, Mexico
| | - Alonso A López-Zavala
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora. Blvd. Rosales S/N, Centro. Hermosillo, SON, CP, 83000, Mexico
| | - Eduardo Ruiz-Bustos
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora. Blvd. Rosales S/N, Centro. Hermosillo, SON, CP, 83000, Mexico
| | - Mónica G Reséndiz-Sandoval
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, Gustavo Enrique Astiazarán Rosas, N0. 46. Hermosillo, SON, CP, 83304, Mexico
| | - Francisco J Castillo-Yañez
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora. Blvd. Rosales S/N, Centro. Hermosillo, SON, CP, 83000, Mexico
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA; Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University. Bryan, TX, 77807, USA.
| | - Aldo A Arvizu-Flores
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora. Blvd. Rosales S/N, Centro. Hermosillo, SON, CP, 83000, Mexico.
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A Kayvirus Distant Homolog of Staphylococcal Virulence Determinants and VISA Biomarker Is a Phage Lytic Enzyme. Viruses 2020; 12:v12030292. [PMID: 32156046 PMCID: PMC7150955 DOI: 10.3390/v12030292] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 01/07/2023] Open
Abstract
Staphylococcal bacteriophages of the Kayvirus genus are candidates for therapeutic applications. One of their proteins, Tgl, is slightly similar to two staphylococcal virulence factors, secreted autolysins of lytic transglycosylase motifs IsaA and SceD. We show that Tgl is a lytic enzyme secreted by the bacterial transport system and localizes to cell peripheries like IsaA and SceD. It causes lysis of E. coli cells expressing the cloned tgl gene, but could be overproduced when depleted of signal peptide. S. aureus cells producing Tgl lysed in the presence of nisin, which mimics the action of phage holin. In vitro, Tgl protein was able to destroy S. aureus cell walls. The production of Tgl decreased S. aureus tolerance to vancomycin, unlike the production of SceD, which is associated with decreased sensitivity to vancomycin. In the genomes of kayviruses, the tgl gene is located a few genes away from the lysK gene, encoding the major endolysin. While lysK is a late phage gene, tgl can be transcribed by a host RNA polymerase, like phage early genes. Taken together, our data indicate that tgl belongs to the kayvirus lytic module and encodes an additional endolysin that can act in concert with LysK in cell lysis.
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Wei K, Ding Y, Yin X, Zhang J, Shen B. Molecular cloning, expression analyses and functional characterization of a goose-type lysozyme gene from Bostrychus sinensis (family: Eleotridae). FISH & SHELLFISH IMMUNOLOGY 2020; 96:41-52. [PMID: 31794842 DOI: 10.1016/j.fsi.2019.11.067] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
In this study, we sequenced and characterized the goose-type lysozyme gene, termed as BsLysG, from the Chinese black sleeper (Bostrychus sinensis). The BsLysG encodes 196 amino acids and contains a soluble bacterial lytic transglycosylases domain, three catalytic residues (Glu72, Asp85 and Asp102) and the GLMQ motif (Gly97, Leu98, Met99 and Gln100). No signal peptide was observed in the BsLysG protein. The genomic DNA of BsLysG contains five exons and four introns. The sequence analyses showed that the BsLysG exhibits high similarity with LysG from other fishes. Phylogenetic analyses showed that the BsLysG is clustered together with its counterparts from other teleost fishes. The Real-time PCR analyses showed that the BsLysG was found to be ubiquitously expressed in ten examined organs in Chinese black sleeper, with predominant expression in spleen, followed by head kidney and peripheral blood. Expression analyses showed that the BsLysG was significantly upregulated in vivo after either pathogen Vibrio parahemolyticus infection or poly (I:C) challenge in peripheral blood, head kidney, liver and spleen organs. The purified recombinant BsLysG (rBsLysG) has optimal activity at 35 °C and pH 5.5. The rBsLysG exhibited antimicrobial activity against two Gram-positive bacteria (Micrococcus lysodeikticus and Staphylococcus aureus) and two Gram-negative bacteria (Escherichia coli and V. parahemolyticus). The Scanning electron microscope (SEM) imaging analyses showed that the rBsLysG-treated V. parahemolyticus cells displayed morphological deformation. These results indicate that the BsLysG is involved in host immune defense against bacterial infection.
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Affiliation(s)
- Ke Wei
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316004, China
| | - Yuehan Ding
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316004, China
| | - Xiaolong Yin
- Zhoushan Fisheries Research Institute, Zhoushan, Zhejiang, 316022, China
| | - Jianshe Zhang
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316004, China.
| | - Bin Shen
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316004, China.
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Mohapatra A, Parida S, Mohanty J, Sahoo PK. Identification and functional characterization of a g-type lysozyme gene of Labeo rohita, an Indian major carp species. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 92:87-98. [PMID: 30439371 DOI: 10.1016/j.dci.2018.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/06/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
Lysozyme, an important secretory innate immune component, possesses antimicrobial activity against broad spectrum of bacteria and viruses. In the present study, complete CDs (558 bps) of g-type lysozyme of rohu (Labeo rohita) was amplified and translated for a putative protein of 185 amino acids. The domain architecture and tertiary structure was also predicted for the protein. Its expression profile was studied in three infection models (bacteria: Aeromonas hydrophila, poly I:C, a dsRNA viral analogue and an ectoparasite: Argulus siamensis) in liver and kidney tissues of rohu. An up-regulation of 630-fold and 420-fold of the gene was observed at 48 h in liver and anterior kidney tissues respectively, after A. hydrophila infection. Significant increase in transcript level was noticed in both liver (0.8-fold) and kidney (480-fold) after 1 h and 12 h of poly I:C induction, respectively. Similarly, expression of lysozyme g transcripts was increased 6000-fold after 7 d of A. siamensis infection in liver tissue. The recombinant protein of g-type lysozyme of rohu (rLr-lysG) of 20.19 kDa was produced in Escherichia coli system and the lysozyme activity of rLr-lysG was found to be most active at pH 6.0 and temperature 35 °C. The potential lytic activity was found to be against A. hydrophila (UL = 0.53) followed by for E. tarda (UL = 0.45) whereas the lytic activity was the least against S. aureus (UL = 0.35) and M. lysodeikticus (UL = 0.34), at pH 6.0 and temperature 35 °C. The normal serum level of protein was estimated using indirect ELISA and was found to be very low (0.12-0.15 μg/ml). These results suggested that g-type lysozyme of rohu might be a potent immunostimulant against microbial infections, with a major role in innate immunity.
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Affiliation(s)
- Amruta Mohapatra
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Sonali Parida
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Jyotirmaya Mohanty
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - P K Sahoo
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India.
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10
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Nishitani Y, Horiuchi A, Aslam M, Kanai T, Atomi H, Miki K. Crystal structures of an archaeal chitinase ChiD and its ligand complexes. Glycobiology 2018; 28:418-426. [PMID: 29800365 DOI: 10.1093/glycob/cwy024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 03/20/2018] [Indexed: 11/13/2022] Open
Abstract
Chitinase D (designated as Pc-ChiD) was found in a hyperthermophilic archaeon, Pyrococcus chitonophagus (previously described as Thermococcus chitonophagus), that was isolated from media containing only chitin as carbon source. Pc-ChiD displays chitinase activity and is thermostable at temperatures up to 95°C, suggesting its potential for industrial use. Pc-ChiD has a secretion signal peptide and two chitin-binding domains (ChBDs) in the N-terminal domain. However, the C-terminal domain shares no sequence similarity with previously identified saccharide-degrading enzymes and does not contain the DXDXE motif conserved in the glycoside hydrolase (GH) 18 family chitinases. To elucidate its overall structure and reaction mechanism, we determined the first crystal structures of Pc-ChiD, both in the ligand-free form and in complexes with substrates. Structure analyses revealed that the C-terminal domain of Pc-ChiD, Pc-ChiD(ΔBD), consists of a third putative substrate-binding domain, which cannot be predicted from the amino acid sequence, and a catalytic domain structurally similar to that found in not the GH18 family but the GH23 family. Based on the similarity with GH23 family chitinase, the catalytic residues of Pc-ChiD were predicted and confirmed by mutagenesis analyses. Moreover, the specific C-terminal 100 residues of Pc-ChiD are important to fix the putative substrate-binding domain next to the catalytic domain, contributing to the structure stability as well as the long chitin chain binding. Our findings reveal the structure of a unique archaeal chitinase that is distinct from previously known members of the GH23 family.
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Affiliation(s)
- Yuichi Nishitani
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ayumi Horiuchi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Mehwish Aslam
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tamotsu Kanai
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.,JST, CREST, Gobancho 7, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.,JST, CREST, Gobancho 7, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.,JST, CREST, Gobancho 7, Chiyoda-ku, Tokyo 102-0076, Japan
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11
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Borišek J, Pintar S, Ogrizek M, Grdadolnik SG, Hodnik V, Turk D, Perdih A, Novič M. Discovery of (phenylureido)piperidinyl benzamides as prospective inhibitors of bacterial autolysin E from Staphylococcus aureus. J Enzyme Inhib Med Chem 2018; 33:1239-1247. [PMID: 30141354 PMCID: PMC6116672 DOI: 10.1080/14756366.2018.1493474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Autolysin E (AtlE) is a cell wall degrading enzyme that catalyzes the hydrolysis of the β-1,4-glycosidic bond between the N-acetylglucosamine and N-acetylmuramic acid units of the bacterial peptidoglycan. Using our recently determined crystal structure of AtlE from Staphylococcus aureus and a combination of pharmacophore modeling, similarity search, and molecular docking, a series of (Phenylureido)piperidinyl benzamides were identified as potential binders and surface plasmon resonance (SPR) and saturation-transfer difference (STD) NMR experiments revealed that discovered compounds bind to AtlE in a lower micromolar range. (phenylureido)piperidinyl benzamides are the first reported non-substrate-like compounds that interact with this enzyme and enable further study of the interaction of small molecules with bacterial AtlE as potential inhibitors of this target.
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Affiliation(s)
- Jure Borišek
- a National Institute of Chemistry , Ljubljana , Slovenia
| | - Sara Pintar
- b Department of Biochemistry, Molecular and Structural Biology , Jozef Stefan Institute , Ljubljana , Slovenia.,c Jozef Stefan International Postgraduate School , Ljubljana , Slovenia
| | - Mitja Ogrizek
- a National Institute of Chemistry , Ljubljana , Slovenia
| | | | - Vesna Hodnik
- d Biotechnical Faculty , Infrastructural Center for Surface Plasmon Resonance , Ljubljana , Slovenia
| | - Dušan Turk
- b Department of Biochemistry, Molecular and Structural Biology , Jozef Stefan Institute , Ljubljana , Slovenia.,e Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins , Ljubljana , Slovenia
| | - Andrej Perdih
- a National Institute of Chemistry , Ljubljana , Slovenia
| | - Marjana Novič
- a National Institute of Chemistry , Ljubljana , Slovenia
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12
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Borišek J, Pintar S, Ogrizek M, Turk D, Perdih A, Novič M. A Water-Assisted Catalytic Mechanism in Glycoside Hydrolases Demonstrated on the Staphylococcus aureus Autolysin E. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01064] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jure Borišek
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Sara Pintar
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
- Jozef Stefan International Postgraduate School, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Mitja Ogrizek
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Dušan Turk
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Marjana Novič
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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13
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Nilojan J, Bathige SDNK, Kugapreethan R, Thulasitha WS, Nam BH, Lee J. Molecular, transcriptional and functional insights into duplicated goose-type lysozymes from Sebastes schlegelii and their potential immunological role. FISH & SHELLFISH IMMUNOLOGY 2017; 67:66-77. [PMID: 28528707 DOI: 10.1016/j.fsi.2017.05.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 05/09/2017] [Accepted: 05/14/2017] [Indexed: 06/07/2023]
Abstract
Black rockfish (Sebastes schlegelii), an important aquaculture species in Korea, has been affected by bacterial diseases leading to a drastic decline in production. Goose-type lysozyme (LysG) is a key enzyme of the innate immune system to eradicate bacterial infections. In this study, two isoforms of LysG from black rockfish, designated as RfLysG1 and RfLysG2, have been identified and characterized at the molecular, transcriptional, and functional levels. The deduced amino acid sequences had the LysG family characteristics and exhibited conserved properties, including active residues and domains. The cDNA sequences of RfLysG1 and RfLysG2 were 1514 bp and 900 bp in length, respectively. The 567-bp open reading frame (ORF) of RfLysG1 encoded a protein of 188 amino acids with molecular mass 20.11 kDa, and the 600-bp ORF of RfLysG2 encoded a polypeptide with 199 amino acids and molecular mass of 22.19 kDa. Homology studies indicated that RfLysG1 showed the highest identity (84.6%) with LysG-B of Oplegnathus fasciatus, while RfLysG2 showed the highest identity (74.4%) with LysG of Siniperca chuatsi. Both sequences possessed a soluble lytic trans-glycosylase domain. Both lacked signal peptide and they were not identified as proteins secreted by non-classical pathway by the SecretomeP server. Transcriptional analysis of the two genes showed constitutive expression, where both genes were highly expressed in blood under normal physiological conditions. In response to the immune challenges lipopolysaccharide (LPS), Streptococcus iniae, and poly I:C injection, the expression of RfLysG1 and RfLysG2 was significantly upregulated in blood and spleen tissues in a time-dependent manner. Turbidimetric assays indicated that both recombinant proteins tagged with maltose-binding protein (MBP) were reactive against several Gram-positive and Gram-negative bacteria, but MBP was inactive. Optimum temperatures for the recombinant RfLysG1 and RfLysG2 were 40 °C and 50 °C, respectively, and both were highly active at pH 3.0. The results provide evidence for the vital immunological role and bacteriolytic potential of RfLysG1 and RfLysG2.
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Affiliation(s)
- Jehanathan Nilojan
- Department of Marine Life Sciences, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - S D N K Bathige
- Department of Marine Life Sciences, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Roopasingam Kugapreethan
- Department of Marine Life Sciences, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - W S Thulasitha
- Department of Marine Life Sciences, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Department of Zoology, University of Jaffna, Jaffna 40000, Sri Lanka
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, 408-1 Sirang-ri, Gijang-up, Gijang-gun, Busan 46083, Republic of Korea
| | - Jehee Lee
- Department of Marine Life Sciences, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea.
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14
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Mihelič M, Vlahoviček-Kahlina K, Renko M, Mesnage S, Doberšek A, Taler-Verčič A, Jakas A, Turk D. The mechanism behind the selection of two different cleavage sites in NAG-NAM polymers. IUCRJ 2017; 4:185-198. [PMID: 28250957 PMCID: PMC5330529 DOI: 10.1107/s2052252517000367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 01/09/2017] [Indexed: 06/06/2023]
Abstract
Peptidoglycan is a giant molecule that forms the cell wall that surrounds bacterial cells. It is composed of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) residues connected by β-(1,4)-glycosidic bonds and cross-linked with short polypeptide chains. Owing to the increasing antibiotic resistance against drugs targeting peptidoglycan synthesis, studies of enzymes involved in the degradation of peptidoglycan, such as N-acetylglucos-aminidases, may expose new, valuable drug targets. The scientific challenge addressed here is how lysozymes, muramidases which are likely to be the most studied enzymes ever, and bacterial N-acetylglucosaminidases discriminate between two glycosidic bonds that are different in sequence yet chemically equivalent in the same NAG-NAM polymers. In spite of more than fifty years of structural studies of lysozyme, it is still not known how the enzyme selects the bond to be cleaved. Using macromolecular crystallography, chemical synthesis and molecular modelling, this study explains how these two groups of enzymes based on an equivalent structural core exhibit a difference in selectivity. The crystal structures of Staphylococcus aureusN-acetylglucosaminidase autolysin E (AtlE) alone and in complex with fragments of peptidoglycan revealed that N-acetylglucosaminidases and muramidases approach the substrate at alternate glycosidic bond positions from opposite sides. The recognition pocket for NAM residues in the active site of N-acetylglucosaminidases may make them a suitable drug target.
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Affiliation(s)
- Marko Mihelič
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | | | - Miha Renko
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Stephane Mesnage
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, England
| | - Andreja Doberšek
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Ajda Taler-Verčič
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Andreja Jakas
- Division of Organic Chemistry, Rudjer Boskovic Institute, Bijenicka cesta 54, 10000 Zagreb, Croatia
| | - Dušan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
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15
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Jin Y, Petricevic M, John A, Raich L, Jenkins H, Portela
De Souza L, Cuskin F, Gilbert H, Rovira C, Goddard-Borger ED, Williams SJ, Davies GJ. A β-Mannanase with a Lysozyme-like Fold and a Novel Molecular Catalytic Mechanism. ACS CENTRAL SCIENCE 2016; 2:896-903. [PMID: 28058278 PMCID: PMC5200933 DOI: 10.1021/acscentsci.6b00232] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Indexed: 06/06/2023]
Abstract
The enzymatic cleavage of β-1,4-mannans is achieved by endo-β-1,4-mannanases, enzymes involved in germination of seeds and microbial hemicellulose degradation, and which have increasing industrial and consumer product applications. β-Mannanases occur in a range of families of the CAZy sequence-based glycoside hydrolase (GH) classification scheme including families 5, 26, and 113. In this work we reveal that β-mannanases of the newly described GH family 134 differ from other mannanase families in both their mechanism and tertiary structure. A representative GH family 134 endo-β-1,4-mannanase from a Streptomyces sp. displays a fold closely related to that of hen egg white lysozyme but acts with inversion of stereochemistry. A Michaelis complex with mannopentaose, and a product complex with mannotriose, reveal ligands with pyranose rings distorted in an unusual inverted chair conformation. Ab initio quantum mechanics/molecular mechanics metadynamics quantified the energetically accessible ring conformations and provided evidence in support of a 1C4 → 3H4‡ → 3S1 conformational itinerary along the reaction coordinate. This work, in concert with that on GH family 124 cellulases, reveals how the lysozyme fold can be co-opted to catalyze the hydrolysis of different polysaccharides in a mechanistically distinct manner.
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Affiliation(s)
- Yi Jin
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, U.K.
| | - Marija Petricevic
- School of Chemistry and Bio21 Molecular Science
and Biotechnology
Institute and Department of Medical Biology, University
of Melbourne, Parkville, Victoria 3010, Australia
| | - Alan John
- School of Chemistry and Bio21 Molecular Science
and Biotechnology
Institute and Department of Medical Biology, University
of Melbourne, Parkville, Victoria 3010, Australia
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
| | - Lluís Raich
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) & IQTCUB, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Huw Jenkins
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, U.K.
| | - Leticia Portela
De Souza
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, U.K.
| | - Fiona Cuskin
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Harry
J. Gilbert
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Carme Rovira
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) & IQTCUB, Universitat de Barcelona, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain
| | - Ethan D. Goddard-Borger
- School of Chemistry and Bio21 Molecular Science
and Biotechnology
Institute and Department of Medical Biology, University
of Melbourne, Parkville, Victoria 3010, Australia
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science
and Biotechnology
Institute and Department of Medical Biology, University
of Melbourne, Parkville, Victoria 3010, Australia
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, U.K.
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16
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Liu QN, Xin ZZ, Zhang DZ, Jiang SH, Chai XY, Li CF, Zhou CL, Tang BP. Molecular identification and expression analysis of a goose-type lysozyme (LysG) gene in yellow catfish Pelteobagrus fulvidraco. FISH & SHELLFISH IMMUNOLOGY 2016; 58:423-428. [PMID: 27645907 DOI: 10.1016/j.fsi.2016.09.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 08/28/2016] [Accepted: 09/15/2016] [Indexed: 06/06/2023]
Abstract
Lysozymes, innate immunity molecules, play a vital role in immune response to pathogens. The yellow catfish Pelteobagrus fulvidraco (Siluriformes: Bagridae) is an economically important fish in China. The aim of this study was to quantify expression of the P. fulvidraco LysG gene (a g-type lysozyme) in response to pathogen-associated molecular patterns (PAMP) challenge. First, the P. fulvidraco LysG gene (PfLysG) was cloned and characterized. The full-length cDNA of PfLysG is 1323 bp, including a 5'-untranslated region (UTR) of 131 bp, a 3'-UTR of 634 bp, and an open reading frame of 558 bp encoding a polypeptide of 185 amino acids, which contains a transglycosylase SLT domain (Pfam01464). The predicted molecular weight of the protein is 20.52 kDa with a pI of 9.08. Two catalytic residues and seven N-acetyl-D-glucosamine binding sites are conserved in the sequence and there is no predicted signal peptide. The deduced PfLysG protein sequence has 84%, 76% and 69% percent identity with the LysGs from Ictalurus furcatus, Danio rerio, and Salmo salar, respectively. The predicted tertiary structure of PfLysG is very similar to that from other animals. Phylogenetic analysis showed that PfLysG is closely related to those from Teleostei. Real-time quantitative reverse transcription-PCR (qPCR) analysis showed that PfLysG was expressed in all examined tissues and most highly expressed in head kidney, spleen, and intestine. After simulated pathogen challenge with lipopolysaccharide and polyriboinosinic polyribocytidylic acid, respectively, the mRNA expression of PfLysG was upregulated significantly at different time points. The results suggest that the identified g-type lysozyme of P. fulvidraco is involved in innate immune responses.
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Affiliation(s)
- Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China
| | - Zhao-Zhe Xin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China
| | - Sen-Hao Jiang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China
| | - Xin-Yue Chai
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China
| | - Chao-Feng Li
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China.
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17
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Ko J, Wan Q, Bathige SDNK, Lee J. Molecular characterization, transcriptional profiling, and antibacterial potential of G-type lysozyme from seahorse (Hippocampus abdominalis). FISH & SHELLFISH IMMUNOLOGY 2016; 58:622-630. [PMID: 27732899 DOI: 10.1016/j.fsi.2016.10.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 10/06/2016] [Accepted: 10/07/2016] [Indexed: 06/06/2023]
Abstract
Lysozymes are a family of enzymes that catalyze the hydrolysis of bacterial cell wall, acting as antimicrobial effectors of the innate immune system. In the present study, an ortholog of goose-type lysozyme (ShLysG) from the big-belly seahorse (Hippocampus abdominalis) was identified and characterized structurally and functionally. The full-length cDNA sequence (1213 bp) of ShLysG is comprised of an open reading frame made up of 552 bp, encoding a polypeptide of 184 amino acid (aa) with a predicted molecular mass of 20 kDa. In silico analysis of ShLysG revealed the absence of signal peptide and the presence of a characteristic bacterial soluble lytic transglycosylase (SLT) domain bearing three catalytic residues (Glu71, Asp84, and Asp95) and seven N-acetyl-d-glucosamine binding sites (Glu71, Asp95, Tyr98, His99, Ile117, Tyr145, and Asn146). Homology analysis demonstrated that the aa sequence of ShLysG shared 60.7-67.4% identity and 72.6-79.3% similarity with the orthologs of other teleosts. Phylogenetic analysis of ShLysG indicated a closest relationship with the ortholog from Gadus morhua. In healthy seahorse, ShLysG mRNA showed a constitutive expression in all the tissues examined, with the highest expression in kidney and the least expression in liver. The ShLysG mRNA levels were also shown significant elevation upon the bacterial and pathogen-associated molecular pattern (PAMPs) challenges. Furthermore, lytic activities of ShLysG recombinant protein were detected against several Gram-negative and Gram-positive bacterial species. Taken together, these results suggest that ShLysG might possess a potential immune defensive role against invading microbial pathogens in seahorse.
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Affiliation(s)
- Jiyeon Ko
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Jeju International Marine Science Research & Education Center, Korea Institute of Ocean Science & Technology (KIOST), Jeju Special Self-Governing Province, 63349, Republic of Korea
| | - Qiang Wan
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea.
| | - S D N K Bathige
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Jehee Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea.
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18
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Sugiyama Y, Gotoh A, Katoh T, Honda Y, Yoshida E, Kurihara S, Ashida H, Kumagai H, Yamamoto K, Kitaoka M, Katayama T. Introduction of H-antigens into oligosaccharides and sugar chains of glycoproteins using highly efficient 1,2-α-l-fucosynthase. Glycobiology 2016; 26:1235-1247. [DOI: 10.1093/glycob/cww085] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 08/16/2016] [Accepted: 08/16/2016] [Indexed: 12/17/2022] Open
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19
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Seppola M, Bakkemo KR, Mikkelsen H, Myrnes B, Helland R, Irwin DM, Nilsen IW. Multiple specialised goose-type lysozymes potentially compensate for an exceptional lack of chicken-type lysozymes in Atlantic cod. Sci Rep 2016; 6:28318. [PMID: 27324690 PMCID: PMC4914998 DOI: 10.1038/srep28318] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/31/2016] [Indexed: 01/05/2023] Open
Abstract
Previous analyses of the Atlantic cod genome showed unique combinations of lacking and expanded number of genes for the immune system. The present study examined lysozyme activity, lysozyme gene distribution and expression in cod. Enzymatic assays employing specific bacterial lysozyme inhibitors provided evidence for presence of g-type, but unexpectedly not for c-type lysozyme activity. Database homology searches failed to identify any c-type lysozyme gene in the cod genome or in expressed sequence tags from cod. In contrast, we identified four g-type lysozyme genes (LygF1a-d) constitutively expressed, although differentially, in all cod organs examined. The active site glutamate residue is replaced by alanine in LygF1a, thus making it enzymatic inactive, while LygF1d was found in two active site variants carrying alanine or glutamate, respectively. In vitro and in vivo infection by the intracellular bacterium Francisella noatunensis gave a significantly reduced LygF1a and b expression but increased expression of the LygF1c and d genes as did also the interferon gamma (IFNγ) cytokine. These results demonstrate a lack of c-type lysozyme that is unprecedented among vertebrates. Our results further indicate that serial gene duplications have produced multiple differentially regulated cod g-type lysozymes with specialised functions potentially compensating for the lack of c-type lysozymes.
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Affiliation(s)
- Marit Seppola
- Department of Medical Biology, UiT-The Arctic University of Norway, Tromsø, Norway
| | | | | | | | - Ronny Helland
- Department of Chemistry, UiT-The Arctic University of Norway, Tromsø, Norway
| | - David M Irwin
- Laboratory Medicine &Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Inge W Nilsen
- Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
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20
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Somboonpatarakun C, Shinya S, Kawaguchi Y, Araki T, Fukamizo T, Klaynongsruang S. A goose-type lysozyme from ostrich (Struthio camelus) egg white: multiple roles of His101 in its enzymatic reaction. Biosci Biotechnol Biochem 2016; 80:264-72. [DOI: 10.1080/09168451.2015.1091716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Abstract
A goose-type lysozyme from ostrich egg white (OEL) was produced by Escherichia coli expression system, and the role of His101 of OEL in the enzymatic reaction was investigated by NMR spectroscopy, thermal unfolding, and theoretical modeling of the enzymatic hydrolysis of hexa-N-acetylchitohexaose, (GlcNAc)6. Although the binding of tri-N-acetylchitotriose, (GlcNAc)3, to OEL perturbed several backbone resonances in the 1H–15N HSQC spectrum, the chemical shift of the backbone resonance of His101 was not significantly affected. However, apparent pKa values of His101 and Lys102 determined from the pH titration curves of the backbone chemical shifts were markedly shifted by (GlcNAc)3 binding. Thermal unfolding experiments and modeling study of (GlcNAc)6 hydrolysis using a His101-mutated OEL (H101A-OEL) revealed that the His101 mutation affected not only sugar residue affinities at subsites −3 and −2 but also the rate constant for bond cleavage. His101 appears to play multiple roles in the substrate binding and the catalytic reaction.
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Affiliation(s)
- Chalermchai Somboonpatarakun
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
| | - Shoko Shinya
- Department of Advanced Bioscience, Kinki University, Nara, Japan
| | - Yuya Kawaguchi
- Department of Bioscience, School of Agriculture, Kyushu Tokai University, Kumamoto, Japan
| | - Tomohiro Araki
- Department of Bioscience, School of Agriculture, Kyushu Tokai University, Kumamoto, Japan
| | - Tamo Fukamizo
- Department of Advanced Bioscience, Kinki University, Nara, Japan
| | - Sompong Klaynongsruang
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen University, Khon Kaen, Thailand
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21
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Kumaresan V, Bhatt P, Ganesh MR, Harikrishnan R, Arasu M, Al-Dhabi NA, Pasupuleti M, Marimuthu K, Arockiaraj J. A novel antimicrobial peptide derived from fish goose type lysozyme disrupts the membrane of Salmonella enterica. Mol Immunol 2015; 68:421-33. [PMID: 26477736 DOI: 10.1016/j.molimm.2015.10.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/30/2015] [Accepted: 10/02/2015] [Indexed: 12/21/2022]
Abstract
In aquaculture, accumulation of antibiotics resulted in development of resistance among bacterial pathogens. Consequently, it became mandatory to find alternative to synthetic antibiotics. Antimicrobial peptides (AMPs) which are described as evolutionary ancient weapons have been considered as promising alternates in recent years. In this study, a novel antimicrobial peptide had been derived from goose type lysozyme (LyzG) which was identified from the cDNA library of freshwater fish Channa striatus (Cs). The identified lysozyme cDNA contains 585 nucleotides which encodes a protein of 194 amino acids. CsLyzG was closely related to Siniperca chuatsi with 92.8% homology. The depicted protein sequence contained a GEWL domain with conserved GLMQ motif, 7 active residues and 2 catalytic residues. Gene expression analysis revealed that CsLyzG was distributed in major immune organs with highest expression in head kidney. Results of temporal expression analysis after bacterial (Aeromonas hydrophila) and fungal (Aphanomyces invadans) challenges indicated a stimulant-dependent expression pattern of CsLyzG. Two antimicrobial peptides IK12 and TS10 were identified from CsLyzG and synthesized. Antibiogram showed that IK12 was active against Salmonella enterica, a major multi-drug resistant (MDR) bacterial pathogen which produces beta lactamase. The IK12 induced loss of cell viability in the bacterial pathogen. Flow cytometry assay revealed that IK12 disrupt the membrane of S. enterica which is confirmed by scanning electron microscope (SEM) analysis that reveals blebs around the bacterial cell membrane. Conclusively, CsLyzG is a potential innate immune component and the identified antimicrobial peptide has great caliber to be used as an ecofriendly antibacterial substance in aquaculture.
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Affiliation(s)
- Venkatesh Kumaresan
- Division of Fisheries Biotechnology & Molecular Biology, Department of Biotechnology, Faculty of Science and Humanities, SRM University, Kattankulathur, 603 203 Chennai, Tamil Nadu, India
| | - Prasanth Bhatt
- Division of Fisheries Biotechnology & Molecular Biology, Department of Biotechnology, Faculty of Science and Humanities, SRM University, Kattankulathur, 603 203 Chennai, Tamil Nadu, India
| | - Munuswamy-Ramanujam Ganesh
- Interdisciplinary Institute of Indian System of Medicine, SRM University, Kattankulathur, 603 203 Chennai, Tamil Nadu, India
| | - Ramasamy Harikrishnan
- Department of Zoology, Pachaiyappa's College for Men, Kanchipuram 631 501 Tamil Nadu, India
| | - MariadhasValan Arasu
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mukesh Pasupuleti
- Lab PCN 206, Microbiology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226 031 Uttar Pradesh, India
| | - Kasi Marimuthu
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Semeling Bedong, 08100 Bedong, Kedah, Malaysia
| | - Jesu Arockiaraj
- Division of Fisheries Biotechnology & Molecular Biology, Department of Biotechnology, Faculty of Science and Humanities, SRM University, Kattankulathur, 603 203 Chennai, Tamil Nadu, India.
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22
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Hussain M, Zahoor T, Anjum FM, Shahid M, Saeed F. Isolation and Characterization of Buffalo Milk Lysozyme. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2015. [DOI: 10.1080/10942912.2013.809540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Buonocore F, Randelli E, Trisolino P, Facchiano A, de Pascale D, Scapigliati G. Molecular characterization, gene structure and antibacterial activity of a g-type lysozyme from the European sea bass (Dicentrarchus labrax L.). Mol Immunol 2014; 62:10-8. [DOI: 10.1016/j.molimm.2014.05.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 05/25/2014] [Indexed: 10/25/2022]
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24
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Sammito M, Meindl K, de Ilarduya IM, Millán C, Artola-Recolons C, Hermoso JA, Usón I. Structure solution with ARCIMBOLDO using fragments derived from distant homology models. FEBS J 2014; 281:4029-45. [PMID: 24976038 DOI: 10.1111/febs.12897] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/19/2014] [Accepted: 06/25/2014] [Indexed: 11/30/2022]
Abstract
Molecular replacement, one of the general methods used to solve the crystallographic phase problem, relies on the availability of suitable models for placement in the unit cell of the unknown structure in order to provide initial phases. ARCIMBOLDO, originally conceived for ab initio phasing, operates at the limit of this approach, using small, very accurate fragments such as polyalanine α-helices. A distant homolog may contain accurate building blocks, but it may not be evident which sub-structure is the most suitable purely from the degree of conservation. Trying out all alternative possibilities in a systematic way is computationally expensive, even if effective. In the present study, the solution of the previously unknown structure of MltE, an outer membrane-anchored endolytic peptidoglycan lytic transglycosylase from Escherichia coli, is described. The asymmetric unit contains a dimer of this 194 amino acid protein. The closest available homolog was the catalytic domain of Slt70 (PDB code 1QTE). Originally, this template was used omitting contiguous spans of aminoacids and setting as many ARCIMBOLDO runs as models, each aiming to locate two copies sequentially with PHASER. Fragment trimming against the correlation coefficient prior to expansion through density modification and autotracing in SHELXE was essential. Analysis of the figures of merit led to the strategy to optimize the search model against the experimental data now implemented within ARCIMBOLDO-SHREDDER (http://chango.ibmb.csic.es/SHREDDER). In this strategy, the initial template is systematically shredded, and fragments are scored against each unique solution of the rotation function. Results are combined into a score per residue and the template is trimmed accordingly.
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Affiliation(s)
- Massimo Sammito
- Instituto de Biología Molecular de Barcelona, Barcelona Science Park, Barcelona, Spain
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25
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Irwin DM. Evolution of the vertebrate goose-type lysozyme gene family. BMC Evol Biol 2014; 14:188. [PMID: 25167808 PMCID: PMC4243810 DOI: 10.1186/s12862-014-0188-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 08/12/2014] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Lysozyme g is an antibacterial enzyme that was first found in the eggs of some birds, but recently has been found in additional species, including non-vertebrates. Some previously characterized lysozyme g sequences are suggested to have altered secretion potential and enzymatic activity, however the distribution of these altered sequences is unknown. Duplicated copies of the lysozyme g gene exist in some species; however, the origins of the duplicates and their roles in altered function are unclear. RESULTS We identified 234 lysozyme g sequences from 118 vertebrate species, including 181 sequences that are full or near full length representing all vertebrate classes except cartilaginous fish. Phylogenetic analysis shows that most lysozyme g gene duplicates are recent or lineage specific events, however three amplification events are more ancient, those in an early amniote, an early mammal, and an early teleost. The older gene duplications are associated with changes in function, including changes in secretion potential and muramidase antibacterial enzymatic activity. CONCLUSIONS Lysozyme g is an essential muramidase enzyme that is widespread in vertebrates. Duplication of the lysozyme g gene, and the retention of non-secreted isozymes that have lost enzymatic activity indicate that lysozyme g has an activity other than the muramidase activity associated with being an antibacterial enzyme.
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Affiliation(s)
- David M Irwin
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto M5S 1A8, Ontario, Canada.
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26
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Bathige SDNK, Umasuthan N, Whang I, Lim BS, Jung HB, Lee J. Evidences for the involvement of an invertebrate goose-type lysozyme in disk abalone immunity: cloning, expression analysis and antimicrobial activity. FISH & SHELLFISH IMMUNOLOGY 2013; 35:1369-1379. [PMID: 23973847 DOI: 10.1016/j.fsi.2013.07.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 07/29/2013] [Accepted: 07/30/2013] [Indexed: 06/02/2023]
Abstract
Lysozymes are ubiquitously distributed enzymes with hydrolytic activity against bacterial peptidoglycan and function to protect organisms from microbial pathogens. In this study, an invertebrate goose-type lysozyme, designated as abLysG, was identified in the disk abalone, Haliotis discus discus. The full-length cDNA of abLysG was 894 bp in length with an open reading frame of 789 bp encoding a polypeptide of 263 amino acids containing a signal peptide and a characteristic soluble lytic transglycosylase domain. Six cysteine residues and two catalytic residues (Glu(142) and Asp(168)) conserved among molluscs were also identified. The 3D homology structural models of abLysG and hen egg white lysozyme had similar conformations of the active sites involved in the binding of substrate. BAC sequence data revealed that the genomic structure of disk abalone g-type lysozyme comprises 7 exons with 6 intervening introns. The deduced amino acid sequence of abLysG shared 45.2-61.6% similarity with those of other molluscs and vertebrates. The TFSEARCH server predicted a variety of transcription factor-binding sites in the 5'-flanking region of the abLysG gene, some of which are involved in transcriptional regulation of the lysozyme gene. abLysG expression was detected in multiple tissues with the highest expression in mantle. Moreover, qPCR analysis of abLysG mRNA expression demonstrated significant up-regulation in gill in response to infection by live bacteria (Vibrio parahaemolyticus and Listeria monocytogenes), virus (viral hemorrhagic septicemia) and bacterial mimics (LPS and PGN). Expression of the recombinant disk abalone g-type lysozyme in Escherichia coli BL21, demonstrated its bacteriolytic activity against several Gram-negative and Gram-positive bacterial species. Collectively these data suggest that abLysG is an antimicrobial enzyme with a potential role in the disk abalone innate immune system to protect it from bacterial and viral infections.
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Affiliation(s)
- S D N K Bathige
- Department of Marine Life Sciences, School of Marine Biomedical Sciences, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea
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27
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Pallara C, Jiménez-García B, Pérez-Cano L, Romero-Durana M, Solernou A, Grosdidier S, Pons C, Moal IH, Fernandez-Recio J. Expanding the frontiers of protein-protein modeling: from docking and scoring to binding affinity predictions and other challenges. Proteins 2013; 81:2192-200. [PMID: 23934865 DOI: 10.1002/prot.24387] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 07/31/2013] [Accepted: 08/01/2013] [Indexed: 11/06/2022]
Abstract
In addition to protein-protein docking, this CAPRI edition included new challenges, like protein-water and protein-sugar interactions, or the prediction of binding affinities and ΔΔG changes upon mutation. Regarding the standard protein-protein docking cases, our approach, mostly based on the pyDock scheme, submitted correct models as predictors and as scorers for 67% and 57% of the evaluated targets, respectively. In this edition, available information on known interface residues hardly made any difference for our predictions. In one of the targets, the inclusion of available experimental small-angle X-ray scattering (SAXS) data using our pyDockSAXS approach slightly improved the predictions. In addition to the standard protein-protein docking assessment, new challenges were proposed. One of the new problems was predicting the position of the interface water molecules, for which we submitted models with 20% and 43% of the water-mediated native contacts predicted as predictors and scorers, respectively. Another new problem was the prediction of protein-carbohydrate binding, where our submitted model was very close to being acceptable. A set of targets were related to the prediction of binding affinities, in which our pyDock scheme was able to discriminate between natural and designed complexes with area under the curve = 83%. It was also proposed to estimate the effect of point mutations on binding affinity. Our approach, based on machine learning methods, showed high rates of correctly classified mutations for all cases. The overall results were highly rewarding, and show that the field is ready to move forward and face new interesting challenges in interactomics.
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Affiliation(s)
- Chiara Pallara
- Joint BSC-IRB Research Programme in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
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28
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Wang T, Ding J, Zhang Y, Wang DC, Liu W. Complex structure of type VI peptidoglycan muramidase effector and a cognate immunity protein. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1889-900. [PMID: 24100309 PMCID: PMC3792639 DOI: 10.1107/s090744491301576x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 06/06/2013] [Indexed: 11/19/2022]
Abstract
The type VI secretion system (T6SS) is a bacterial protein-export machine that is capable of delivering virulence effectors between Gram-negative bacteria. The T6SS of Pseudomonas aeruginosa transports two lytic enzymes, Tse1 and Tse3, to degrade cell-wall peptidoglycan in the periplasm of rival bacteria that are competing for niches via amidase and muramidase activities, respectively. Two cognate immunity proteins, Tsi1 and Tsi3, are produced by the bacterium to inactivate the two antibacterial effectors, thereby protecting its siblings from self-intoxication. Recently, Tse1-Tsi1 has been structurally characterized. Here, the structure of the Tse3-Tsi3 complex is reported at 1.9 Å resolution. The results reveal that Tse3 contains a C-terminal catalytic domain that adopts a soluble lytic transglycosylase (SLT) fold in which three calcium-binding sites were surprisingly observed close to the catalytic Glu residue. The electrostatic properties of the substrate-binding groove are also distinctive from those of known structures with a similar fold. All of these features imply that a unique catalytic mechanism is utilized by Tse3 in cleaving glycosidic bonds. Tsi3 comprises a single domain showing a β-sandwich architecture that is reminiscent of the immunoglobulin fold. Three loops of Tsi3 insert deeply into the groove of Tse3 and completely occlude its active site, which forms the structural basis of Tse3 inactivation. This work is the first crystallographic report describing the three-dimensional structure of the Tse3-Tsi3 effector-immunity pair.
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Affiliation(s)
- Tianyu Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Jinjing Ding
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Ying Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Da-Cheng Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Wei Liu
- Institute of Immunology, The Third Military Medical University, Chongqing 400038, People’s Republic of China
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29
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Xu Q, Chiu HJ, Farr CL, Jaroszewski L, Knuth MW, Miller MD, Lesley SA, Godzik A, Elsliger MA, Deacon AM, Wilson IA. Structures of a bifunctional cell wall hydrolase CwlT containing a novel bacterial lysozyme and an NlpC/P60 DL-endopeptidase. J Mol Biol 2013; 426:169-84. [PMID: 24051416 DOI: 10.1016/j.jmb.2013.09.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/07/2013] [Accepted: 09/11/2013] [Indexed: 11/17/2022]
Abstract
Tn916-like conjugative transposons carrying antibiotic resistance genes are found in a diverse range of bacteria. Orf14 within the conjugation module encodes a bifunctional cell wall hydrolase CwlT that consists of an N-terminal bacterial lysozyme domain (N-acetylmuramidase, bLysG) and a C-terminal NlpC/P60 domain (γ-d-glutamyl-l-diamino acid endopeptidase) and is expected to play an important role in the spread of the transposons. We determined the crystal structures of CwlT from two pathogens, Staphylococcus aureus Mu50 (SaCwlT) and Clostridium difficile 630 (CdCwlT). These structures reveal that NlpC/P60 and LysG domains are compact and conserved modules, connected by a short flexible linker. The LysG domain represents a novel family of widely distributed bacterial lysozymes. The overall structure and the active site of bLysG bear significant similarity to other members of the glycoside hydrolase family 23 (GH23), such as the g-type lysozyme (LysG) and Escherichia coli lytic transglycosylase MltE. The active site of bLysG contains a unique structural and sequence signature (DxxQSSES+S) that is important for coordinating a catalytic water. Molecular modeling suggests that the bLysG domain may recognize glycan in a similar manner to MltE. The C-terminal NlpC/P60 domain contains a conserved active site (Cys-His-His-Tyr) that appears to be specific to murein tetrapeptide. Access to the active site is likely regulated by isomerism of a side chain atop the catalytic cysteine, allowing substrate entry or product release (open state), or catalysis (closed state).
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Affiliation(s)
- Qingping Xu
- Joint Center for Structural Genomics (http://www.jcsg.org); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics (http://www.jcsg.org); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Carol L Farr
- Joint Center for Structural Genomics (http://www.jcsg.org); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics (http://www.jcsg.org); Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Mark W Knuth
- Joint Center for Structural Genomics (http://www.jcsg.org); Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Mitchell D Miller
- Joint Center for Structural Genomics (http://www.jcsg.org); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Scott A Lesley
- Joint Center for Structural Genomics (http://www.jcsg.org); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Adam Godzik
- Joint Center for Structural Genomics (http://www.jcsg.org); Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics (http://www.jcsg.org); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ashley M Deacon
- Joint Center for Structural Genomics (http://www.jcsg.org); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ian A Wilson
- Joint Center for Structural Genomics (http://www.jcsg.org); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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30
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Li L, Zhang W, Liu Q, Gao Y, Gao Y, Wang Y, Wang DZ, Li Z, Wang T. Structural Insights on the bacteriolytic and self-protection mechanism of muramidase effector Tse3 in Pseudomonas aeruginosa. J Biol Chem 2013; 288:30607-30613. [PMID: 24025333 DOI: 10.1074/jbc.c113.506097] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The warfare among microbial species as well as between pathogens and hosts is fierce, complicated, and continuous. In Pseudomonas aeruginosa, the muramidase effector Tse3 (Type VI secretion exported 3) can be injected into the periplasm of neighboring bacterial competitors by a Type VI secretion apparatus, eventually leading to cell lysis and death. However, P. aeruginosa protects itself from lysis by expressing immune protein Tsi3 (Type six secretion immunity 3). Here, we report the crystal structure of the Tse3-Tsi3 complex at 1.8 Å resolution, revealing that Tse3 possesses one open accessible, goose-type lysozyme-like domain with peptidoglycan hydrolysis activity. Calcium ions bind specifically in the Tse3 active site and are identified to be crucial for its bacteriolytic activity. In combination with biochemical studies, the structural basis of self-protection mechanism of Tsi3 is also elucidated, thus providing an understanding and new insights into the effectors of Type VI secretion system.
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Affiliation(s)
- Lianbo Li
- From the Laboratory for Computational Chemistry and Drug Design and
| | - Weili Zhang
- From the Laboratory for Computational Chemistry and Drug Design and
| | - Qisong Liu
- Key Laboratory of Chemical Genomics, School of Chemical Biology & Biotechnology, Peking University, Shenzhen Graduate School, Shenzhen 518055, China
| | - Yu Gao
- From the Laboratory for Computational Chemistry and Drug Design and
| | - Ying Gao
- From the Laboratory for Computational Chemistry and Drug Design and
| | - Yun Wang
- From the Laboratory for Computational Chemistry and Drug Design and
| | - David Zhigang Wang
- Key Laboratory of Chemical Genomics, School of Chemical Biology & Biotechnology, Peking University, Shenzhen Graduate School, Shenzhen 518055, China.
| | - Zigang Li
- Key Laboratory of Chemical Genomics, School of Chemical Biology & Biotechnology, Peking University, Shenzhen Graduate School, Shenzhen 518055, China.
| | - Tao Wang
- From the Laboratory for Computational Chemistry and Drug Design and.
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31
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Wang R, Feng J, Li C, Liu S, Zhang Y, Liu Z. Four lysozymes (one c-type and three g-type) in catfish are drastically but differentially induced after bacterial infection. FISH & SHELLFISH IMMUNOLOGY 2013; 35:136-145. [PMID: 23639933 DOI: 10.1016/j.fsi.2013.04.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/22/2013] [Accepted: 04/13/2013] [Indexed: 06/02/2023]
Abstract
Lysozyme is an important component of the innate immune system. In this study, four lysozyme genes including one c-type lysozyme and three g-type lysozymes were identified from channel catfish (Ictalurus punctatus). The lysozyme genes are highly conserved in their structural features as compared to those from other species. Phylogenetic analyses were conducted allowing annotation of these genes. Additional analyses using conserved syntenies allowed determination of orthologies for the c-type lysozyme. Phylogenetic analysis indicated that the g-type lysozyme may have gone through species-specific gene duplications leading to multiple copies in some teleost species. Channel catfish possessed three copies of the g-type lysozyme genes. Expression analysis revealed that the catfish lysozyme genes were expressed in a broad range of tissues. The highest levels of expression were found in head kidney, liver, spleen, and trunk kidney, compatible with the immune functions of these tissues/organs. The c-type and g-type lysozymes were drastically induced after bacterial infection, but exhibited large differences in the extent of induction and the tissue with the highest level of induction, with the g-type lysozyme being most highly induced in the head kidney whereas the other three lysozymes being most highly induced in the liver, suggesting their cooperative actions in the immune responses but difference in their detailed functions.
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Affiliation(s)
- Ruijia Wang
- Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
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Arimori T, Kawamoto N, Shinya S, Okazaki N, Nakazawa M, Miyatake K, Fukamizo T, Ueda M, Tamada T. Crystal structures of the catalytic domain of a novel glycohydrolase family 23 chitinase from Ralstonia sp. A-471 reveals a unique arrangement of the catalytic residues for inverting chitin hydrolysis. J Biol Chem 2013; 288:18696-706. [PMID: 23658014 DOI: 10.1074/jbc.m113.462135] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chitinase C from Ralstonia sp. A-471 (Ra-ChiC) has a catalytic domain sequence similar to goose-type (G-type) lysozymes and, unlike other chitinases, belongs to glycohydrolase (GH) family 23. Using NMR spectroscopy, however, Ra-ChiC was found to interact only with the chitin dimer but not with the peptidoglycan fragment. Here we report the crystal structures of wild-type, E141Q, and E162Q of the catalytic domain of Ra-ChiC with or without chitin oligosaccharides. Ra-ChiC has a substrate-binding site including a tunnel-shaped cavity, which determines the substrate specificity. Mutation analyses based on this structural information indicated that a highly conserved Glu-141 acts as a catalytic acid, and that Asp-226 located at the roof of the tunnel activates a water molecule as a catalytic base. The unique arrangement of the catalytic residues makes a clear contrast to the other GH23 members and also to inverting GH19 chitinases.
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Affiliation(s)
- Takao Arimori
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
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Leysen S, Vanderkelen L, Weeks SD, Michiels CW, Strelkov SV. Structural basis of bacterial defense against g-type lysozyme-based innate immunity. Cell Mol Life Sci 2013; 70:1113-22. [PMID: 23086131 PMCID: PMC11113182 DOI: 10.1007/s00018-012-1184-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 09/21/2012] [Accepted: 09/27/2012] [Indexed: 10/27/2022]
Abstract
Gram-negative bacteria can produce specific proteinaceous inhibitors to defend themselves against the lytic action of host lysozymes. So far, four different lysozyme inhibitor families have been identified. Here, we report the crystal structure of the Escherichia coli periplasmic lysozyme inhibitor of g-type lysozyme (PliG-Ec) in complex with Atlantic salmon g-type lysozyme (SalG) at a resolution of 0.95 Å, which is exceptionally high for a complex of two proteins. The structure reveals for the first time the mechanism of g-type lysozyme inhibition by the PliG family. The latter contains two specific conserved regions that are essential for its inhibitory activity. The inhibitory complex formation is based on a double 'key-lock' mechanism. The first key-lock element is formed by the insertion of two conserved PliG regions into the active site of the lysozyme. The second element is defined by a distinct pocket of PliG accommodating a lysozyme loop. Computational analysis indicates that this pocket represents a suitable site for small molecule binding, which opens an avenue for the development of novel antibacterial agents that suppress the inhibitory activity of PliG.
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Affiliation(s)
- S. Leysen
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Herestraat 49 bus 822, 3000 Leuven, Belgium
| | - L. Vanderkelen
- Laboratory of Food Microbiology, Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - S. D. Weeks
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Herestraat 49 bus 822, 3000 Leuven, Belgium
| | - C. W. Michiels
- Laboratory of Food Microbiology, Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - S. V. Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Herestraat 49 bus 822, 3000 Leuven, Belgium
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Wang Q, Zhang L, Zhao J, You L, Wu H. Two goose-type lysozymes in Mytilus galloprovincialis: possible function diversification and adaptive evolution. PLoS One 2012; 7:e45148. [PMID: 23028813 PMCID: PMC3448621 DOI: 10.1371/journal.pone.0045148] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 08/14/2012] [Indexed: 11/18/2022] Open
Abstract
Two goose-type lysozymes (designated as MGgLYZ1 and MGgLYZ2) were identified from the mussel Mytilus galloprovincialis. MGgLYZ1 mRNA was widely expressed in the examined tissues and responded sensitively to bacterial challenge in hemocytes, while MGgLYZ2 mRNA was predominately expressed and performed its functions in hepatopancreas. However, immunolocalization analysis showed that both these lysozymes were expressed in all examined tissues with the exception of adductor muscle. Recombinant MGgLYZ1 and MGgLYZ2 could inhibit the growth of several Gram-positive and Gram-negative bacteria, and they both showed the highest activity against Pseudomonas putida with the minimum inhibitory concentration (MIC) of 0.95-1.91 µM and 1.20-2.40 µM, respectively. Protein sequences analysis revealed that MGgLYZ2 had lower isoelectric point and less protease cutting sites than MGgLYZ1. Recombinant MGgLYZ2 exhibited relative high activity at acidic pH of 4-5, while MGgLYZ1 have an optimum pH of 6. These results indicated MGgLYZ2 adapted to acidic environment and perhaps play an important role in digestion. Genomic structure analysis suggested that both MGgLYZ1 and MGgLYZ2 genes are composed of six exons with same length and five introns, indicating these genes were conserved and might originate from gene duplication during the evolution. Selection pressure analysis showed that MGgLYZ1 was under nearly neutral selection while MGgLYZ2 evolved under positive selection pressure with three positively selected amino acid residues (Y(102), L(200) and S(202)) detected in the mature peptide. All these findings suggested MGgLYZ2 perhaps served as a digestive lysozyme under positive selection pressure during the evolution while MGgLYZ1 was mainly involved in innate immune responses.
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Affiliation(s)
| | | | - Jianmin Zhao
- Key Laboratory of Coastal Zone Environmental Processes, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, PR China
- * E-mail: (JZ); (HW)
| | | | - Huifeng Wu
- Key Laboratory of Coastal Zone Environmental Processes, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, PR China
- * E-mail: (JZ); (HW)
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Ponce M, Salas-Leiton E, Garcia-Cegarra A, Boglino A, Coste O, Infante C, Gisbert E, Rebordinos L, Manchado M. Genomic characterization, phylogeny and gene regulation of g-type lysozyme in sole (Solea senegalensis). FISH & SHELLFISH IMMUNOLOGY 2011; 31:925-937. [PMID: 21906680 DOI: 10.1016/j.fsi.2011.08.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 08/05/2011] [Accepted: 08/19/2011] [Indexed: 05/31/2023]
Abstract
The g-type lysozyme is a key protein of the innate immune system to fight bacterial infections. In this study we cloned and characterized the gene encoding for g-type lysozyme in Senegalese sole (Solea senegalensis). The deduced amino acid sequence comprised 195 residues containing the three conserved catalytic residues and two cysteines. A BAC analysis revealed that the gene is structured in 5 exons and 4 introns. Also, two polyadenylation signals that generate two cDNAs differing in 3'-UTR length were detected. Promoter analysis showed the presence of the main cis-acting elements involved in the transcriptional regulation of the gene. At genomic level, the g-type lysozyme was associated with mucolipin 1 and the peptidoglycan recognition protein 2 conforming a cluster of antidefensive genes with a well-conserved synteny across Percomorpha. FISH analysis using the BAC clone revealed a single hybridization signal located in an acrocentric chromosome pair. The phylogenetic analysis confirmed that the g-type lysozyme represents a complex group in fish that has been shaped by gene duplications and diversification with several positions under Darwinian selection. Expression analysis in juvenile tissues indicated that transcript levels were higher in gills, spleen and heart. During development, gene expression activated just at the beginning of metamorphosis, increasing progressively until climax. Hormonal treatments demonstrated that this gene was regulated positively by thyroid hormones during development and negatively by dexamethasone. In contrast, no response was observed after all-trans retinoic acid or 4-diethylaminobenzaldehyde treatments. Finally, treatments using lipopolysaccharide, lipoteichoic acid, peptidoglycan, zymosan and poly(I:C) activated gene expression in a time- and tissue-specific manner. Taken together, data indicate that g-type lysozyme is a high evolutionary conserved gene that diversified to adapt to changing environment and pathogen conditions. Gene expression can be activated by diverse pathogen stimuli and modulated by physiological factors with important consequences for the aquaculture of this species.
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Affiliation(s)
- Marian Ponce
- IFAPA centro El Toruño, Junta de Andalucía, Camino Tiro de pichón s/n, 11500 El Puerto de Santa María, Cádiz, Spain
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36
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Shinya S, Ohnuma T, Kawamura S, Torikata T, Nishimura S, Katoh E, Fukamizo T. Interaction of a goose-type lysozyme with chitin oligosaccharides as determined by NMR spectroscopy. ACTA ACUST UNITED AC 2011; 150:569-77. [DOI: 10.1093/jb/mvr101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Artola-Recolons C, Carrasco-López C, Llarrull LI, Kumarasiri M, Lastochkin E, Martínez de Ilarduya I, Meindl K, Usón I, Mobashery S, Hermoso JA. High-resolution crystal structure of MltE, an outer membrane-anchored endolytic peptidoglycan lytic transglycosylase from Escherichia coli. Biochemistry 2011; 50:2384-6. [PMID: 21341761 DOI: 10.1021/bi200085y] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The crystal structure of the first endolytic peptidoglycan lytic transglycosylase MltE from Escherichia coli is reported here. The degradative activity of this enzyme initiates the process of cell wall recycling, which is an integral event in the existence of bacteria. The structure sheds light on how MltE recognizes its substrate, the cell wall peptidoglycan. It also explains the ability of this endolytic enzyme to cleave in the middle of the peptidoglycan chains. Furthermore, the structure reveals how the enzyme is sequestered on the inner leaflet of the outer membrane.
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Affiliation(s)
- Cecilia Artola-Recolons
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
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38
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Vanderkelen L, Van Herreweghe JM, Vanoirbeek KGA, Baggerman G, Myrnes B, Declerck PJ, Nilsen IW, Michiels CW, Callewaert L. Identification of a bacterial inhibitor against g-type lysozyme. Cell Mol Life Sci 2011; 68:1053-64. [PMID: 20734102 PMCID: PMC11115080 DOI: 10.1007/s00018-010-0507-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 07/12/2010] [Accepted: 08/10/2010] [Indexed: 01/17/2023]
Abstract
Lysozymes are antibacterial effectors of the innate immune system in animals that hydrolyze peptidoglycan. Bacteria have evolved protective mechanisms that contribute to lysozyme tolerance such as the production of lysozyme inhibitors, but only inhibitors of chicken (c-) and invertebrate (i-) type lysozyme have been identified. We here report the discovery of a novel Escherichia coli inhibitor specific for goose (g-) type lysozymes, which we designate PliG (periplasmic lysozyme inhibitor of g-type lysozyme). Although it does not inhibit c- or i-type lysozymes, PliG shares a structural sequence motif with the previously described PliI and MliC/PliC lysozyme inhibitor families, suggesting a common ancestry and mode of action. Deletion of pliG increased the sensitivity of E. coli to g-type lysozyme. The existence of inhibitors against all major types of animal lysozyme and their contribution to lysozyme tolerance suggest that lysozyme inhibitors may play a role in bacterial interactions with animal hosts.
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Affiliation(s)
- L. Vanderkelen
- Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - J. M. Van Herreweghe
- Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - K. G. A. Vanoirbeek
- Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - G. Baggerman
- Prometa, Interfaculty Centre for Proteomics and Metabolomics, Katholieke Universiteit Leuven, O&N II Herestraat 49, 3000 Leuven, Belgium
| | - B. Myrnes
- Fish Health and Marine Bioprospecting, Nofima Marin, P.O. Box 6122, 9291 Tromsø, Norway
| | - P. J. Declerck
- Laboratory for Pharmaceutical Biology, Katholieke Universiteit Leuven, O&N II Herestraat 49, 3000 Leuven, Belgium
| | - I. W. Nilsen
- Fish Health and Marine Bioprospecting, Nofima Marin, P.O. Box 6122, 9291 Tromsø, Norway
| | - C. W. Michiels
- Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
| | - L. Callewaert
- Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
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Whang I, Lee Y, Lee S, Oh MJ, Jung SJ, Choi CY, Lee WS, Kim HS, Kim SJ, Lee J. Characterization and expression analysis of a goose-type lysozyme from the rock bream Oplegnathus fasciatus, and antimicrobial activity of its recombinant protein. FISH & SHELLFISH IMMUNOLOGY 2011; 30:532-542. [PMID: 21167286 DOI: 10.1016/j.fsi.2010.11.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 11/10/2010] [Accepted: 11/28/2010] [Indexed: 05/30/2023]
Abstract
Lysozyme (muramidase) represents an important defense molecule of the fish innate immune system. Known for its bactericidal properties, lysozyme catalyzes the hydrolysis of β-(1,4)-glycosidic bonds between the N-acetyl glucosamine and N-acetyl muramic acid in the peptidoglycan layer of bacterial cell walls. In this study, the complete coding sequence of a g-type lysozyme (RBgLyz) was identified in the Oplegnathus fasciatus rock bream fish genome by means of multi-tissue normalized cDNA pyrosequencing using Roche 454 GS-FLX™ technology. RBgLyz is composed of 669 bp, with a 567 bp open reading frame that encodes 188 amino acids. Protein motif searches indicated that RBgLyz contains the soluble lytic transglycosylase domain involved in maintaining cell wall integrity. Furthermore, RBgLyz shares significant identity (81.4%) with Chinese perch Siniperca chuatsi. Quantitative real-time RT-PCR analysis results showed that RBgLyz transcripts are constitutively expressed in various tissues from healthy rock breams. In order to determine RBgLyz function in immunity, its expression was analyzed in head kidney following exposure to known immune stimulants or pathogens. RBgLyz transcripts were significantly up-regulated in response to challenge with lipopolysaccharide (LPS) and Edwardsiella tarda, as compared to non-injected control fish. Polyinosinic:polycytidylic acid (poly I:C) dsRNA stimulated a moderate expression of RBgLyz, as did Streptococcus iniae but to a lesser extent. There were no specific time-dependent effects on RBgLyz mRNA expression observed in response to rock bream iridovirus (RBIV) infection. Taken together, the gene expression results indicated that g-type lysozyme plays a role in the innate immune response to LPS, poly I:C, E. tarda and S. iniae in rock bream. Thus, we generated recombinant RBgLyz in an Escherichia coli expression system and characterized its antimicrobial activity. Our results indicated that recombinant RBgLyz had lytic activity against Gram-negative Vibrio salmonicida, Gram-positive Listeria monocytogenes, S. iniae and Micrococcus lysodeikticus. In addition, observations by scanning electron microscope (SEM) confirmed that the cell morphology of M. lysodeikticus was altered in the presence of recombinant RBgLyz.
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Affiliation(s)
- Ilson Whang
- Department of Life Sciences, College of Natural Sciences, Jeju National University, Jeju Special Self-Governing Province 690-756, Republic of Korea
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40
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Zhao L, Sun JS, Sun L. The g-type lysozyme of Scophthalmus maximus has a broad substrate spectrum and is involved in the immune response against bacterial infection. FISH & SHELLFISH IMMUNOLOGY 2011; 30:630-637. [PMID: 21185386 DOI: 10.1016/j.fsi.2010.12.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 12/15/2010] [Accepted: 12/15/2010] [Indexed: 05/30/2023]
Abstract
Lysozyme is a muramidase that inflicts damage on bacterial cell wall by catalyzing the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine in peptidoglycan. Lysozymes are classified into several types, one of which is the goose-type (g-type). In this study, we identified and analyzed a g-type lysozyme (SmLysG) from turbot Scophthalmus maximus. The deduced amino acid sequence of SmLysG contains 193 residues and is most closely related to that of the g-type lysozyme of Scophthalmus rhombus (94% overall identity). SmLysG possesses a Goose Egg White Lysozyme (GEWL) domain with conserved residues essential for catalytic activity. Recombinant SmLysG (rSmLysG) purified from yeast exhibits strong lysozyme activity against Micrococcus luteus. Enzyme assays showed that the optimal temperature and pH of rSmLysG are 30°C and pH 7.0, respectively. Substrate spectrum analysis indicated that rSmLysG inhibited the growth of a number of important fish pathogens of both Gram-negative and Gram-positive natures. SmLysG transcription was detected in multiple tissues and was upregulated in kidney and spleen by experimental challenges with lipopolysaccharide and bacterial pathogens that are, respectively, sensitive to and resistant against the lytic effect of rSmLysG. Comparative analysis showed that although bacterial infection also induced the expression of c-type lysozyme, the induction levels were much lower than those of SmLysG. Taken together, these results indicate that SmLysG is a functional g-type lysozyme with a wide working range and is involved in innate immune defense against general bacterial infection.
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Affiliation(s)
- Lu Zhao
- Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
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41
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Wohlkönig A, Huet J, Looze Y, Wintjens R. Structural relationships in the lysozyme superfamily: significant evidence for glycoside hydrolase signature motifs. PLoS One 2010; 5:e15388. [PMID: 21085702 PMCID: PMC2976769 DOI: 10.1371/journal.pone.0015388] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 08/31/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Chitin is a polysaccharide that forms the hard, outer shell of arthropods and the cell walls of fungi and some algae. Peptidoglycan is a polymer of sugars and amino acids constituting the cell walls of most bacteria. Enzymes that are able to hydrolyze these cell membrane polymers generally play important roles for protecting plants and animals against infection with insects and pathogens. A particular group of such glycoside hydrolase enzymes share some common features in their three-dimensional structure and in their molecular mechanism, forming the lysozyme superfamily. RESULTS Besides having a similar fold, all known catalytic domains of glycoside hydrolase proteins of lysozyme superfamily (families and subfamilies GH19, GH22, GH23, GH24 and GH46) share in common two structural elements: the central helix of the all-α domain, which invariably contains the catalytic glutamate residue acting as general-acid catalyst, and a β-hairpin pointed towards the substrate binding cleft. The invariant β-hairpin structure is interestingly found to display the highest amino acid conservation in aligned sequences of a given family, thereby allowing to define signature motifs for each GH family. Most of such signature motifs are found to have promising performances for searching sequence databases. Our structural analysis further indicates that the GH motifs participate in enzymatic catalysis essentially by containing the catalytic water positioning residue of inverting mechanism. CONCLUSIONS The seven families and subfamilies of the lysozyme superfamily all have in common a β-hairpin structure which displays a family-specific sequence motif. These GH β-hairpin motifs contain potentially important residues for the catalytic activity, thereby suggesting the participation of the GH motif to catalysis and also revealing a common catalytic scheme utilized by enzymes of the lysozyme superfamily.
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Affiliation(s)
- Alexandre Wohlkönig
- Structural Biology Brussels and Molecular and Cellular Interactions, VIB, Brussels, Belgium
| | - Joëlle Huet
- Laboratoire de Chimie Générale, Institut de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium
| | - Yvan Looze
- Laboratoire de Chimie Générale, Institut de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium
| | - René Wintjens
- Laboratoire de Chimie Générale, Institut de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium
- Interdisciplinary Research Institute, USR 3078 CNRS, Villeneuve d'Ascq, France
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Maruyama Y, Ochiai A, Itoh T, Mikami B, Hashimoto W, Murata K. Mutational studies of the peptidoglycan hydrolase FlgJ of Sphingomonas sp. strain A1. J Basic Microbiol 2010; 50:311-7. [PMID: 20586063 DOI: 10.1002/jobm.200900249] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The flagellar protein FlgJ, a member of glycoside hydrolase family 73, has N- and C-terminal domains that are responsible for flagellar rod assembly and peptidoglycan hydrolysis, respectively. The crystal structure of the C-terminal domain of SPH1045 (SPH1045-C), the FlgJ from Sphingomonas sp. strain A1, showed a long cleft formed by two lobes, alpha and beta. In this study, seven site-specific mutants of residues in the cleft were prepared and analyzed. Enzyme activity was reduced most significantly in mutants E185A and Y281A, followed by E224A. A comparison of the crystal structure of the inactive mutant E185A with that of other related enzymes revealed that Glu185 is structurally reasonable as the proton donor and that Tyr281 is close to Glu185. Glu224 is, however, far from the catalytic site, which is inconsistent with the decreased activity exhibited by E224A. The structural flexibility of Glu224 and its neighboring residues observed in SPH1045-C may indicate that this region is able to change its conformation upon substrate binding.
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Affiliation(s)
- Yukie Maruyama
- Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
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Ye X, Zhang L, Tian Y, Tan A, Bai J, Li S. Identification and expression analysis of the g-type and c-type lysozymes in grass carp Ctenopharyngodon idellus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2010; 34:501-509. [PMID: 20034515 DOI: 10.1016/j.dci.2009.12.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 12/15/2009] [Accepted: 12/15/2009] [Indexed: 05/28/2023]
Abstract
Lysozyme is an important molecule of innate immune system for the defense against bacterial infections. We identified two genes encoding g-type and c-type lysozymes from grass carp Ctenopharyngodon idellus by the RACE method. The deduced amino acids of both lysozymes possessed typical structural residues and conserved catalytic sites similar to their counterparts across the species. In contrast, there was only 8.6% similarity of amino acid sequence between these two lysozymes. Phylogenetic analyses revealed that these two genes evolved at different rate. C-type lysozyme of grass carp was diverged early in the evolutionary history. Moreover, the expression patterns of these two genes differed. The mRNA levels of both genes were increased after bacterial infection, but the up-regulation of g-type lysozyme was much stronger than that of c-type lysozyme. We also showed that the c-type and g-type recombinant lysozymes possessed different lytic activities against fish bacterial pathogens. These results confirmed that both lysozymes play important roles in the defense of grass carp against bacterial infections. The g-type lysozyme may be induced for the defense against bacterial infections, while c-type lysozyme might be the main molecule for the house-keeping defense under normal conditions. These two types of lysozymes likely use different mechanisms to regulate their expressions.
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Affiliation(s)
- Xing Ye
- Pearl River Fisheries Research Institute, Key Laboratory of Tropical & Subtropical Fish Breeding & Cultivation, Chinese Academy of Fishery Sciences, No. 1 Xing Yu Road, Guangzhou, PR China.
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Kyomuhendo P, Myrnes B, Brandsdal BO, Smalås AO, Nilsen IW, Helland R. Thermodynamics and structure of a salmon cold active goose-type lysozyme. Comp Biochem Physiol B Biochem Mol Biol 2010; 156:254-63. [PMID: 20398783 DOI: 10.1016/j.cbpb.2010.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Revised: 04/06/2010] [Accepted: 04/06/2010] [Indexed: 11/27/2022]
Abstract
Atlantic salmon goose-type lysozyme (SalG) was previously shown to display features of cold-adaptation as well as renaturation following heat treatment. In this study differential scanning calorimetry (DSC) was carried out to investigate unfolding and potential refolding, while X-ray crystallography was used to study structural factors contributing to the temperature-related characteristics. The recombinant SalG has a melting temperature (T(m)) of 36.8 degrees C under thermal denaturation conditions and regains activity after returning to permissive (low) temperature. Furthermore, refolding is dramatically reduced in solutions with high SalG concentrations, coupled with significant protein precipitation. The structural features of SalG closely resemble those of other g-type lysozymes. However, the N-terminal region of SalG is less anchored to the rest of the molecule due to the absence of disulphide bonds, thus, contributing significantly to the low T(m) of SalG. The absence of disulphide bonds and the distribution of salt bridges may at the same time ease refolding leading to renaturation.
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45
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