101
|
Chen J, An Y, Kumar A, Liu Z. Improvement of chitinase Pachi with nematicidal activities by random mutagenesis. Int J Biol Macromol 2016; 96:171-176. [PMID: 27989482 DOI: 10.1016/j.ijbiomac.2016.11.093] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 11/23/2016] [Accepted: 11/24/2016] [Indexed: 11/18/2022]
Abstract
Chitinase, an enzyme that can degrade the main compositions of insect intestine and cuticle, has been used in the bio-control field. Our previous work has reported the chitinase Pachi with nematicidal activity (Caenorhabditis elegans). In the present study, to improve the chitinolytic and nematicidal activities of Pachi, a random mutant library was constructed by error-prone PCR and screened by bacteriophage T7-based high-throughput screening system. One mutant, PachiN35D was obtained from about 10, 000 clones. The kinetics analysis revealed that PachiN35D exhibited a 63% decrease in Km value against chitosan, a 2.1-fold enhancement in kcat/Km value and a 1.2-fold increase in specific activity over the wild-type Pachi. Moreover, the mortality analysis against Caenorhabditis elegans showed that the 50% lethal concentration (LC50) of PachiN35D is 309.6±1.1μg/ml and a 20% increase in nematicidal activity over the wild-type Pachi (with a LC50 value of 387.3±31.7μg/ml). The structure modeling and superimposition indicated that the substitution N35D reduced the distance between substrate and substrate-binding site Asp141, finally resulting in an increase in substrate affinity, catalytic efficiency and specific activity. These results provide useful information for the study of structure-function relationship of Pachi and lay a foundation for its potential applications in agro-biotechnology.
Collapse
Affiliation(s)
- Junpeng Chen
- College of Life Science and Technology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430 070, China
| | - Yangdongfang An
- College of Life Science and Technology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430 070, China
| | - Ashok Kumar
- College of Life Science and Technology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430 070, China
| | - Ziduo Liu
- College of Life Science and Technology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430 070, China.
| |
Collapse
|
102
|
Suginta W, Sirimontree P, Sritho N, Ohnuma T, Fukamizo T. The chitin-binding domain of a GH-18 chitinase from Vibrio harveyi is crucial for chitin-chitinase interactions. Int J Biol Macromol 2016; 93:1111-1117. [DOI: 10.1016/j.ijbiomac.2016.09.066] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 09/06/2016] [Accepted: 09/18/2016] [Indexed: 11/26/2022]
|
103
|
Vaikuntapu PR, Rambabu S, Madhuprakash J, Podile AR. A new chitinase-D from a plant growth promoting Serratia marcescens GPS5 for enzymatic conversion of chitin. BIORESOURCE TECHNOLOGY 2016; 220:200-207. [PMID: 27567481 DOI: 10.1016/j.biortech.2016.08.055] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 08/05/2016] [Accepted: 08/06/2016] [Indexed: 06/06/2023]
Abstract
The current study describes heterologous expression and biochemical characterization of single-modular chitinase-D from Serratia marcescens (SmChiD) with unprecedented catalytic properties which include chitobiase and transglycosylation (TG) activities besides hydrolytic activity. Without accessory domains, SmChiD, hydrolyzed insoluble polymeric chitin substrates like colloidal, α- and β-chitin. Activity studies on CHOS with degree of polymerization (DP) 2-6 as substrate revealed that SmChiD hydrolyzed DP2 with a chitobiase activity and showed TG activity on CHOS with DP3-6, producing longer chain CHOS. But, the TG products were further hydrolyzed to shorter chain CHOS with DP1-2 products. SmChiD with its unique catalytic properties, could be a potential enzyme for the production of long chain CHOS and also for the preparation of efficient enzyme cocktails for chitin degradation.
Collapse
Affiliation(s)
- Papa Rao Vaikuntapu
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India
| | - Samudrala Rambabu
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India
| | - Jogi Madhuprakash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India
| | - Appa Rao Podile
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India.
| |
Collapse
|
104
|
Khan FI, Bisetty K, Gu KR, Singh S, Permaul K, Hassan MI, Wei DQ. Molecular dynamics simulation of chitinase I from Thermomyces lanuginosus SSBP to ensure optimal activity. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1237024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Faez Iqbal Khan
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, China
| | - Krishna Bisetty
- Department of Chemistry, Durban University of Technology, Durban, South Africa
| | - Ke-Ren Gu
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, China
| | - Suren Singh
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | - Kugen Permaul
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, India
| | - Dong-Qing Wei
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, China
| |
Collapse
|
105
|
Gaber Y, Mekasha S, Vaaje-Kolstad G, Eijsink VG, Fraaije MW. Characterization of a chitinase from the cellulolytic actinomycete Thermobifida fusca. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1253-1259. [DOI: 10.1016/j.bbapap.2016.04.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/22/2016] [Accepted: 04/20/2016] [Indexed: 01/19/2023]
|
106
|
The Details of Glycolipid Glycan Hydrolysis by the Structural Analysis of a Family 123 Glycoside Hydrolase from Clostridium perfringens. J Mol Biol 2016; 428:3253-3265. [DOI: 10.1016/j.jmb.2016.03.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/17/2016] [Accepted: 03/21/2016] [Indexed: 01/02/2023]
|
107
|
Di Rosa M, Brundo VM, Malaguarnera L. New insights on chitinases immunologic activities. World J Immunol 2016; 6:96-104. [DOI: 10.5411/wji.v6.i2.96] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 10/29/2015] [Accepted: 04/11/2016] [Indexed: 02/05/2023] Open
Abstract
Mammalian chitinases and the related chilectins (ChiLs) belong to the GH18 family, which hydrolyse the glycosidic bond of chitin by a substrate-assisted mechanism. Chitin the fundamental component in the coating of numerous living species is the most abundant natural biopolymer. Mounting evidence suggest that the function of the majority of the mammalian chitinases is not exclusive to catalyze the hydrolysis of chitin producing pathogens, but include crucial role specific in the immunologic activities. The chitinases and chitinase-like proteins are expressed in response to different proinflammatory cues in various tissues by activated macrophages, neutrophils and in different monocyte-derived cell lines. The mechanism and molecular interaction of chitinases in relation to immune regulation embrace bacterial infection, inflammation, dismetabolic and degenerative disease. The aim of this review is to update the reader with regard to the role of chitinases proposed in the recent innate and adaptive immunity literature. The deep scrutiny of this family of enzymes could be a useful base for further studies addressed to the development of potential procedure directing these molecules as diagnostic and prognostic markers for numerous immune and inflammatory diseases.
Collapse
|
108
|
Xu J, Xu X, Tian L, Wang G, Zhang X, Wang X, Guo W. Discovery and identification of candidate genes from the chitinase gene family for Verticillium dahliae resistance in cotton. Sci Rep 2016; 6:29022. [PMID: 27354165 PMCID: PMC4926273 DOI: 10.1038/srep29022] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/14/2016] [Indexed: 12/02/2022] Open
Abstract
Verticillium dahliae, a destructive and soil-borne fungal pathogen, causes massive losses in cotton yields. However, the resistance mechanism to V. dahilae in cotton is still poorly understood. Accumulating evidence indicates that chitinases are crucial hydrolytic enzymes, which attack fungal pathogens by catalyzing the fungal cell wall degradation. As a large gene family, to date, the chitinase genes (Chis) have not been systematically analyzed and effectively utilized in cotton. Here, we identified 47, 49, 92, and 116 Chis from four sequenced cotton species, diploid Gossypium raimondii (D5), G. arboreum (A2), tetraploid G. hirsutum acc. TM-1 (AD1), and G. barbadense acc. 3-79 (AD2), respectively. The orthologous genes were not one-to-one correspondence in the diploid and tetraploid cotton species, implying changes in the number of Chis in different cotton species during the evolution of Gossypium. Phylogenetic classification indicated that these Chis could be classified into six groups, with distinguishable structural characteristics. The expression patterns of Chis indicated their various expressions in different organs and tissues, and in the V. dahliae response. Silencing of Chi23, Chi32, or Chi47 in cotton significantly impaired the resistance to V. dahliae, suggesting these genes might act as positive regulators in disease resistance to V. dahliae.
Collapse
Affiliation(s)
- Jun Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoyang Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Liangliang Tian
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Guilin Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Xueying Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinyu Wang
- College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
109
|
Alteen M, Oehler V, Nemčovičová I, Wilson IB, Vocadlo DJ, Gloster TM. Mechanism of Human Nucleocytoplasmic Hexosaminidase D. Biochemistry 2016; 55:2735-47. [PMID: 27149221 PMCID: PMC4878814 DOI: 10.1021/acs.biochem.5b01285] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 04/13/2016] [Indexed: 12/23/2022]
Abstract
Mammalian β-hexosaminidases have been shown to play essential roles in cellular physiology and health. These enzymes are responsible for the cleavage of the monosaccharides N-acetylglucosamine (GlcNAc) and N-acetylgalactosamine (GalNAc) from cellular substrates. One of these β-hexosaminidases, hexosaminidase D (HexD), encoded by the HEXDC gene, has received little attention. No mechanistic studies have focused on the role of this unusual nucleocytoplasmically localized β-hexosaminidase, and its cellular function remains unknown. Using a series of kinetic and mechanistic investigations into HexD, we define the precise catalytic mechanism of this enzyme and establish the identities of key enzymic residues. The preparation of synthetic aryl N-acetylgalactosaminide substrates for HexD in combination with measurements of kinetic parameters for wild-type and mutant enzymes, linear free energy analyses of the enzyme-catalyzed hydrolysis of these substrates, evaluation of the reaction by nuclear magnetic resonance, and inhibition studies collectively reveal the detailed mechanism of action employed by HexD. HexD is a retaining glycosidase that operates using a substrate-assisted catalytic mechanism, has a preference for galactosaminide over glucosaminide substrates, and shows a pH optimum in its second-order rate constant at pH 6.5-7.0. The catalytically important residues are Asp148 and Glu149, with Glu149 serving as the general acid/base residue and Asp148 as the polarizing residue. HexD is inhibited by Gal-NAG-thiazoline (Ki = 420 nM). The fundamental insights gained from this study will aid in the development of potent and selective probes for HexD, which will serve as useful tools to improve our understanding of the physiological role played by this unusual enzyme.
Collapse
Affiliation(s)
- Matthew
G. Alteen
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A
1S6, Canada
- Biomedical
Sciences Research Complex, University of
St Andrews, North Haugh,
St Andrews, Fife KY16 9ST, U.K.
| | - Verena Oehler
- Biomedical
Sciences Research Complex, University of
St Andrews, North Haugh,
St Andrews, Fife KY16 9ST, U.K.
| | - Ivana Nemčovičová
- Department
für Chemie, Universität für
Bodenkultur, Muthgasse
18, A-1190 Wien, Austria
| | - Iain B.
H. Wilson
- Department
für Chemie, Universität für
Bodenkultur, Muthgasse
18, A-1190 Wien, Austria
| | - David J. Vocadlo
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A
1S6, Canada
| | - Tracey M. Gloster
- Biomedical
Sciences Research Complex, University of
St Andrews, North Haugh,
St Andrews, Fife KY16 9ST, U.K.
| |
Collapse
|
110
|
Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism. Sci Rep 2016; 6:23473. [PMID: 27032335 PMCID: PMC4817029 DOI: 10.1038/srep23473] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/25/2016] [Indexed: 11/25/2022] Open
Abstract
Glycoside hydrolases (GHs) play fundamental roles in the decomposition of lignocellulosic biomaterials. Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. The Ig-like module is pivoting the packing and unpacking motions of CBM46 relative to CD in the assembly of the binding subsite. This is the first example of a multidomain GH relying on large amplitude motions of the CBM46 for assembly of the catalytically competent form of the enzyme.
Collapse
|
111
|
Jana S, Hamre AG, Wildberger P, Holen MM, Eijsink VGH, Beckham GT, Sørlie M, Payne CM. Aromatic-Mediated Carbohydrate Recognition in Processive Serratia marcescens Chitinases. J Phys Chem B 2016; 120:1236-49. [PMID: 26824449 DOI: 10.1021/acs.jpcb.5b12610] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microorganisms use a host of enzymes, including processive glycoside hydrolases, to deconstruct recalcitrant polysaccharides to sugars. Processive glycoside hydrolases closely associate with polymer chains and repeatedly cleave glycosidic linkages without dissociating from the crystalline surface after each hydrolytic step; they are typically the most abundant enzymes in both natural secretomes and industrial cocktails by virtue of their significant hydrolytic potential. The ubiquity of aromatic residues lining the enzyme catalytic tunnels and clefts is a notable feature of processive glycoside hydrolases. We hypothesized that these aromatic residues have uniquely defined roles, such as substrate chain acquisition and binding in the catalytic tunnel, that are defined by their local environment and position relative to the substrate and the catalytic center. Here, we investigated this hypothesis with variants of Serratia marcescens family 18 processive chitinases ChiA and ChiB. We applied molecular simulation and free energy calculations to assess active site dynamics and ligand binding free energies. Isothermal titration calorimetry provided further insight into enthalpic and entropic contributions to ligand binding free energy. Thus, the roles of six aromatic residues, Trp-167, Trp-275, and Phe-396 in ChiA, and Trp-97, Trp-220, and Phe-190 in ChiB, have been examined. We observed that point mutation of the tryptophan residues to alanine results in unfavorable changes in the free energy of binding relative to wild-type. The most drastic effects were observed for residues positioned at the "entrances" of the deep substrate-binding clefts and known to be important for processivity. Interestingly, phenylalanine mutations in ChiA and ChiB had little to no effect on chito-oligomer binding, in accordance with the limited effects of their removal on chitinase functionality.
Collapse
Affiliation(s)
- Suvamay Jana
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506-0046, United States
| | - Anne Grethe Hamre
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Patricia Wildberger
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Matilde Mengkrog Holen
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Vincent G H Eijsink
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory , Golden, Colorado 80401, United States
| | - Morten Sørlie
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506-0046, United States
| |
Collapse
|
112
|
Structural and Biochemical Insights into the Peptidoglycan Hydrolase Domain of FlgJ from Salmonella typhimurium. PLoS One 2016; 11:e0149204. [PMID: 26871950 PMCID: PMC4752226 DOI: 10.1371/journal.pone.0149204] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 01/28/2016] [Indexed: 11/19/2022] Open
Abstract
FlgJ is a glycoside hydrolase (GH) enzyme belonging to the Carbohydrate Active enZyme (CAZy) family GH73. It facilitates passage of the bacterial flagellum through the peptidoglycan (PG) layer by cleaving the β-1,4 glycosidic bond between N-acetylglucosamine and N-acetylmuramic acid sugars that comprise the glycan strands of PG. Here we describe the crystal structure of the GH domain of FlgJ from bacterial pathogen Salmonella typhimurium (StFlgJ). Interestingly, the active site of StFlgJ was blocked by the C-terminal α-helix of a neighbouring symmetry mate and a β-hairpin containing the putative catalytic glutamic acid residue Glu223 was poorly resolved and could not be completely modeled into the electron density, suggesting it is flexible. Previous reports have shown that the GH73 enzyme Auto from Listeria monocytogenes is inhibited by an N-terminal α-helix that may occlude the active site in similar fashion. To investigate if the C-terminus of StFlgJ inhibits GH activity, the glycolytic activity of StFlgJ was assessed with and without the C-terminal α-helix. The GH activity of StFlgJ was unaffected by the presence or absence of the α-helix, suggesting it is not involved in regulating activity. Removal of the C-terminal α-helix did, however, allow a crystal structure of the domain to be obtained where the flexible β-hairpin containing residue Glu223 was entirely resolved. The β-hairpin was positioned such that the active site groove was fully solvent-exposed, placing Glu223 nearly 21.6 Å away from the putative general acid/base residue Glu184, which is too far apart for these two residues to coordinate glycosidic bond hydrolysis. The mobile nature of the StFlgJ β-hairpin is consistent with structural studies of related GH73 enzymes, suggesting that a dynamic active site may be common to many GH73 enzymes, in which the active site opens to capture substrate and then closes to correctly orient active site residues for catalysis.
Collapse
|
113
|
Nguyen-Thi N, Doucet N. Combining chitinase C and N-acetylhexosaminidase from Streptomyces coelicolor A3(2) provides an efficient way to synthesize N-acetylglucosamine from crystalline chitin. J Biotechnol 2016; 220:25-32. [DOI: 10.1016/j.jbiotec.2015.12.038] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 11/25/2015] [Accepted: 12/30/2015] [Indexed: 11/24/2022]
|
114
|
Microbiome and Biocatalytic Bacteria in Monkey Cup (Nepenthes Pitcher) Digestive Fluid. Sci Rep 2016; 6:20016. [PMID: 26817720 PMCID: PMC4730220 DOI: 10.1038/srep20016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 12/07/2015] [Indexed: 02/08/2023] Open
Abstract
Tropical carnivorous plant, Nepenthes, locally known as “monkey cup”, utilises its pitcher as a passive trap to capture insects. It then secretes enzymes into the pitcher fluid to digest the insects for nutrients acquisition. However, little is known about the microbiota and their activity in its pitcher fluid. Eighteen bacteria phyla were detected from the metagenome study in the Nepenthes pitcher fluid. Proteobacteria, Bacteroidetes and Actinobacteria are the dominant phyla in the Nepenthes pitcher fluid. We also performed culturomics approach by isolating 18 bacteria from the Nepenthes pitcher fluid. Most of the bacterial isolates possess chitinolytic, proteolytic, amylolytic, and cellulolytic and xylanolytic activities. Fifteen putative chitinase genes were identified from the whole genome analysis on the genomes of the 18 bacteria isolated from Nepenthes pitcher fluid and expressed for chitinase assay. Of these, six clones possessed chitinase activity. In conclusion, our metagenome result shows that the Nepenthes pitcher fluid contains vast bacterial diversity and the culturomic studies confirmed the presence of biocatalytic bacteria within the Nepenthes pitcher juice which may act in symbiosis for the turn over of insects trapped in the Nepenthes pitcher fluid.
Collapse
|
115
|
Di Rosa M, Distefano G, Zorena K, Malaguarnera L. Chitinases and immunity: Ancestral molecules with new functions. Immunobiology 2015; 221:399-411. [PMID: 26686909 DOI: 10.1016/j.imbio.2015.11.014] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 11/30/2015] [Indexed: 02/07/2023]
Abstract
Chitinases belonging to 18 glycosyl hydrolase family is an ancient gene family that is widely expressed from prokaryotes to eukaryotes. In humans, despite the absence of endogenous chitin, a number of Chitinases and Chitinase-like Proteins (C/CLPs) have been identified. Chitinases with enzymatic activity have a chitin binding domain containing six cysteine residues responsible for their binding to chitin. In contrast, CLPs do not contain such typical chitin-binding domains, but still can bind to chitin with high affinity. Molecular phylogenetic analyses suggest that active Chitinases result from an early gene duplication event. Further duplication events, followed by mutations leading to loss of chitinase activity, allowed evolution of the chi-lectins. For the majority of the mammalian chitinases the last decades have witnessed the appearance of a substantial number of studies describing their expression differentially regulated during more specific immunologic activities. It is becoming increasingly clear that their function is not exclusive to catalyse the hydrolysis of chitin producing pathogens, but include crucial role in bacterial infections and inflammatory diseases. Here we provide an overview of all family members to shed light on the mechanisms and molecular interactions of Chitinases and CLPs in relation to immune response regulation, in order to delineate their future utilization as diagnostic and prognostic markers for numerous diseases.
Collapse
Affiliation(s)
- Michelino Di Rosa
- Department of Biomedical and Biotechnology Sciences, University of Catania, Italy
| | - Gisella Distefano
- Department of Biomedical and Biotechnology Sciences, University of Catania, Italy
| | - Katarzyna Zorena
- Department of Immunobiology and Environment Microbiology Medical University of Gdańsk, Poland
| | - Lucia Malaguarnera
- Department of Biomedical and Biotechnology Sciences, University of Catania, Italy.
| |
Collapse
|
116
|
Hamre AG, Jana S, Reppert NK, Payne CM, Sørlie M. Processivity, Substrate Positioning, and Binding: The Role of Polar Residues in a Family 18 Glycoside Hydrolase. Biochemistry 2015; 54:7292-306. [PMID: 26503416 DOI: 10.1021/acs.biochem.5b00830] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzymatic degradation of recalcitrant polysaccharides such as cellulose (β-1,4-linked glucose) and chitin (β-1,4-linked N-acetylglucosamine) by glycoside hydrolases (GHs) is of significant biological and economical importance. In nature, depolymerization is primarily accomplished by processive GHs, which remain attached to the substrate between subsequent hydrolytic reactions. Recent computational efforts have suggested that the processive ability of a GH is directly linked to the ligand binding free energy. The contribution of individual aromatic residues in the active site of these enzymes has been extensively studied. In this study, we offer the first experimental evidence confirming correlation of binding free energy and degree of processivity and evidence that polar residues are essential for maintaining processive ability. Exchanging Thr(276) with Ala in substrate binding subsite -2 in the processive ChiA of Serratia marcescens results in a decrease in both the enthalpy (2.6 and 3.8 kcal/mol) and free energy (0.5 and 2.2 kcal/mol) for the binding to the substrate (GlcNAc)6 and the inhibitor allosamidin, respectively, compared to that of the wild type. Moreover, the initial apparent processivity as measured by [(GlcNAc)2]/[GlcNAc] ratios (17.1 ± 0.4) and chitin degradation efficiency (20%) are greatly reduced for ChiA-T276A versus those of the wild type (30.1 ± 1.5 and 75%, respectively). Mutation of Arg(172) to Ala reduces the level of recognition and positioning of the substrate into the active site. Molecular dynamics simulations indicate ChiA-R172A behaves like the wild type, but the dynamics of ChiA-T276A are greatly influenced by mutation, which is reflective of their influence on processivity.
Collapse
Affiliation(s)
- Anne Grethe Hamre
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås, Norway
| | - Suvamay Jana
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Nicole K Reppert
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås, Norway
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Morten Sørlie
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås, Norway
| |
Collapse
|
117
|
Chitinases from Bacteria to Human: Properties, Applications, and Future Perspectives. Enzyme Res 2015; 2015:791907. [PMID: 26664744 PMCID: PMC4668315 DOI: 10.1155/2015/791907] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/29/2015] [Accepted: 11/01/2015] [Indexed: 01/24/2023] Open
Abstract
Chitin is the second most plenteous polysaccharide in nature after cellulose, present in cell walls of several fungi, exoskeletons of insects, and crustacean shells. Chitin does not accumulate in the environment due to presence of bacterial chitinases, despite its abundance. These enzymes are able to degrade chitin present in the cell walls of fungi as well as the exoskeletons of insect. They have shown being the potential agents for biological control of the plant diseases caused by various pathogenic fungi and insect pests and thus can be used as an alternative to chemical pesticides. There has been steady increase in demand of chitin derivatives, obtained by action of chitinases on chitin polymer for various industrial, clinical, and pharmaceutical purposes. Hence, this review focuses on properties and applications of chitinases starting from bacteria, followed by fungi, insects, plants, and vertebrates. Designing of chitinase by applying directed laboratory evolution and rational approaches for improved catalytic activity for cost-effective field applications has also been explored.
Collapse
|
118
|
Langner T, Göhre V. Fungal chitinases: function, regulation, and potential roles in plant/pathogen interactions. Curr Genet 2015; 62:243-54. [PMID: 26527115 DOI: 10.1007/s00294-015-0530-x] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 12/13/2022]
Abstract
In the past decades our knowledge about fungal cell wall architecture increased tremendously and led to the identification of many enzymes involved in polysaccharide synthesis and remodeling, which are also of biotechnological interest. Fungal cell walls play an important role in conferring mechanic stability during cell division and polar growth. Additionally, in phytopathogenic fungi the cell wall is the first structure that gets into intimate contact with the host plant. A major constituent of fungal cell walls is chitin, a homopolymer of N-acetylglucosamine units. To ensure plasticity, polymeric chitin needs continuous remodeling which is maintained by chitinolytic enzymes, including lytic polysaccharide monooxygenases N-acetylglucosaminidases, and chitinases. Depending on the species and lifestyle of fungi, there is great variation in the number of encoded chitinases and their function. Chitinases can have housekeeping function in plasticizing the cell wall or can act more specifically during cell separation, nutritional chitin acquisition, or competitive interaction with other fungi. Although chitinase research made huge progress in the last decades, our knowledge about their role in phytopathogenic fungi is still scarce. Recent findings in the dimorphic basidiomycete Ustilago maydis show that chitinases play different physiological functions throughout the life cycle and raise questions about their role during plant-fungus interactions. In this work we summarize these functions, mechanisms of chitinase regulation and their putative role during pathogen/host interactions.
Collapse
Affiliation(s)
- Thorsten Langner
- Institute for Microbiology, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Vera Göhre
- Institute for Microbiology, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany.
| |
Collapse
|
119
|
Inverse relationship between chitobiase and transglycosylation activities of chitinase-D from Serratia proteamaculans revealed by mutational and biophysical analyses. Sci Rep 2015; 5:15657. [PMID: 26493546 PMCID: PMC4616163 DOI: 10.1038/srep15657] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
Serratia proteamaculans chitinase-D (SpChiD) has a unique combination of hydrolytic and transglycosylation (TG) activities. The TG activity of SpChiD can be used for large-scale production of chito-oligosaccharides (CHOS). The multiple activities (hydrolytic and/or chitobiase activities and TG) of SpChiD appear to be strongly influenced by the substrate-binding cleft. Here, we report the unique property of SpChiD substrate-binding cleft, wherein, the residues Tyr28, Val35 and Thr36 control chitobiase activity and the residues Trp160 and Trp290 are crucial for TG activity. Mutants with reduced (V35G and T36G/F) or no (SpChiDΔ30–42 and Y28A) chitobiase activity produced higher amounts of the quantifiable even-chain TG product with degree of polymerization (DP)-6, indicating that the chitobiase and TG activities are inversely related. In addition to its unprecedented catalytic properties, unlike other chitinases, the single modular SpChiD showed dual unfolding transitions. Ligand-induced thermal stability studies with the catalytically inactive mutant of SpChiD (E153A) showed that the transition temperature increased upon binding of CHOS with DP2–6. Isothermal titration calorimetry experiments revealed the exceptionally high binding affinities for E153A to CHOS with DP2–6. These observations strongly support that the architecture of SpChiD substrate-binding cleft adopted to control chitobiase and TG activities, in addition to usual chitinase-mediated hydrolysis.
Collapse
|
120
|
Substrate-binding specificity of chitinase and chitosanase as revealed by active-site architecture analysis. Carbohydr Res 2015; 418:50-56. [PMID: 26545262 DOI: 10.1016/j.carres.2015.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/03/2015] [Accepted: 10/06/2015] [Indexed: 11/21/2022]
Abstract
Chitinases and chitosanases, referred to as chitinolytic enzymes, are two important categories of glycoside hydrolases (GH) that play a key role in degrading chitin and chitosan, two naturally abundant polysaccharides. Here, we investigate the active site architecture of the major chitosanase (GH8, GH46) and chitinase families (GH18, GH19). Both charged (Glu, His, Arg, Asp) and aromatic amino acids (Tyr, Trp, Phe) are observed with higher frequency within chitinolytic active sites as compared to elsewhere in the enzyme structure, indicating significant roles related to enzyme function. Hydrogen bonds between chitinolytic enzymes and the substrate C2 functional groups, i.e. amino groups and N-acetyl groups, drive substrate recognition, while non-specific CH-π interactions between aromatic residues and substrate mainly contribute to tighter binding and enhanced processivity evident in GH8 and GH18 enzymes. For different families of chitinolytic enzymes, the number, type, and position of substrate atoms bound in the active site vary, resulting in different substrate-binding specificities. The data presented here explain the synergistic action of multiple enzyme families at a molecular level and provide a more reasonable method for functional annotation, which can be further applied toward the practical engineering of chitinases and chitosanases.
Collapse
|
121
|
Tibullo D, Di Rosa M, Giallongo C, La Cava P, Parrinello NL, Romano A, Conticello C, Brundo MV, Saccone S, Malaguarnera L, Di Raimondo F. Bortezomib modulates CHIT1 and YKL40 in monocyte-derived osteoclast and in myeloma cells. Front Pharmacol 2015; 6:226. [PMID: 26528182 PMCID: PMC4604315 DOI: 10.3389/fphar.2015.00226] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/22/2015] [Indexed: 11/15/2022] Open
Abstract
Osteolytic bone disease is a common manifestation of multiple myeloma (MM) that leads to progressive skeleton destruction and is the most severe cause of morbidity in MM patients. It results from increased osteolytic activity and decrease osteoblastic function. Activation of mammalian chitinases chitotriosidase (CHIT1) and YKL40 is associated with osteoclast (OCs) differentiation and bone digestion. In the current study, we investigated the effect of two Bortezomib’s concentration (2.5 and 5 nM) on osteoclastogenesis by analyzing regulation of chitinase expression. OCs exposition to bortezomib (BO) was able to inhibit the expression of different OCs markers such as RANK, CTSK, TRAP, and MMP9. In addition BO-treatment reduced CHIT1 enzymatic activity and both CHIT1 and YKL40 mRNA expression levels and cytoplasmatic and secreted protein. Moreover, immunofluorescence evaluation of mature OCs showed that BO was able to translocate YKL40 into the nucleus, while CHIT1 remained into the cytoplasm. Since MM cell lines such as U266, SKM-M1 and MM1 showed high levels of CHIT1 activity, we analyzed bone resorption ability of U266 using dentin disk assay resorption pits. Silencing chitinase proteins in U266 cell line with specific small interfering RNA, resulted in pits number reduction on dentine disks. In conclusion, we showed that BO decreases osteoclastogenesis and reduces bone resorption in OCs and U266 cell line by modulating the chitinases CHIT1 and YKL40. These results indicate that chitinases may be a therapeutic target for bone disease in MM patients.
Collapse
Affiliation(s)
- Daniele Tibullo
- Section of Hematology, Department of Surgery and Medical Specialties, University of Catania , Catania, Italy
| | - Michelino Di Rosa
- Department of Biomedical and Biotechnology Sciences, University of Catania , Catania, Italy
| | - Cesarina Giallongo
- Section of Hematology, Department of Surgery and Medical Specialties, University of Catania , Catania, Italy
| | - Piera La Cava
- Section of Hematology, Department of Surgery and Medical Specialties, University of Catania , Catania, Italy
| | - Nunziatina L Parrinello
- Section of Hematology, Department of Surgery and Medical Specialties, University of Catania , Catania, Italy
| | - Alessandra Romano
- Section of Hematology, Department of Surgery and Medical Specialties, University of Catania , Catania, Italy
| | - Concetta Conticello
- Section of Hematology, Department of Surgery and Medical Specialties, University of Catania , Catania, Italy
| | - Maria V Brundo
- Department of Biological, Geological and Environmental Sciences, University of Catania , Catania, Italy
| | - Salvatore Saccone
- Department of Biological, Geological and Environmental Sciences, University of Catania , Catania, Italy
| | - Lucia Malaguarnera
- Department of Biomedical and Biotechnology Sciences, University of Catania , Catania, Italy
| | - Francesco Di Raimondo
- Section of Hematology, Department of Surgery and Medical Specialties, University of Catania , Catania, Italy
| |
Collapse
|
122
|
Stockinger LW, Eide KB, Dybvik AI, Sletta H, Vårum KM, Eijsink VG, Tøndervik A, Sørlie M. The effect of the carbohydrate binding module on substrate degradation by the human chitotriosidase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1494-501. [DOI: 10.1016/j.bbapap.2015.06.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 05/29/2015] [Accepted: 06/23/2015] [Indexed: 11/25/2022]
|
123
|
Bamford NC, Snarr BD, Gravelat FN, Little DJ, Lee MJ, Zacharias CA, Chabot JC, Geller AM, Baptista SD, Baker P, Robinson H, Howell PL, Sheppard DC. Sph3 Is a Glycoside Hydrolase Required for the Biosynthesis of Galactosaminogalactan in Aspergillus fumigatus. J Biol Chem 2015; 290:27438-50. [PMID: 26342082 DOI: 10.1074/jbc.m115.679050] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Indexed: 11/06/2022] Open
Abstract
Aspergillus fumigatus is the most virulent species within the Aspergillus genus and causes invasive infections with high mortality rates. The exopolysaccharide galactosaminogalactan (GAG) contributes to the virulence of A. fumigatus. A co-regulated five-gene cluster has been identified and proposed to encode the proteins required for GAG biosynthesis. One of these genes, sph3, is predicted to encode a protein belonging to the spherulin 4 family, a protein family with no known function. Construction of an sph3-deficient mutant demonstrated that the gene is necessary for GAG production. To determine the role of Sph3 in GAG biosynthesis, we determined the structure of Aspergillus clavatus Sph3 to 1.25 Å. The structure revealed a (β/α)8 fold, with similarities to glycoside hydrolase families 18, 27, and 84. Recombinant Sph3 displayed hydrolytic activity against both purified and cell wall-associated GAG. Structural and sequence alignments identified three conserved acidic residues, Asp-166, Glu-167, and Glu-222, that are located within the putative active site groove. In vitro and in vivo mutagenesis analysis demonstrated that all three residues are important for activity. Variants of Asp-166 yielded the greatest decrease in activity suggesting a role in catalysis. This work shows that Sph3 is a glycoside hydrolase essential for GAG production and defines a new glycoside hydrolase family, GH135.
Collapse
Affiliation(s)
- Natalie C Bamford
- From the Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada, the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Brendan D Snarr
- the Departments of Microbiology and Immunology and Medicine, McGill University, Montréal, Québec H4A 3J1, Canada, and
| | - Fabrice N Gravelat
- the Departments of Microbiology and Immunology and Medicine, McGill University, Montréal, Québec H4A 3J1, Canada, and
| | - Dustin J Little
- From the Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada, the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Mark J Lee
- the Departments of Microbiology and Immunology and Medicine, McGill University, Montréal, Québec H4A 3J1, Canada, and
| | - Caitlin A Zacharias
- the Departments of Microbiology and Immunology and Medicine, McGill University, Montréal, Québec H4A 3J1, Canada, and
| | - Josée C Chabot
- the Departments of Microbiology and Immunology and Medicine, McGill University, Montréal, Québec H4A 3J1, Canada, and
| | - Alexander M Geller
- the Departments of Microbiology and Immunology and Medicine, McGill University, Montréal, Québec H4A 3J1, Canada, and
| | - Stefanie D Baptista
- the Departments of Microbiology and Immunology and Medicine, McGill University, Montréal, Québec H4A 3J1, Canada, and
| | - Perrin Baker
- From the Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Howard Robinson
- the Photon Sciences Division, Brookhaven National Laboratory, Upton, New York 11973-5000
| | - P Lynne Howell
- From the Program in Molecular Structure and Function, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada, the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada,
| | - Donald C Sheppard
- the Departments of Microbiology and Immunology and Medicine, McGill University, Montréal, Québec H4A 3J1, Canada, and
| |
Collapse
|
124
|
Bjerga GEK, Williamson AK. Cold shock induction of recombinant Arctic environmental genes. BMC Biotechnol 2015; 15:78. [PMID: 26286037 PMCID: PMC4544801 DOI: 10.1186/s12896-015-0185-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 07/24/2015] [Indexed: 11/16/2022] Open
Abstract
Background Heterologous expression of psychrophilic enzymes in E. coli is particularly challenging due to their intrinsic instability. The low stability is regarded as a consequence of adaptation that allow them to function at low temperatures. Recombinant production presents a significant barrier to their exploitation for commercial applications in industry. Methods As part of an enzyme discovery project we have investigated the utility of a cold-shock inducible promoter for low-temperature expression of five diverse genes derived from the metagenomes of marine Arctic sediments. After evaluation of their production, we further optimized for soluble production by building a vector suite from which the environmental genes could be expressed as fusions with solubility tags. Results We found that the low-temperature optimized system produced high expression levels for all putatively cold-active proteins, as well as reducing host toxicity for several candidates. As a proof of concept, activity assays with one of the candidates, a putative chitinase, showed that functional protein was obtained using the low-temperature optimized vector suite. Conclusions We conclude that a cold-shock inducible system is advantageous for the heterologous expression of psychrophilic proteins, and may also be useful for expression of toxic mesophilic and thermophilic proteins where properties of the proteins are deleterious to the host cell growth. Electronic supplementary material The online version of this article (doi:10.1186/s12896-015-0185-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Gro Elin Kjæreng Bjerga
- Norstruct, Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway. .,Centre for Applied Biotechnology, Uni Research AS, Thormøhlensgt. 55, N-5008, Bergen, Norway.
| | - Adele Kim Williamson
- Norstruct, Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway.
| |
Collapse
|
125
|
Modulation of the transglycosylation activity of plant family GH18 chitinase by removing or introducing a tryptophan side chain. FEBS Lett 2015. [DOI: 10.1016/j.febslet.2015.07.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
126
|
Hamre AG, Jana S, Holen MM, Mathiesen G, Väljamäe P, Payne CM, Sørlie M. Thermodynamic Relationships with Processivity in Serratia marcescens Family 18 Chitinases. J Phys Chem B 2015; 119:9601-13. [PMID: 26154587 DOI: 10.1021/acs.jpcb.5b03817] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzymatic degradation of recalcitrant polysaccharides is accomplished by synergistic enzyme cocktails of glycoside hydrolases (GHs) and accessory enzymes. Many GHs are processive which means that they remain attached to the substrate in between subsequent hydrolytic reactions. Chitinases are GHs that catalyze the hydrolysis of chitin (β-1,4-linked N-acetylglucosamine). Previously, a relationship between active site topology and processivity has been suggested while recent computational efforts have suggested a link between the degree of processivity and ligand binding free energy. We have investigated these relationships by employing computational (molecular dynamics (MD)) and experimental (isothermal titration calorimetry (ITC)) approaches to gain insight into the thermodynamics of substrate binding to Serratia marcescens chitinases ChiA, ChiB, and ChiC. We show that increased processive ability indeed corresponds to more favorable binding free energy and that this likely is a general feature of GHs. Moreover, ligand binding in ChiB is entropically driven; in ChiC it is enthalpically driven, and the enthalpic and entropic contributions to ligand binding in ChiA are equal. Furthermore, water is shown to be especially important in ChiA-binding. This work provides new insight into oligosaccharide binding, getting us one step closer to understand how GHs efficiently degrade recalcitrant polysaccharides.
Collapse
Affiliation(s)
- Anne Grethe Hamre
- †Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. 5003, N-1432 Ås, Norway
| | - Suvamay Jana
- ‡Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Matilde Mengkrog Holen
- †Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. 5003, N-1432 Ås, Norway
| | - Geir Mathiesen
- †Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. 5003, N-1432 Ås, Norway
| | - Priit Väljamäe
- §Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Christina M Payne
- ‡Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Morten Sørlie
- †Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. 5003, N-1432 Ås, Norway
| |
Collapse
|
127
|
Fadel F, Zhao Y, Cachau R, Cousido-Siah A, Ruiz FX, Harlos K, Howard E, Mitschler A, Podjarny A. New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM. ACTA ACUST UNITED AC 2015; 71:1455-70. [PMID: 26143917 DOI: 10.1107/s139900471500783x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/21/2015] [Indexed: 11/10/2022]
Abstract
Chitotriosidase (CHIT1) is a human chitinase belonging to the highly conserved glycosyl hydrolase family 18 (GH18). GH18 enzymes hydrolyze chitin, an N-acetylglucosamine polymer synthesized by lower organisms for structural purposes. Recently, CHIT1 has attracted attention owing to its upregulation in immune-system disorders and as a marker of Gaucher disease. The 39 kDa catalytic domain shows a conserved cluster of three acidic residues, Glu140, Asp138 and Asp136, involved in the hydrolysis reaction. Under an excess concentration of substrate, CHIT1 and other homologues perform an additional activity, transglycosylation. To understand the catalytic mechanism of GH18 chitinases and the dual enzymatic activity, the structure and mechanism of CHIT1 were analyzed in detail. The resolution of the crystals of the catalytic domain was improved from 1.65 Å (PDB entry 1waw) to 0.95-1.10 Å for the apo and pseudo-apo forms and the complex with chitobiose, allowing the determination of the protonation states within the active site. This information was extended by hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. The results suggest a new mechanism involving changes in the conformation and protonation state of the catalytic triad, as well as a new role for Tyr27, providing new insights into the hydrolysis and transglycosylation activities.
Collapse
Affiliation(s)
- Firas Fadel
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Headington, Oxford, England
| | - Raul Cachau
- Leidos Biomedical Research Inc. Advanced Biomedical Computer Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Alexandra Cousido-Siah
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Francesc X Ruiz
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Headington, Oxford, England
| | - Eduardo Howard
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Andre Mitschler
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Alberto Podjarny
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| |
Collapse
|
128
|
Wheatley RW, Huber RE. An allolactose trapped at the lacZ β-galactosidase active site with its galactosyl moiety in a (4)H3 conformation provides insights into the formation, conformation, and stabilization of the transition state. Biochem Cell Biol 2015; 93:531-40. [PMID: 26291713 DOI: 10.1139/bcb-2015-0037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
When lactose was incubated with G794A-β-galactosidase (a variant with a "closed" active site loop that binds transition state analogs well) an allolactose was trapped with its Gal moiety in a (4)H3 conformation, similar to the oxocarbenium ion-like conformation expected of the transition state. The numerous interactions formed between the (4)H3 structure and β-galactosidase indicate that this structure is representative of the transition state. This conformation is also very similar to that of d-galactono-1,5-lactone, a good transition state analog. Evidence indicates that substrates take up the (4)H3 conformation during migration from the shallow to the deep mode. Steric forces utilizing His418 and other residues are important for positioning the O1 leaving group into a quasi-axial position. An electrostatic interaction between the O5 of the distorted Gal and Tyr503 as well as C-H-π bonds with Trp568 are also significant. Computational studies of the energy of sugar ring distortion show that the β-galactosidase reaction itinerary is driven by energetic considerations in utilization of a (4)H3 transition state with a novel (4)C1-(4)H3-(4)C1 conformation itinerary. To our knowledge, this is the first X-ray crystallographic structural demonstration that the transition state of a natural substrate of a glycosidase has a (4)H3 conformation.
Collapse
Affiliation(s)
- Robert W Wheatley
- Biochemistry Division, Faculty of Science, University of Calgary, Calgary, AB T2N 1N4, Canada.,Biochemistry Division, Faculty of Science, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Reuben E Huber
- Biochemistry Division, Faculty of Science, University of Calgary, Calgary, AB T2N 1N4, Canada.,Biochemistry Division, Faculty of Science, University of Calgary, Calgary, AB T2N 1N4, Canada
| |
Collapse
|
129
|
Sugawara A, Maita N, Gouda H, Yamamoto T, Hirose T, Kimura S, Saito Y, Nakano H, Kasai T, Nakano H, Shiomi K, Hirono S, Watanabe T, Taniguchi H, O̅mura S, Sunazuka T. Creation of Customized Bioactivity within a 14-Membered Macrolide Scaffold: Design, Synthesis, and Biological Evaluation Using a Family-18 Chitinase. J Med Chem 2015; 58:4984-97. [DOI: 10.1021/acs.jmedchem.5b00175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Akihiro Sugawara
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Nobuo Maita
- Institute
for Enzyme Research, University of Tokushima, 3-18-15 Kuramotocho, Tokushima City, Tokushima, 770-8503, Japan
| | - Hiroaki Gouda
- School
of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Tsuyoshi Yamamoto
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Tomoyasu Hirose
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Saori Kimura
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yoshifumi Saito
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Hayato Nakano
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Takako Kasai
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Hirofumi Nakano
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Kazuro Shiomi
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Shuichi Hirono
- School
of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Takeshi Watanabe
- Department
of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
| | - Hisaaki Taniguchi
- Institute
for Enzyme Research, University of Tokushima, 3-18-15 Kuramotocho, Tokushima City, Tokushima, 770-8503, Japan
| | - Satoshi O̅mura
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Toshiaki Sunazuka
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| |
Collapse
|
130
|
The directionality of processive enzymes acting on recalcitrant polysaccharides is reflected in the kinetic signatures of oligomer degradation. FEBS Lett 2015; 589:1807-12. [DOI: 10.1016/j.febslet.2015.05.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 04/17/2015] [Accepted: 05/20/2015] [Indexed: 11/18/2022]
|
131
|
Di Rosa M, Sanfilippo C, Libra M, Musumeci G, Malaguarnera L. Different pediatric brain tumors are associated with different gene expression profiling. Acta Histochem 2015; 117:477-85. [PMID: 25792036 DOI: 10.1016/j.acthis.2015.02.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 01/30/2015] [Accepted: 02/09/2015] [Indexed: 02/07/2023]
Abstract
Malignant brain tumors are the most common pediatric solid tumors and are the leading cause of death from childhood cancers. These tumors include several histologic subtypes. Due to the particular properties of brain tumors, such as growth and division, examination of brain tumors and the analysis of results are not simple. Up to date there is a dearth of useful biomarkers that have been validated and clinically implemented for pediatric brain tumors. In order to identify the new genetic alterations we recognized, using microarray dataset, chitinases as new potential biomarkers of CNS tumors. The modulation of chitinases was confirmed also in the different histologic subtypes. Our study revealed that distinct patterns of chitinases expression characterize the diverse histological subtypes. In addition evaluating other lisosomal enzymes such as glycosidases and proteases we found that NEU4, CTBS and GBA2 belonging to glycosidases family and CTSC, CTSK and CTSF belonging to proteases family were differently modulated. Future investigations are needed to be performed before some of these enzymes could finally be used as biomarkers of specific types of CNS neoplasms.
Collapse
|
132
|
Umemoto N, Kanda Y, Ohnuma T, Osawa T, Numata T, Sakuda S, Taira T, Fukamizo T. Crystal structures and inhibitor binding properties of plant class V chitinases: the cycad enzyme exhibits unique structural and functional features. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:54-66. [PMID: 25652217 DOI: 10.1111/tpj.12785] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 01/09/2015] [Accepted: 01/30/2015] [Indexed: 06/04/2023]
Abstract
A class V (glycoside hydrolase family 18) chitinase from the cycad Cycas revoluta (CrChiA) is a plant chitinase that has been reported to possess efficient transglycosylation (TG) activity. We solved the crystal structure of CrChiA, and compared it with those of class V chitinases from Nicotiana tabacum (NtChiV) and Arabidopsis thaliana (AtChiC), which do not efficiently catalyze the TG reaction. All three chitinases had a similar (α/β)8 barrel fold with an (α + β) insertion domain. In the acceptor binding site (+1, +2 and +3) of CrChiA, the Trp168 side chain was found to stack face-to-face with the +3 sugar. However, this interaction was not found in the identical regions of NtChiV and AtChiC. In the DxDxE motif, which is essential for catalysis, the carboxyl group of the middle Asp (Asp117) was always oriented toward the catalytic acid Glu119 in CrChiA, whereas the corresponding Asp in NtChiV and AtChiC was oriented toward the first Asp. These structural features of CrChiA appear to be responsible for the efficient TG activity. When binding of the inhibitor allosamidin was evaluated using isothermal titration calorimetry, the changes in binding free energy of the three chitinases were found to be similar to each other, i.e. between -9.5 and -9.8 kcal mol(-1) . However, solvation and conformational entropy changes in CrChiA were markedly different from those in NtChiV and AtChiC, but similar to those of chitinase A from Serratia marcescens (SmChiA), which also exhibits significant TG activity. These results provide insight into the molecular mechanism underlying the TG reaction and the molecular evolution from bacterial chitinases to plant class V chitinases.
Collapse
Affiliation(s)
- Naoyuki Umemoto
- Department of Advanced Bioscience, Kinki University, 3327-204 Nakamachi, Nara, 631-8505, Japan
| | | | | | | | | | | | | | | |
Collapse
|
133
|
Zhang Y, Zhao Z, Liu H. Deriving Chemically Essential Interactions Based on Active Site Alignments and Quantum Chemical Calculations: A Case Study on Glycoside Hydrolases. ACS Catal 2015. [DOI: 10.1021/cs501709d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yinliang Zhang
- School
of Life Sciences, University of Science and Technology of China, 443 Huangshan Road, Hefei, Anhui 230027, China
| | - Zheng Zhao
- Hefei
Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Haiyan Liu
- School
of Life Sciences, University of Science and Technology of China, 443 Huangshan Road, Hefei, Anhui 230027, China
- Hefei National Laboratory for Physical Sciences at the Microscales, Hefei, Anhui 230027, China
- Hefei
Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| |
Collapse
|
134
|
Jitonnom J, Sattayanon C, Kungwan N, Hannongbua S. A DFT study of the unusual substrate-assisted mechanism of Serratia marcescens chitinase B reveals the role of solvent and mutational effect on catalysis. J Mol Graph Model 2015; 56:53-9. [DOI: 10.1016/j.jmgm.2014.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 12/05/2014] [Accepted: 12/08/2014] [Indexed: 11/29/2022]
|
135
|
Sulzenbacher G, Roig-Zamboni V, Peumans WJ, Henrissat B, van Damme EJM, Bourne Y. Structural basis for carbohydrate binding properties of a plant chitinase-like agglutinin with conserved catalytic machinery. J Struct Biol 2015; 190:115-21. [PMID: 25727185 DOI: 10.1016/j.jsb.2015.01.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 01/24/2015] [Accepted: 01/27/2015] [Indexed: 01/13/2023]
Abstract
A new chitinase-like agglutinin, RobpsCRA, related to family GH18 chitinases, has previously been identified in black locust (Robinia pseudoacacia) bark. The crystal structure of RobpsCRA at 1.85Å resolution reveals unusual molecular determinants responsible for the lack of its ancestral chitinase activity. Unlike other chitinase-like proteins, which lack chitinase catalytic residues, RobpsCRA has conserved its catalytic machinery. However, concerted rearrangements of loop regions coupled to non-conservative substitutions of aromatic residues central to the chitin-binding groove explain the lack of hydrolytic activity against chitin and the switch toward recognition of high-mannose type N-glycans. Identification of close homologs in flowering plants with conservation of sequence motifs associated to the structural adaptations seen in RobpsCRA defines an emerging class of agglutinins, as emphasized by a phylogenetic analysis, that are likely to share a similar carbohydrate binding specificity for high-mannose type N-glycans. This study illustrates the recent evolution and molecular adaptation of a versatile TIM-barrel scaffold within the ancestral GH18 family.
Collapse
Affiliation(s)
- Gerlind Sulzenbacher
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Véronique Roig-Zamboni
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Willy J Peumans
- Department of Molecular Biotechnology, Laboratory of Biochemistry and Glycobiology, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Bernard Henrissat
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Els J M van Damme
- Department of Molecular Biotechnology, Laboratory of Biochemistry and Glycobiology, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Yves Bourne
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France.
| |
Collapse
|
136
|
Effects of C-Terminal Domain Truncation on Enzyme Properties of Serratia marcescens Chitinase C. Appl Biochem Biotechnol 2015; 175:3617-27. [DOI: 10.1007/s12010-015-1530-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/27/2015] [Indexed: 10/24/2022]
|
137
|
Genome-wide analysis and differential expression of chitinases in banana against root lesion nematode (Pratylenchus coffeae) and eumusa leaf spot (Mycosphaerella eumusae) pathogens. Appl Biochem Biotechnol 2015; 175:3585-98. [PMID: 25820355 DOI: 10.1007/s12010-015-1528-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 01/26/2015] [Indexed: 10/24/2022]
Abstract
Knowledge on structure and conserved domain of Musa chitinase isoforms and their responses to various biotic stresses will give a lead to select the suitable chitinase isoform for developing biotic stress-resistant genotypes. Hence, in this study, chitinase sequences available in the Musa genome hub were analyzed for their gene structure, conserved domain, as well as intron and exon regions. To identify the Musa chitinase isoforms involved in Pratylenchus coffeae (root lesion nematode) and Mycosphaerella eumusae (eumusa leaf spot) resistant mechanisms, differential gene expression analysis was carried out in P. coffeae- and M. eumusae-challenged resistant and susceptible banana genotypes. This study revealed that more number of chitinase isoforms (CIs) were responses upon eumusa leaf spot stress than nematode stress. The nematode challenge studies revealed that class II chitinase (GSMUA_Achr9G16770_001) was significantly overexpressed with 6.75-fold (with high fragments per kilobase of exon per million fragments mapped (FPKM)) in resistant genotype (Karthobiumtham-ABB) than susceptible (Nendran-AAB) genotype, whereas when M. eumusae was challenge inoculated, two class III CIs (GSMUA_Achr9G25580_001 and GSMUA_Achr8G27880_001) were overexpressed in resistant genotype (Manoranjitham-AAA) than the susceptible genotype (Grand Naine-AAA). However, none of the CIs were found to be commonly overexpressed under both stress conditions. This study reiterated that the chitinase genes are responding differently to different biotic stresses in their respective resistant genotypes.
Collapse
|
138
|
Ni H, Zeng S, Qin X, Sun X, Zhang S, Zhao X, Yu Z, Li L. Molecular docking and site-directed mutagenesis of a Bacillus thuringiensis chitinase to improve chitinolytic, synergistic lepidopteran-larvicidal and nematicidal activities. Int J Biol Sci 2015; 11:304-15. [PMID: 25678849 PMCID: PMC4323370 DOI: 10.7150/ijbs.10632] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/24/2014] [Indexed: 11/05/2022] Open
Abstract
Bacterial chitinases are useful in the biocontrol of agriculturally important pests and fungal pathogens. However, the utility of naturally occurring bacterial chitinases is often limited by their low enzyme activity. In this study, we constructed mutants of a Bacillus thuringiensis chitinase with enhanced activity based on homology modeling, molecular docking, and the site-directed mutagenesis of target residues to modify spatial positions, steric hindrances, or hydrophilicity/hydrophobicity. We first identified a gene from B. thuringiensis YBT-9602 that encodes a chitinase (Chi9602) belonging to glycosyl hydrolase family 18 with conserved substrate-binding and substrate-catalytic motifs. We constructed a structural model of a truncated version of Chi9602 (Chi960235-459) containing the substrate-binding domain using the homologous 1ITX protein of Bacillus circulans as the template. We performed molecular docking analysis of Chi960235-459 using di-N-acetyl-D-glucosamine as the ligand. We then selected 10 residues of interest from the docking area for the site-directed mutagenesis experiments and expression in Escherichia coli. Assays of the chitinolytic activity of the purified chitinases revealed that the three mutants exhibited increased chitinolytic activity. The ChiW50A mutant exhibited a greater than 60 % increase in chitinolytic activity, with similar pH, temperature and metal ion requirements, compared to wild-type Chi9602. Furthermore, ChiW50A exhibited pest-controlling activity and antifungal activity. Remarkable synergistic effects of this mutant with B. thuringiensis spore-crystal preparations against Helicoverpa armigera and Caenorhabditis elegans larvae and obvious activity against several plant-pathogenic fungi were observed.
Collapse
Affiliation(s)
- Hong Ni
- 1. State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, China ; 2. Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan 430062, Hubei, China
| | - Siquan Zeng
- 2. Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan 430062, Hubei, China
| | - Xu Qin
- 1. State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xiaowen Sun
- 2. Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan 430062, Hubei, China
| | - Shan Zhang
- 2. Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan 430062, Hubei, China
| | - Xiuyun Zhao
- 1. State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Ziniu Yu
- 1. State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Lin Li
- 1. State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| |
Collapse
|
139
|
Thiery E, Reniers J, Wouters J, Vincent SP. Stereoselective Synthesis of Boat-Locked Glycosides Designed as Glycosyl Hydrolase Conformational Probes. European J Org Chem 2015. [DOI: 10.1002/ejoc.201403363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
140
|
Sugimoto H, Nakamura K, Nishino Y, Idezawa Y, Fujinuma A, Suzuki K, Watanabe T. Differences in the roles of the two surface-exposed tyrosine residues, Y240 and Y481, of Serratia marcescens chitinase B during processive degradation of crystalline chitin. J GEN APPL MICROBIOL 2015; 61:255-61. [DOI: 10.2323/jgam.61.255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Hayuki Sugimoto
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University
- Graduate School of Science and Technology, Niigata University
| | - Keita Nakamura
- Graduate School of Science and Technology, Niigata University
| | - Yuji Nishino
- Graduate School of Science and Technology, Niigata University
| | - Yuta Idezawa
- Graduate School of Science and Technology, Niigata University
| | - Akiko Fujinuma
- Graduate School of Science and Technology, Niigata University
| | - Kazushi Suzuki
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University
- Graduate School of Science and Technology, Niigata University
| | - Takeshi Watanabe
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University
- Graduate School of Science and Technology, Niigata University
| |
Collapse
|
141
|
Ranok A, Wongsantichon J, Robinson RC, Suginta W. Structural and thermodynamic insights into chitooligosaccharide binding to human cartilage chitinase 3-like protein 2 (CHI3L2 or YKL-39). J Biol Chem 2014; 290:2617-29. [PMID: 25477513 DOI: 10.1074/jbc.m114.588905] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Four crystal structures of human YKL-39 were solved in the absence and presence of chitooligosaccharides. The structure of YKL-39 comprises a major (β/α)8 triose-phosphate isomerase barrel domain and a small α + β insertion domain. Structural analysis demonstrates that YKL-39 interacts with chitooligosaccharides through hydrogen bonds and hydrophobic interactions. The binding of chitin fragments induces local conformational changes that facilitate tight binding. Compared with other GH-18 members, YKL-39 has the least extended chitin-binding cleft, containing five subsites for sugars, namely (-3)(-2)(-1)(+1)(+2), with Trp-360 playing a prominent role in the sugar-protein interactions at the center of the chitin-binding cleft. Evaluation of binding affinities obtained from isothermal titration calorimetry and intrinsic fluorescence spectroscopy suggests that YKL-39 binds to chitooligosaccharides with Kd values in the micromolar concentration range and that the binding energies increase with the chain length. There were no significant differences between the Kd values of chitopentaose and chitohexaose, supporting the structural evidence for the five binding subsite topology. Thermodynamic analysis indicates that binding of chitooligosaccharide to YKL-39 is mainly driven by enthalpy.
Collapse
Affiliation(s)
- Araya Ranok
- From the Biochemistry-Electrochemistry Research Unit, School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Jantana Wongsantichon
- the Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Biopolis Drive, Singapore 138673, Singapore, and
| | - Robert C Robinson
- the Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Biopolis Drive, Singapore 138673, Singapore, and the Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Wipa Suginta
- From the Biochemistry-Electrochemistry Research Unit, School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand,
| |
Collapse
|
142
|
Sirimontree P, Suginta W, Sritho N, Kanda Y, Shinya S, Ohnuma T, Fukamizo T. Mutation strategies for obtaining chitooligosaccharides with longer chains by transglycosylation reaction of family GH18 chitinase. Biosci Biotechnol Biochem 2014; 78:2014-21. [DOI: 10.1080/09168451.2014.948373] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Abstract
Enhancing the transglycosylation (TG) activity of glycoside hydrolases does not always result in the production of oligosaccharides with longer chains, because the TG products are often decomposed into shorter oligosaccharides. Here, we investigated the mutation strategies for obtaining chitooligosaccharides with longer chains by means of TG reaction catalyzed by family GH18 chitinase A from Vibrio harveyi (VhChiA). HPLC analysis of the TG products from incubation of chitooligosaccharide substrates, GlcNAcn, with several mutant VhChiAs suggested that mutant W570G (mutation of Trp570 to Gly) and mutant D392N (mutation of Asp392 to Asn) significantly enhanced TG activity, but the TG products were immediately hydrolyzed into shorter GlcNAcn. On the other hand, the TG products obtained from mutants D313A and D313N (mutations of Asp313 to Ala and Asn, respectively) were not further hydrolyzed, leading to the accumulation of oligosaccharides with longer chains. The data obtained from the mutant VhChiAs suggested that mutations of Asp313, the middle aspartic acid residue of the DxDxE catalytic motif, to Ala and Asn are most effective for obtaining chitooligosaccharides with longer chains.
Collapse
Affiliation(s)
- Paknisa Sirimontree
- Biochemistry-Electrochemistry Research Unit, Schools of Chemistry and Biochemistry, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Wipa Suginta
- Biochemistry-Electrochemistry Research Unit, Schools of Chemistry and Biochemistry, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Natchanok Sritho
- Biochemistry-Electrochemistry Research Unit, Schools of Chemistry and Biochemistry, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Yuka Kanda
- Department of Advanced Biosciences, Kinki University, Nara, Japan
| | - Shoko Shinya
- Department of Advanced Biosciences, Kinki University, Nara, Japan
| | - Takayuki Ohnuma
- Department of Advanced Biosciences, Kinki University, Nara, Japan
| | - Tamo Fukamizo
- Department of Advanced Biosciences, Kinki University, Nara, Japan
| |
Collapse
|
143
|
Teng Z, Sun C, Liu S, Wang H, Zhang S. Functional characterization of chitinase-3 reveals involvement of chitinases in early embryo immunity in zebrafish. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 46:489-498. [PMID: 24968080 DOI: 10.1016/j.dci.2014.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/14/2014] [Accepted: 06/16/2014] [Indexed: 06/03/2023]
Abstract
The function and mechanism of chitinases in early embryonic development remain largely unknown. We show here that recombinant chitinase-3 (rChi3) is able to hydrolyze the artificial chitin substrate, 4-methylumbelliferyl-β-D-N,N',N″-triacetylchitotrioside, and to bind to and inhibit the growth of the fungus Candida albicans, implicating that Chi3 plays a dual function in innate immunity and chitin-bearing food digestion in zebrafish. This is further corroborated by the expression profile of Chi3 in the liver and gut, which are both immune- and digestion-relevant organs. Compared with rChi3, rChi3-CD lacking CBD still retains partial capacity to bind to C. albicans, but its enzymatic and antifungal activities are significantly reduced. By contrast, rChi3-E140N with the putative catalytic residue E140 mutated shows little affinity to chitin, and its enzymatic and antifungal activities are nearly completely lost. These suggest that both enzymatic and antifungal activities of Chi3 are dependent on the presence of CBD and E140. We also clearly demonstrate that in zebrafish, both the embryo extract and the developing embryo display antifungal activity against C. albicans, and all the findings point to chitinase-3 (Chi3) being a newly-identified factor involved in the antifungal activity. Taken together, a dual function in both innate immunity and food digestion in embryo is proposed for zebrafish Chi3. It also provides a new angle to understand the immune role of chitinases in early embryonic development of animals.
Collapse
Affiliation(s)
- Zinan Teng
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity, Department of Marine Biology, Ocean University of China, Qingdao 266003, China
| | - Chen Sun
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity, Department of Marine Biology, Ocean University of China, Qingdao 266003, China
| | - Shousheng Liu
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity, Department of Marine Biology, Ocean University of China, Qingdao 266003, China
| | - Hongmiao Wang
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity, Department of Marine Biology, Ocean University of China, Qingdao 266003, China
| | - Shicui Zhang
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity, Department of Marine Biology, Ocean University of China, Qingdao 266003, China.
| |
Collapse
|
144
|
Bellinzoni M, Haouz A, Miras I, Magnet S, André-Leroux G, Mukherjee R, Shepard W, Cole ST, Alzari PM. Structural studies suggest a peptidoglycan hydrolase function for the Mycobacterium tuberculosis Tat-secreted protein Rv2525c. J Struct Biol 2014; 188:156-64. [PMID: 25260828 DOI: 10.1016/j.jsb.2014.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/08/2014] [Accepted: 09/16/2014] [Indexed: 11/18/2022]
Abstract
Among the few proteins shown to be secreted by the Tat system in Mycobacterium tuberculosis, Rv2525c is of particular interest, since its gene is conserved in the minimal genome of Mycobacterium leprae. Previous evidence linked this protein to cell wall metabolism and sensitivity to β-lactams. We describe here the crystal structure of Rv2525c that shows a TIM barrel-like fold characteristic of glycoside hydrolases of the GH25 family, which includes prokaryotic and phage-encoded peptidoglycan hydrolases. Structural comparison with other members of this family combined with substrate docking suggest that, although the 'neighbouring group' catalytic mechanism proposed for this family still appears as the most plausible, the identity of residues involved in catalysis in GH25 hydrolases might need to be revised.
Collapse
Affiliation(s)
- Marco Bellinzoni
- Institut Pasteur, Unité de Microbiologie Structurale and CNRS-UMR3528, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Ahmed Haouz
- Institut Pasteur, Plateforme de Cristallographie (CNRS-UMR3528), 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Isabelle Miras
- Institut Pasteur, Plateforme de Cristallographie (CNRS-UMR3528), 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Sophie Magnet
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - Gwénaëlle André-Leroux
- Institut Pasteur, Unité de Microbiologie Structurale and CNRS-UMR3528, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France; Unité Mathématique, Informatique et Génome (MIG), INRA, Domaine de Vilvert, 78352 Jouy en Josas Cedex, France
| | - Raju Mukherjee
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - William Shepard
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, 91192 Gif-sur-Yvette Cedex, France
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - Pedro M Alzari
- Institut Pasteur, Unité de Microbiologie Structurale and CNRS-UMR3528, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| |
Collapse
|
145
|
Di Rosa M, Szychlinska MA, Tibullo D, Malaguarnera L, Musumeci G. Expression of CHI3L1 and CHIT1 in osteoarthritic rat cartilage model. A morphological study. Eur J Histochem 2014; 58:2423. [PMID: 25308850 PMCID: PMC4194398 DOI: 10.4081/ejh.2014.2423] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/02/2014] [Accepted: 07/02/2014] [Indexed: 02/07/2023] Open
Abstract
Osteoarthritis is a degenerative joint disease, which affects millions of people around the world. It occurs when the protective cartilage at the end of bones wears over time, leading to loss of flexibility of the joint, pain and stiffness. The cause of osteoarthritis is unknown, but its development is associated with different factors, such as metabolic, genetic, mechanical and inflammatory ones. In recent years the biological role of chitinases has been studied in relation to different inflammatory diseases and more in particular the elevated levels of human cartilage glycoprotein 39 (CHI3L1) and chitotriosidase (CHIT1) have been reported in a variety of diseases including chronic inflammation and degenerative disorders. The aim of this study was to investigate, by immunohistochemistry, the distribution of CHI3L1 and CHIT1 in osteoarthritic and normal rat articular cartilage, to discover their potential role in the development of this disease. The hypothesis was that the expression of chitinases could increase in OA disease. Immunohistochemical analysis showed that CHI3L1 and CHIT1 staining was very strong in osteoarthritic cartilage, especially in the superficial areas of the cartilage most exposed to mechanical load, while it was weak or absent in normal cartilage. These findings suggest that these two chitinases could be functionally associated with the development of osteoarthritis and could be used as markers, so in the future they could have a role in the daily clinical practice to stage the severity of the disease. However, the longer-term in vivoand in vitro studies are needed to understand the exact mechanism of these molecules, their receptors and activities on cartilage tissue.
Collapse
|
146
|
Mutagenesis and molecular dynamics simulations revealed the chitooligosaccharide entry and exit points for chitinase D from Serratia proteamaculans. Biochim Biophys Acta Gen Subj 2014; 1840:2685-94. [DOI: 10.1016/j.bbagen.2014.06.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 05/27/2014] [Accepted: 06/18/2014] [Indexed: 12/17/2022]
|
147
|
Gooyit M, Tricoche N, Lustigman S, Janda KD. Dual protonophore-chitinase inhibitors dramatically affect O. volvulus molting. J Med Chem 2014; 57:5792-9. [PMID: 24918716 PMCID: PMC4216208 DOI: 10.1021/jm5006435] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The
L3-stage-specific chitinase OvCHT1 has been implicated in the
development of Onchocerca volvulus,
the causative agent of onchocerciasis. Closantel, a known anthelmintic
drug, was previously discovered as a potent and specific OvCHT1 inhibitor.
As closantel is also a known protonophore, we performed a simple scaffold
modulation to map out the structural features that are relevant for
its individual or dual biochemical roles. Furthermore, we present
that either OvCHT1 inhibition or protonophoric activity was capable
of affecting O. volvulus L3 molting
and that the presence of both activities in a single molecule yielded
more potent inhibition of the nematode’s developmental process.
Collapse
Affiliation(s)
- Major Gooyit
- Departments of Chemistry and Immunology and Microbial Science, The Skaggs Institute for Chemical Biology, and The Worm Institute of Research and Medicine, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | | | | | | |
Collapse
|
148
|
Shinya S, Urasaki A, Ohnuma T, Taira T, Suzuki A, Ogata M, Usui T, Lampela O, Juffer AH, Fukamizo T. Interaction of di-N-acetylchitobiosyl moranoline with a family GH19 chitinase from moss, Bryum coronatum. Glycobiology 2014; 24:945-55. [PMID: 24907709 DOI: 10.1093/glycob/cwu052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Tri-N-acetylchitotriosyl moranoline, (GlcNAc)3-M, was previously shown to strongly inhibit lysozyme (Ogata M, Umemoto N, Ohnuma T, Numata T, Suzuki A, Usui T, Fukamizo T. 2013. A novel transition-state analogue for lysozyme, 4-O-β-tri-Nacetylchitotriosyl moranoline, provided evidence supporting the covalent glycosyl-enzyme intermediate. J Biol Chem. 288:6072-6082). The findings prompted us to examine the interaction of di-N-acetylchitobiosyl moranoline, (GlcNAc)2-M, with a family GH19 chitinase from moss, Bryum coronatum (BcChi19A). Thermal unfolding experiments using BcChi19A and the catalytic acid-deficient mutant (BcChi19A-E61A) revealed that the transition temperature (Tm) was elevated by 4.3 and 5.8°C, respectively, upon the addition of (GlcNAc)2-M, while the chitin dimer, (GlcNAc)2, elevated Tm only by 1.0 and 1.4°C, respectively. By means of isothermal titration calorimetry, binding free energy changes for the interactions of (GlcNAc)3 and (GlcNAc)2-M with BcChi19A-E61A were determined to be -5.2 and -6.6 kcal/mol, respectively, while (GlcNAc)2 was found to interact with BcChi19A-E61A with markedly lower affinity. nuclear magnetic resonance titration experiments using (15)N-labeled BcChi19A and BcChi19A-E61A revealed that both (GlcNAc)2 and (GlcNAc)2-M interact with the region surrounding the catalytic center of the enzyme and that the interaction of (GlcNAc)2-M is markedly stronger than that of (GlcNAc)2 for both enzymes. However, (GlcNAc)2-M was found to moderately inhibit the hydrolytic reaction of chitin oligosaccharides catalyzed by BcChi19A (IC50 = 130-620 μM). A molecular dynamics simulation of BcChi19A in complex with (GlcNAc)2-M revealed that the complex is quite stable and the binding mode does not significantly change during the simulation. The moranoline moiety of (GlcNAc)2-M did not fit into the catalytic cleft (subsite -1) but was rather in contact with subsite +1. This situation may result in the moderate inhibition toward the BcChi19A-catalyzed hydrolysis.
Collapse
Affiliation(s)
- Shoko Shinya
- Department of Advanced Bioscience, Kinki University, 3327-204, Nakamachi, Nara 631-8505, Japan
| | - Atsushi Urasaki
- Department of Advanced Bioscience, Kinki University, 3327-204, Nakamachi, Nara 631-8505, Japan
| | - Takayuki Ohnuma
- Department of Advanced Bioscience, Kinki University, 3327-204, Nakamachi, Nara 631-8505, Japan
| | - Toki Taira
- Department of Bioscience and Biotechnology, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Akari Suzuki
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Makoto Ogata
- Department of Chemistry and Biochemistry, Fukushima National College of Technology, 30 Nagao, Iwaki, Fukushima 970-8034, Japan
| | - Taichi Usui
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Outi Lampela
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu 90014, Finland
| | - André H Juffer
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu 90014, Finland
| | - Tamo Fukamizo
- Department of Advanced Bioscience, Kinki University, 3327-204, Nakamachi, Nara 631-8505, Japan
| |
Collapse
|
149
|
Knott BC, Crowley MF, Himmel ME, Ståhlberg J, Beckham GT. Carbohydrate-protein interactions that drive processive polysaccharide translocation in enzymes revealed from a computational study of cellobiohydrolase processivity. J Am Chem Soc 2014; 136:8810-9. [PMID: 24869982 DOI: 10.1021/ja504074g] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Translocation of carbohydrate polymers through protein tunnels and clefts is a ubiquitous biochemical phenomenon in proteins such as polysaccharide synthases, glycoside hydrolases, and carbohydrate-binding modules. Although static snapshots of carbohydrate polymer binding in proteins have long been studied via crystallography and spectroscopy, the molecular details of polysaccharide chain processivity have not been elucidated. Here, we employ simulation to examine how a cellulose chain translocates by a disaccharide unit during the processive cycle of a glycoside hydrolase family 7 cellobiohydrolase. Our results demonstrate that these biologically and industrially important enzymes employ a two-step mechanism for chain threading to form a Michaelis complex and that the free energy barrier to chain threading is significantly lower than the hydrolysis barrier. Taken with previous studies, our findings suggest that the rate-limiting step in enzymatic cellulose degradation is the glycosylation reaction, not chain processivity. Based on the simulations, we find that strong electrostatic interactions with polar residues that are conserved in GH7 cellobiohydrolases, but not in GH7 endoglucanases, at the leading glucosyl ring provide the thermodynamic driving force for polysaccharide chain translocation. Also, we consider the role of aromatic-carbohydrate interactions, which are widespread in carbohydrate-active enzymes and have long been associated with processivity. Our analysis suggests that the primary role for these aromatic residues is to provide tunnel shape and guide the carbohydrate chain to the active site. More broadly, this work elucidates the role of common protein motifs found in carbohydrate-active enzymes that synthesize or depolymerize polysaccharides by chain translocation mechanisms coupled to catalysis.
Collapse
Affiliation(s)
- Brandon C Knott
- National Bioenergy Center and ‡Biosciences Center, National Renewable Energy Laboratory , Golden, Colorado 80401, United States
| | | | | | | | | |
Collapse
|
150
|
Towards a molecular-level theory of carbohydrate processivity in glycoside hydrolases. Curr Opin Biotechnol 2014; 27:96-106. [DOI: 10.1016/j.copbio.2013.12.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 12/04/2013] [Indexed: 10/25/2022]
|