1
|
Radzlin N, Mohamad Ali MS, Goh KM, Yaakop AS, Zakaria II, Kahar UM. Exploring a novel GH13_5 α-amylase from Jeotgalibacillus malaysiensis D5 T for raw starch hydrolysis. AMB Express 2024; 14:71. [PMID: 38874807 PMCID: PMC11178733 DOI: 10.1186/s13568-024-01722-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024] Open
Abstract
α-Amylase plays a crucial role in the industrial degradation of starch. The genus Jeotgalibacillus of the underexplored marine bacteria family Caryophanaceae has not been investigated in terms of α-amylase production. Herein, we report the comprehensive analysis of an α-amylase (AmyJM) from Jeotgalibacillus malaysiensis D5T (= DSM28777T = KCTC33550T). Protein phylogenetic analysis indicated that AmyJM belongs to glycoside hydrolase family 13 subfamily 5 (GH13_5) and exhibits low sequence identity with known α-amylases, with its closest counterpart being the GH13_5 α-amylase from Bacillus sp. KSM-K38 (51.05% identity). Purified AmyJM (molecular mass of 70 kDa) is stable at a pH range of 5.5-9.0 and optimally active at pH 7.5. The optimum temperature for AmyJM is 40 °C, where the enzyme is reasonably stable at this temperature. Similar to other α-amylases, the presence of CaCl2 enhanced both the activity and stability of AmyJM. AmyJM exhibited activity toward raw and gelatinized forms of starches and related α-glucans, generating a mixture of reducing sugars, such as glucose, maltose, maltotriose, maltotetraose, and maltopentaose. In raw starch hydrolysis, AmyJM exhibited its highest efficiency (51.10% degradation) in hydrolyzing raw wheat starch after 3-h incubation at 40 °C. Under the same conditions, AmyJM also hydrolyzed tapioca, sago, potato, rice, and corn raw starches, yielding 16.01-30.05%. These findings highlight the potential of AmyJM as a biocatalyst for the saccharification of raw starches, particularly those derived from wheat.
Collapse
Affiliation(s)
- Nurfatini Radzlin
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, 43000, Kajang, Selangor, Malaysia
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Enzyme Technology Laboratory, Institute Bioscience, Universiti Putra Malaysia, 43400, Serdang, Malaysia
| | - Kian Mau Goh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Amira Suriaty Yaakop
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Pulau Pinang, Malaysia
| | - Iffah Izzati Zakaria
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, 43000, Kajang, Selangor, Malaysia.
| | - Ummirul Mukminin Kahar
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, 43000, Kajang, Selangor, Malaysia.
| |
Collapse
|
2
|
Xi S, Ban X, Kong H, Li C, Gu Z, Li Z. Conserved residues at the family and subfamily levels determine enzyme activity and substrate binding in glycoside hydrolase family 13. Int J Biol Macromol 2023; 253:126980. [PMID: 37729992 DOI: 10.1016/j.ijbiomac.2023.126980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/24/2023] [Accepted: 09/16/2023] [Indexed: 09/22/2023]
Abstract
Site-directed mutagenesis is a valuable strategy for modifying enzymes, but the lack of understanding of conserved residues regulating glycosidase function hinders enzyme design. We analyzed 1662 enzyme sequences to identify conserved amino acids in maltohexaose-forming amylase at both family and subfamily levels. Several conserved residues at the family level (G37, P45, R52, Y57, D101, V103, H106, G230, R232, D234, E264, H330, D331, and G360) were found, mutations of which resulted in reduced enzyme activity or inactivation. At the subfamily level, several conserved residues (L65, E67, F68, D111, E114, R126, R147, F154, W156, F161, G163, D165, W218H, V342, W345, and F346) were identified, which primarily facilitate substrate binding in the enzyme's active site, as shown by molecular dynamics and kinetic assays. Our findings provide critical insights into conserved residues essential for catalysis and can inform targeted enzyme design in protein engineering.
Collapse
Affiliation(s)
- Shixia Xi
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Xiaofeng Ban
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Haocun Kong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Caiming Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, People's Republic of China.
| |
Collapse
|
3
|
Metagenomics reveal the role of microorganism and GH genes contribute to Sichuan South-road dark tea quality formation during pile fermentation. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
|
4
|
Understanding CGTase action through the relationship between starch structure and cyclodextrin formation. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2020.106316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
5
|
Liu Z, Li J, Jie C, Wu B, Hao N. A multifunctional α-amylase BSGH13 from Bacillus subtilis BS-5 possessing endoglucanase and xylanase activities. Int J Biol Macromol 2021; 171:166-176. [PMID: 33421464 DOI: 10.1016/j.ijbiomac.2021.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/25/2020] [Accepted: 01/01/2021] [Indexed: 10/22/2022]
Abstract
Exploring new multifunctional enzymes and understanding the mechanisms of catalytic promiscuity will be of enormous industrial and academic values. In the present study, we reported the discovery and characterization of a multifunctional enzyme BSGH13 from Bacillus subtilis BS-5. Remarkably, BSGH13 possessed α-amylase, endoglucanase, and xylanase activities. To our knowledge, this was the first report on an amylase from Bacillus species having additional endoglucanase and xylanase activities. Subsequently, we analyzed the effects of aromatic residues substitution at each site of the active site architecture on ligand-binding affinity and catalytic specificity of BSGH13 by a combination of virtual mutation and site-directed mutagenesis approaches. Our results indicated that the introduction of aromatic amino acids Phe or Trp at the positions L182 and L183 altered the local interaction network of BSGH13 towards different substrates, thus changing the multifunctional properties of BSGH13. Moreover, we provided an expanded perspective on studies of multifunctional enzymes.
Collapse
Affiliation(s)
- Zhaoxing Liu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China
| | - Jiahuang Li
- School of Biopharmacy, China Pharmaceutical University, 639 Longmian avenue, Nanjing 211198, Jiangsu, China
| | - Chen Jie
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China.
| | - Ning Hao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing 211816, Jiangsu, China.
| |
Collapse
|
6
|
Garcia-Gonzalez M, Minguet-Lobato M, Plou FJ, Fernandez-Lobato M. Molecular characterization and heterologous expression of two α-glucosidases from Metschnikowia spp, both producers of honey sugars. Microb Cell Fact 2020; 19:140. [PMID: 32652991 PMCID: PMC7353701 DOI: 10.1186/s12934-020-01397-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/07/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND α-Glucosidases are widely distributed enzymes with a varied substrate specificity that are traditionally used in biotechnological industries based on oligo- and polysaccharides as starting materials. According to amino acid sequence homology, α-glucosidases are included into two major families, GH13 and GH31. The members of family GH13 contain several α-glucosidases with confirmed hydrolytic activity on sucrose. Previously, a sucrose splitting activity from the nectar colonizing yeast Metschnikowia reukaufii which produced rare sugars with α-(1→1), α-(1→3) and α-(1→6) glycosidic linkages from sucrose was described. RESULTS In this study, genes codifying for α-glucosidases from the nectaries yeast M. gruessii and M. reukaufii were characterised and heterologously expressed in Escherichia coli for the first time. Recombinant proteins (Mg-αGlu and Mr-αGlu) were purified and biochemically analysed. Both enzymes mainly displayed hydrolytic activity towards sucrose, maltose and p-nitrophenyl-α-D-glucopyranoside. Structural analysis of these proteins allowed the identification of common features from the α-amylase family, in particular from glycoside hydrolases that belong to family GH13. The three acidic residues comprising the catalytic triad were identified and their relevance for the protein hydrolytic mechanism confirmed by site-directed mutagenesis. Recombinant enzymes produced oligosaccharides naturally present in honey employing sucrose as initial substrate and gave rise to mixtures with the same products profile (isomelezitose, trehalulose, erlose, melezitose, theanderose and esculose) previously obtained with M. reukaufii cell extracts. Furthermore, the same enzymatic activity was detected with its orthologous Mg-αGlu from M. gruessii. Interestingly, the isomelezitose amounts obtained in reactions mediated by the recombinant proteins, ~ 170 g/L, were the highest reported so far. CONCLUSIONS Mg/Mr-αGlu were heterologously overproduced and their biochemical and structural characteristics analysed. The recombinant α-glucosidases displayed excellent properties in terms of mild reaction conditions, in addition to pH and thermal stability. Besides, the enzymes produced a rare mixture of hetero-gluco-oligosaccharides by transglucosylation, mainly isomelezitose and trehalulose. These compounds are natural constituents of honey which purification from this natural source is quite unviable, what make these enzymes very interesting for the biotechnological industry. Finally, it should be remarked that these sugars have potential applications as food additives due to their suitable sweetness, viscosity and humectant capacity.
Collapse
Affiliation(s)
- Martin Garcia-Gonzalez
- Department of Molecular Biology, Centre for Molecular Biology Severo Ochoa (CSIC-UAM), University Autonomous from Madrid. C/Nicolás Cabrera, 1. Cantoblanco, 28049, Madrid, Spain
| | - Marina Minguet-Lobato
- Department of Molecular Biology, Centre for Molecular Biology Severo Ochoa (CSIC-UAM), University Autonomous from Madrid. C/Nicolás Cabrera, 1. Cantoblanco, 28049, Madrid, Spain
| | - Francisco J Plou
- Institute of Catalysis and Petrochemistry, CSIC, C/Marie Curie, 2. Cantoblanco, 28049, Madrid, Spain
| | - Maria Fernandez-Lobato
- Department of Molecular Biology, Centre for Molecular Biology Severo Ochoa (CSIC-UAM), University Autonomous from Madrid. C/Nicolás Cabrera, 1. Cantoblanco, 28049, Madrid, Spain.
| |
Collapse
|
7
|
Bi J, Chen S, Zhao X, Nie Y, Xu Y. Computation-aided engineering of starch-debranching pullulanase from Bacillus thermoleovorans for enhanced thermostability. Appl Microbiol Biotechnol 2020; 104:7551-7562. [PMID: 32632476 DOI: 10.1007/s00253-020-10764-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/17/2020] [Accepted: 06/30/2020] [Indexed: 12/26/2022]
Abstract
Pullulanases are widely used in food, medicine, and other industries because they specifically hydrolyze α-1,6-glycosidic linkages in starch and oligosaccharides. In addition, high-temperature thermostable pullulanase has multiple advantages, including decreasing saccharification solution viscosity accompanied with enhanced mass transfer and reducing microbial contamination in starch hydrolysis. However, thermophilic pullulanase availability remains limited. Additionally, most do not meet starch-manufacturing requirements due to weak thermostability. Here, we developed a computation-aided strategy to engineer the thermophilic pullulanase from Bacillus thermoleovorans. First, three computational design predictors (FoldX, I-Mutant 3.0, and dDFIRE) were combined to predict stability changes introduced by mutations. After excluding conserved and catalytic sites, 17 mutants were identified. After further experimental verification, we confirmed six positive mutants. Among them, the G692M mutant had the highest thermostability improvement, with 3.8 °C increased Tm and 2.1-fold longer half-life than the wild type at 70 °C. We then characterized the mechanism underlying increased thermostability, such as rigidity enhancement, closer conformation, and strengthened motion correlation using root mean square fluctuation (RMSF), principal component analysis (PCA), dynamic cross-correlation map (DCCM), and free energy landscape (FEL) analysis. KEY POINTS: • A computation-aided strategy was developed to engineer pullulanase thermostability. • Seventeen mutants were identified by combining three computational design predictors. • The G692M mutant was obtained with increased Tmand half-life at 70 °C.
Collapse
Affiliation(s)
- Jiahua Bi
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Shuhui Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xianghan Zhao
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China. .,Suqian Industrial Technology Research Institute of Jiangnan University, Suqian, 223814, China.
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| |
Collapse
|
8
|
Andersen S, Svensson B, Møller MS. Roles of the N-terminal domain and remote substrate binding subsites in activity of the debranching barley limit dextrinase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140294. [DOI: 10.1016/j.bbapap.2019.140294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/15/2019] [Accepted: 10/10/2019] [Indexed: 11/28/2022]
|
9
|
Wang J, Zhang Y, Wang X, Shang J, Li Y, Zhang H, Lu F, Liu F. Biochemical characterization and molecular mechanism of acid denaturation of a novel α-amylase from Aspergillus niger. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
10
|
|
11
|
Andrade AC, Fróes A, Lopes FÁC, Thompson FL, Krüger RH, Dinsdale E, Bruce T. Diversity of Microbial Carbohydrate-Active enZYmes (CAZYmes) Associated with Freshwater and Soil Samples from Caatinga Biome. MICROBIAL ECOLOGY 2017; 74:89-105. [PMID: 28070679 DOI: 10.1007/s00248-016-0911-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/05/2016] [Indexed: 06/06/2023]
Abstract
Semi-arid and arid areas occupy about 33% of terrestrial ecosystems. However, little information is available about microbial diversity in the semi-arid Caatinga, which represents a unique biome that extends to about 11% of the Brazilian territory and is home to extraordinary diversity and high endemism level of species. In this study, we characterized the diversity of microbial genes associated with biomass conversion (carbohydrate-active enzymes, or so-called CAZYmes) in soil and freshwater of the Caatinga. Our results showed distinct CAZYme profiles in the soil and freshwater samples. Glycoside hydrolases and glycosyltransferases were the most abundant CAZYme families, with glycoside hydrolases more dominant in soil (∼44%) and glycosyltransferases more abundant in freshwater (∼50%). The abundances of individual glycoside hydrolase, glycosyltransferase, and carbohydrate-binding module subfamilies varied widely between soil and water samples. A predominance of glycoside hydrolases was observed in soil, and a higher contribution of enzymes involved in carbohydrate biosynthesis was observed in freshwater. The main taxa associated with the CAZYme sequences were Planctomycetia (relative abundance in soil, 29%) and Alphaproteobacteria (relative abundance in freshwater, 27%). Approximately 5-7% of CAZYme sequences showed low similarity with sequences deposited in non-redundant databases, suggesting putative homologues. Our findings represent a first attempt to describe specific microbial CAZYme profiles for environmental samples. Characterizing these enzyme groups associated with the conversion of carbohydrates in nature will improve our understanding of the significant roles of enzymes in the carbon cycle. We identified a CAZYme signature that can be used to discriminate between soil and freshwater samples, and this signature may be related to the microbial species adapted to the habitat. The data show the potential ecological roles of the CAZYme repertoire and associated biotechnological applications.
Collapse
Affiliation(s)
- Ana Camila Andrade
- Faculdade de Tecnologia e Ciências, Grupo de Biotecnologia Ambiental, Department of Bioenergy, Salvador, Brazil
| | - Adriana Fróes
- Laboratory of Microbiology, Institute of Biology, and SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Fabiano L Thompson
- Laboratory of Microbiology, Institute of Biology, and SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | | | - Thiago Bruce
- Faculdade de Tecnologia e Ciências, Grupo de Biotecnologia Ambiental, Department of Bioenergy, Salvador, Brazil.
- Department of Biology, San Diego State University, San Diego, CA, USA.
- Institute of Biology, Microbiology department, Universidade Federal da Bahia (UFBA), Rio de Janeiro, Brazil.
| |
Collapse
|
12
|
Cao H, Yang X, Jin L, Han W, Zhang Y. Module recombination and functional integration of oligosaccharide-producing multifunctional amylase. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.08.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
13
|
Ligand-binding specificity and promiscuity of the main lignocellulolytic enzyme families as revealed by active-site architecture analysis. Sci Rep 2016; 6:23605. [PMID: 27009476 PMCID: PMC4806347 DOI: 10.1038/srep23605] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/09/2016] [Indexed: 02/02/2023] Open
Abstract
Biomass can be converted into sugars by a series of lignocellulolytic enzymes, which belong to the glycoside hydrolase (GH) families summarized in CAZy databases. Here, using a structural bioinformatics method, we analyzed the active site architecture of the main lignocellulolytic enzyme families. The aromatic amino acids Trp/Tyr and polar amino acids Glu/Asp/Asn/Gln/Arg occurred at higher frequencies in the active site architecture than in the whole enzyme structure. And the number of potential subsites was significantly different among different families. In the cellulase and xylanase families, the conserved amino acids in the active site architecture were mostly found at the −2 to +1 subsites, while in β-glucosidase they were mainly concentrated at the −1 subsite. Families with more conserved binding amino acid residues displayed strong selectivity for their ligands, while those with fewer conserved binding amino acid residues often exhibited promiscuity when recognizing ligands. Enzymes with different activities also tended to bind different hydroxyl oxygen atoms on the ligand. These results may help us to better understand the common and unique structural bases of enzyme-ligand recognition from different families and provide a theoretical basis for the functional evolution and rational design of major lignocellulolytic enzymes.
Collapse
|
14
|
Kahar UM, Ng CL, Chan KG, Goh KM. Characterization of a type I pullulanase from Anoxybacillus sp. SK3-4 reveals an unusual substrate hydrolysis. Appl Microbiol Biotechnol 2016; 100:6291-6307. [DOI: 10.1007/s00253-016-7451-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/05/2016] [Accepted: 03/08/2016] [Indexed: 11/29/2022]
|
15
|
Chai KP, Othman NFB, Teh AH, Ho KL, Chan KG, Shamsir MS, Goh KM, Ng CL. Crystal structure of Anoxybacillus α-amylase provides insights into maltose binding of a new glycosyl hydrolase subclass. Sci Rep 2016; 6:23126. [PMID: 26975884 PMCID: PMC4791539 DOI: 10.1038/srep23126] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 02/17/2016] [Indexed: 11/18/2022] Open
Abstract
A new subfamily of glycosyl hydrolase family GH13 was recently proposed for α-amylases from Anoxybacillus species (ASKA and ADTA), Geobacillus thermoleovorans (GTA, Pizzo, and GtamyII), Bacillus aquimaris (BaqA), and 95 other putative protein homologues. To understand this new GH13 subfamily, we report crystal structures of truncated ASKA (TASKA). ASKA is a thermostable enzyme capable of producing high levels of maltose. Unlike GTA, biochemical analysis showed that Ca2+ ion supplementation enhances the catalytic activities of ASKA and TASKA. The crystal structures reveal the presence of four Ca2+ ion binding sites, with three of these binding sites are highly conserved among Anoxybacillus α-amylases. This work provides structural insights into this new GH13 subfamily both in the apo form and in complex with maltose. Furthermore, structural comparison of TASKA and GTA provides an overview of the conformational changes accompanying maltose binding at each subsite.
Collapse
Affiliation(s)
- Kian Piaw Chai
- Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering, 81310 Skudai, Johor, Malaysia
| | - Noor Farhan Binti Othman
- Universiti Kebangsaan Malaysia, Institute of Systems Biology, 43600 UKM Bangi, Selangor, Malaysia
| | - Aik-Hong Teh
- Universiti Sains Malaysia, Centre for Chemical Biology, 11800 Penang, Malaysia
| | - Kok Lian Ho
- Universiti Putra Malaysia, Department of Pathology, Faculty of Medicine and Health Sciences, 43400 Serdang, Selangor, Malaysia
| | - Kok-Gan Chan
- University of Malaya, Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, 50603 Kuala Lumpur, Malaysia
| | - Mohd Shahir Shamsir
- Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering, 81310 Skudai, Johor, Malaysia
| | - Kian Mau Goh
- Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering, 81310 Skudai, Johor, Malaysia
| | - Chyan Leong Ng
- Universiti Kebangsaan Malaysia, Institute of Systems Biology, 43600 UKM Bangi, Selangor, Malaysia
| |
Collapse
|
16
|
Identification of a novel alkaline amylopullulanase from a gut metagenome of Hermetia illucens. Int J Biol Macromol 2016; 82:514-21. [DOI: 10.1016/j.ijbiomac.2015.10.067] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/19/2015] [Accepted: 10/20/2015] [Indexed: 10/22/2022]
|
17
|
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
|
18
|
Chen F, Xie T, Yue Y, Qian S, Chao Y, Pei J. Molecular dynamic analysis of mutant Y195I α-cyclodextrin glycosyltransferase with switched product specificity from α-cyclodextrin to γ-cyclodextrin. J Mol Model 2015. [PMID: 26216223 DOI: 10.1007/s00894-015-2734-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alpha-cyclodextrin (α-CD) glycosyltransferase (α-CGTase) can convert starch into α-CD blended with various proportions of β-cyclodextrin (β-CD) and/or γ-cyclodextrin (γ-CD). In this study, we verified the catalytic characteristics of purified Y195I α-CGTase and elucidated the mechanism of action with molecular dynamic (MD) simulations. We found that purified Y195I α-CGTase produced less α-CD, slightly more β-CD, and significantly more γ-CD than wild-type α-CGTase. Correspondingly, α-CD-based K m values increased, and β-CD- and γ-CD-based K m values decreased. MD simulation studies revealed that the dynamic trajectories of the substrate oligosaccharide chain in the mutant CGTase binding site were significantly different from those in the wild-type enzyme, with reduced hydrophobic interaction, finally resulting in different product specificity and more γ-CD formation.
Collapse
Affiliation(s)
- Fangjin Chen
- Center for Quantitative Biology, AAIS, Peking University, Beijing, China, 100871
| | | | | | | | | | | |
Collapse
|
19
|
Melzer S, Sonnendecker C, Föllner C, Zimmermann W. Stepwise error-prone PCR and DNA shuffling changed the pH activity range and product specificity of the cyclodextrin glucanotransferase from an alkaliphilic Bacillus sp. FEBS Open Bio 2015; 5:528-34. [PMID: 26155461 PMCID: PMC4491590 DOI: 10.1016/j.fob.2015.06.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/29/2015] [Accepted: 06/04/2015] [Indexed: 01/26/2023] Open
Abstract
We performed random mutagenesis experiments with a cyclodextrin glucanotransferase. Error-prone PCR and DNA shuffling steps were combined. Variants with a broad pH activity range could be obtained. Several variants showed increased product specificity for γ-cyclodextrin.
Cyclodextrin glucanotransferase (EC 2.4.1.19) from the alkaliphilic Bacillus sp. G-825-6 converts starch mainly to γ-cyclodextrin (CD8). A combination of error-prone PCR and DNA shuffling was used to obtain variants of this enzyme with higher product specificity for CD8 and a broad pH activity range. The variant S54 with seven amino acid substitutions showed a 1.2-fold increase in CD8-synthesizing activity and the product ratio of CD7:CD8 was shifted to 1:7 compared to 1:3 of the wild-type enzyme. Nine amino acid substitutions of the cyclodextrin glucanotransferase were performed to generate the variant S35 active in a pH range 4.0–10.0. Compared to the wild-type enzyme which is inactive below pH 6.0, S35 retained 70% of its CD8-synthesizing activity at pH 4.0.
Collapse
Affiliation(s)
- Susanne Melzer
- Institute of Biochemistry, Department of Microbiology and Bioprocess Technology, Leipzig University, Johannisallee 23, 04103 Leipzig, Germany
| | - Christian Sonnendecker
- Institute of Biochemistry, Department of Microbiology and Bioprocess Technology, Leipzig University, Johannisallee 23, 04103 Leipzig, Germany
| | - Christina Föllner
- Institute of Biochemistry, Department of Microbiology and Bioprocess Technology, Leipzig University, Johannisallee 23, 04103 Leipzig, Germany
| | - Wolfgang Zimmermann
- Institute of Biochemistry, Department of Microbiology and Bioprocess Technology, Leipzig University, Johannisallee 23, 04103 Leipzig, Germany
| |
Collapse
|
20
|
Li C, Wu AC, Go RM, Malouf J, Turner MS, Malde AK, Mark AE, Gilbert RG. The characterization of modified starch branching enzymes: toward the control of starch chain-length distributions. PLoS One 2015; 10:e0125507. [PMID: 25874689 PMCID: PMC4395411 DOI: 10.1371/journal.pone.0125507] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 03/21/2015] [Indexed: 11/18/2022] Open
Abstract
Starch is a complex branched glucose polymer whose branch molecular weight distribution (the chain-length distribution, CLD) influences nutritionally important properties such as digestion rate. Chain-stopping in starch biosynthesis is by starch branching enzyme (SBE). Site-directed mutagenesis was used to modify SBEIIa from Zea mays (mSBEIIa) to produce mutants, each differing in a single conserved amino-acid residue. Products at different times from in vitro branching were debranched and the time evolution of the CLD measured by size-exclusion chromatography. The results confirm that Tyr352, Glu513, and Ser349 are important for mSBEIIa activity while Arg456 is important for determining the position at which the linear glucan is cut. The mutant mSBEIIa enzymes have different activities and suggest the length of the transferred chain can be varied by mutation. The work shows analysis of the molecular weight distribution can yield information regarding the enzyme branching sites useful for development of plants yielding starch with improved functionality.
Collapse
Affiliation(s)
- Cheng Li
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Centre for Nutrition and Food Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Alex Chi Wu
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Centre for Nutrition and Food Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Rob Marc Go
- Centre for Nutrition and Food Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Jacob Malouf
- Centre for Nutrition and Food Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Mark S. Turner
- Centre for Nutrition and Food Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Alpeshkumar K. Malde
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Alan E. Mark
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Robert G. Gilbert
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Centre for Nutrition and Food Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
- * E-mail:
| |
Collapse
|
21
|
Oligosaccharide and Substrate Binding in the Starch Debranching Enzyme Barley Limit Dextrinase. J Mol Biol 2015; 427:1263-1277. [DOI: 10.1016/j.jmb.2014.12.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 12/20/2014] [Accepted: 12/27/2014] [Indexed: 11/21/2022]
|
22
|
Qiao Y, Peng Q, Yan J, Wang H, Ding H, Shi B. Gene cloning and enzymatic characterization of alkali-tolerant type I pullulanase from Exiguobacterium acetylicum. Lett Appl Microbiol 2014; 60:52-9. [DOI: 10.1111/lam.12333] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Y. Qiao
- Feed Research Institute; Chinese Academy of Agricultural Sciences; Beijing China
| | - Q. Peng
- Feed Research Institute; Chinese Academy of Agricultural Sciences; Beijing China
| | - J. Yan
- Feed Research Institute; Chinese Academy of Agricultural Sciences; Beijing China
| | - H. Wang
- Feed Research Institute; Chinese Academy of Agricultural Sciences; Beijing China
| | - H. Ding
- Feed Research Institute; Chinese Academy of Agricultural Sciences; Beijing China
| | - B. Shi
- Feed Research Institute; Chinese Academy of Agricultural Sciences; Beijing China
| |
Collapse
|
23
|
Han R, Li J, Shin HD, Chen RR, Du G, Liu L, Chen J. Recent advances in discovery, heterologous expression, and molecular engineering of cyclodextrin glycosyltransferase for versatile applications. Biotechnol Adv 2013; 32:415-28. [PMID: 24361954 DOI: 10.1016/j.biotechadv.2013.12.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 12/04/2013] [Accepted: 12/16/2013] [Indexed: 12/30/2022]
Abstract
Cyclodextrin glycosyltransferase (CGTase) is an important enzyme with multiple functions, in particular the production of cyclodextrins. It is also widely applied in baking and carbohydrate glycosylation because it participates in various types of catalytic reactions. New applications are being found with novel CGTases being isolated from various organisms. Heterologous expression is performed for the overproduction of CGTases to meet the requirements of these applications. In addition, various directed evolution techniques have been applied to modify the molecular structure of CGTase for improved performance in industrial applications. In recent years, substantial progress has been made in the heterologous expression and molecular engineering of CGTases. In this review, we systematically summarize the heterologous expression strategies used for enhancing the production of CGTases. We also outline and discuss the molecular engineering approaches used to improve the production, secretion, and properties (e.g., product and substrate specificity, catalytic efficiency, and thermal stability) of CGTase.
Collapse
Affiliation(s)
- Ruizhi Han
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, Wuxi 214122, China
| | - Hyun-Dong Shin
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta 30332, USA
| | - Rachel R Chen
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta 30332, USA
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, Wuxi 214122, China.
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, Wuxi 214122, China.
| | - Jian Chen
- National Engineering of Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
24
|
Daudé D, Topham CM, Remaud-Siméon M, André I. Probing impact of active site residue mutations on stability and activity of Neisseria polysaccharea amylosucrase. Protein Sci 2013; 22:1754-65. [PMID: 24115119 DOI: 10.1002/pro.2375] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 09/10/2013] [Indexed: 11/06/2022]
Abstract
The amylosucrase from Neisseria polysaccharea is a transglucosidase from the GH13 family of glycoside-hydrolases that naturally catalyzes the synthesis of α-glucans from the widely available donor sucrose. Interestingly, natural molecular evolution has modeled a dense hydrogen bond network at subsite -1 responsible for the specific recognition of sucrose and conversely, it has loosened interactions at the subsite +1 creating a highly promiscuous subsite +1. The residues forming these subsites are considered to be likely involved in the activity as well as the overall stability of the enzyme. To assess their role, a structure-based approach was followed to reshape the subsite -1. A strategy based on stability change predictions, using the FoldX algorithm, was considered to identify the best candidates for site-directed mutagenesis and guide the construction of a small targeted library. A miniaturized purification protocol was developed and both mutant stability and substrate promiscuity were explored. A range of 8 °C between extreme melting temperature values was observed and some variants were able to synthesize series of oligosaccharides with distributions differing from that of the parental enzyme. The crucial role of subsite -1 was thus highlighted and the biocatalysts generated can now be considered as starting points for further engineering purposes.
Collapse
Affiliation(s)
- David Daudé
- Université de Toulouse; INSA, UPS,INP, LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France; CNRS, UMR5504, F-31400, Toulouse, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France
| | | | | | | |
Collapse
|
25
|
Iterative saturation mutagenesis of -6 subsite residues in cyclodextrin glycosyltransferase from Paenibacillus macerans to improve maltodextrin specificity for 2-O-D-glucopyranosyl-L-ascorbic acid synthesis. Appl Environ Microbiol 2013; 79:7562-8. [PMID: 24077706 DOI: 10.1128/aem.02918-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2-O-d-Glucopyranosyl-l-ascorbic acid (AA-2G), a stable l-ascorbic acid derivative, is usually synthesized by cyclodextrin glycosyltransferase (CGTase), which contains nine substrate-binding subsites (from +2 to -7). In this study, iterative saturation mutagenesis (ISM) was performed on the -6 subsite residues (Y167, G179, G180, and N193) in the CGTase from Paenibacillus macerans to improve its specificity for maltodextrin, which is a cheap and easily soluble glycosyl donor for AA-2G synthesis. Site saturation mutagenesis of four sites-Y167, G179, G180, and N193-was first performed and revealed that four mutants-Y167S, G179R, N193R, and G180R-produced AA-2G yields higher than those of other mutant and wild-type CGTases. ISM was then conducted with the best positive mutant as a template. Under optimal conditions, mutant Y167S/G179K/N193R/G180R produced the highest AA-2G titer of 2.12 g/liter, which was 84% higher than that (1.15 g/liter) produced by the wild-type CGTase. Kinetics analysis of AA-2G synthesis using mutant CGTases confirmed the enhanced maltodextrin specificity and showed that compared to the wild-type CGTase, the mutants had no cyclization activity but high hydrolysis and disproportionation activities. A possible mechanism for the enhanced substrate specificity was also analyzed through structure modeling of the mutant and wild-type CGTases. These results indicated that the -6 subsite played crucial roles in the substrate binding and catalytic reactions of CGTase and that the obtained CGTase mutants, especially Y167S/G179K/N193R/G180R, are promising starting points for further development through protein engineering.
Collapse
|
26
|
Song B, Yue Y, Xie T, Qian S, Chao Y. Mutation of Tyrosine167Histidine at Remote Substrate Binding Subsite −6 in α-Cyclodextrin Glycosyltransferase Enhancing α-Cyclodextrin Specificity by Directed Evolution. Mol Biotechnol 2013; 56:232-9. [DOI: 10.1007/s12033-013-9699-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
27
|
Trp358 is a key residue for the multiple catalytic activities of multifunctional amylase OPMA-N from Bacillus sp. ZW2531-1. Appl Microbiol Biotechnol 2013; 98:2101-11. [DOI: 10.1007/s00253-013-5085-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 06/22/2013] [Accepted: 06/25/2013] [Indexed: 11/29/2022]
|
28
|
Guan Q, Guo X, Han T, Wei M, Jin M, Zeng F, Liu L, Li Z, Wang Y, Cheong GW, Zhang S, Jia B. Cloning, purification and biochemical characterisation of an organic solvent-, detergent-, and thermo-stable amylopullulanase from Thermococcus kodakarensis KOD1. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
29
|
Chen W, Xie T, Shao Y, Chen F. Phylogenomic relationships between amylolytic enzymes from 85 strains of fungi. PLoS One 2012; 7:e49679. [PMID: 23166747 PMCID: PMC3499471 DOI: 10.1371/journal.pone.0049679] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 10/12/2012] [Indexed: 01/09/2023] Open
Abstract
Fungal amylolytic enzymes, including α-amylase, gluocoamylase and α-glucosidase, have been extensively exploited in diverse industrial applications such as high fructose syrup production, paper making, food processing and ethanol production. In this paper, amylolytic genes of 85 strains of fungi from the phyla Ascomycota, Basidiomycota, Chytridiomycota and Zygomycota were annotated on the genomic scale according to the classification of glycoside hydrolase (GH) from the Carbohydrate-Active enZymes (CAZy) Database. Comparisons of gene abundance in the fungi suggested that the repertoire of amylolytic genes adapted to their respective lifestyles. Amylolytic enzymes in family GH13 were divided into four distinct clades identified as heterologous α- amylases, eukaryotic α-amylases, bacterial and fungal α-amylases and GH13 α-glucosidases. Family GH15 had two branches, one for gluocoamylases, and the other with currently unknown function. GH31 α-glucosidases showed diverse branches consisting of neutral α-glucosidases, lysosomal acid α-glucosidases and a new clade phylogenetically related to the bacterial counterparts. Distribution of starch-binding domains in above fungal amylolytic enzymes was related to the enzyme source and phylogeny. Finally, likely scenarios for the evolution of amylolytic enzymes in fungi based on phylogenetic analyses were proposed. Our results provide new insights into evolutionary relationships among subgroups of fungal amylolytic enzymes and fungal evolutionary adaptation to ecological conditions.
Collapse
Affiliation(s)
- Wanping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Ting Xie
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Yanchun Shao
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei Province, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Fusheng Chen
- National Key Laboratory of Agro-Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, China
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei Province, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
- * E-mail:
| |
Collapse
|
30
|
Leemhuis H, Pijning T, Dobruchowska JM, Dijkstra BW, Dijkhuizen L. Glycosidic bond specificity of glucansucrases: on the role of acceptor substrate binding residues. BIOCATAL BIOTRANSFOR 2012. [DOI: 10.3109/10242422.2012.676301] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
31
|
Noguchi J, Chaen K, Vu NT, Akasaka T, Shimada H, Nakashima T, Nishi A, Satoh H, Omori T, Kakuta Y, Kimura M. Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding. Glycobiology 2011; 21:1108-16. [DOI: 10.1093/glycob/cwr049] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
32
|
Kumar V. Identification of the sequence motif of glycoside hydrolase 13 family members. Bioinformation 2011; 6:61-3. [PMID: 21544166 PMCID: PMC3082856 DOI: 10.6026/97320630006061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 02/07/2011] [Indexed: 11/23/2022] Open
Abstract
A bioinformatics analysis of sequences of enzymes of the glycoside hydrolase (GH) 13 family members such as α-amylase, cyclodextrin glycosyltransferase (CGTase), branching enzyme and cyclomaltodextrinase has been carried out in order to find out the sequence motifs that govern the reactions specificities of these enzymes by using hidden Markov model (HMM) profile. This analysis suggests the existence of such sequence motifs and residues of these motifs constituting the -1 to +3 catalytic subsites of the enzyme. Hence, by introducing mutations in the residues of these four subsites, one can change the reaction specificities of the enzymes. In general it has been observed that α -amylase sequence motif have low sequence conservation than rest of the motifs of the GH13 family members.
Collapse
Affiliation(s)
- Vikash Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| |
Collapse
|
33
|
Computer-aided subsite mapping of α-amylases. Carbohydr Res 2011; 346:410-5. [DOI: 10.1016/j.carres.2010.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 11/30/2010] [Accepted: 12/03/2010] [Indexed: 11/19/2022]
|
34
|
Mori T, Nishimoto T, Okura T, Chaen H, Fukuda S. Cloning, Sequencing and Expression of the Genes Encoding Cyclic .ALPHA.-Maltosyl-(1.RAR.6)-maltose Hydrolase and .ALPHA.-Glucosidase from an Arthrobacter globiformis Strain. J Appl Glycosci (1999) 2011. [DOI: 10.5458/jag.jag.jag-2010_011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
35
|
Kumar V. Identification of the conserved spatial position of key active-site atoms in glycoside hydrolase 13 family members. Carbohydr Res 2010; 345:1564-9. [PMID: 20557875 DOI: 10.1016/j.carres.2010.04.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 04/22/2010] [Accepted: 04/27/2010] [Indexed: 11/30/2022]
Abstract
A computational study on the glycoside hydrolase 13 (GH13) family of the CAZy database has been carried out at the atomic level in order to identify the conserved positions that may be responsible for recognition of the substrate. Analysis with substrate analog-, inhibitor-, or product-bound 3D structures was carried out to find the atomic spatial arrangement of the amino acids that make -2, -1, +1, and +2 subsites and water oxygen atoms around the ligand. The identified conserved positions of subsites were independent from the nature of the amino acid. The -1 and +1 subsites have more conserved positions than the -2 and +2 subsites. Some of the clusters of the -1 and +1 subsites have atoms of the same chemical nature. A spatially conserved position for water, which is stabilized by a hydrogen bond with the carboxyl group of a proton donor (Glu) and Asp of the catalytic triad, was found in the -1 subsite of 75% of the enzymes subjected to analysis. This position could be the region of hydrolytic water.
Collapse
Affiliation(s)
- Vikash Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, India.
| |
Collapse
|