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Rai R, Samanta D, Goh KM, Chadha BS, Sani RK. Biochemical unravelling of the endoxylanase activity in a bifunctional GH39 enzyme cloned and expressed from thermophilic Geobacillus sp. WSUCF1. Int J Biol Macromol 2024; 257:128679. [PMID: 38072346 DOI: 10.1016/j.ijbiomac.2023.128679] [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: 06/13/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 01/27/2024]
Abstract
The glycoside hydrolase family 39 (GH39) proteins are renowned for their extremophilic and multifunctional enzymatic properties, yet the molecular mechanisms underpinning these unique characteristics continue to be an active subject of research. In this study, we introduce WsuXyn, a GH39 protein with a molecular weight of 58 kDa, originating from the thermophilic Geobacillus sp. WSUCF1. Previously reported for its exceptional thermostable β-xylosidase activity, WsuXyn has recently demonstrated a significant endoxylanase activity (3752 U·mg-1) against beechwood xylan, indicating towards its bifunctional nature. Physicochemical characterization revealed that WsuXyn exhibits optimal endoxylanase activity at 70 °C and pH 7.0. Thermal stability assessments revealed that the enzyme is resilient to elevated temperatures, with a half-life of 168 h. Key kinetic parameters highlight the exceptional catalytic efficiency and strong affinity of the protein for xylan substrate. Moreover, WsuXyn-mediated hydrolysis of beechwood xylan has achieved 77 % xylan conversion, with xylose as the primary product. Structural analysis, amalgamated with docking simulations, has revealed strong binding forces between xylotetraose and the protein, with key amino acid residues, including Glu278, Tyr230, Glu160, Gly202, Cys201, Glu324, and Tyr283, playing pivotal roles in these interactions. Therefore, WsuXyn holds a strong promise for biodegradation and value-added product generation through lignocellulosic biomass conversion.
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Affiliation(s)
- Rohit Rai
- Faculty of Applied Medical Sciences, Lovely Professional University, Phagwara 144411, India.
| | - Dipayan Samanta
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia
| | | | - Rajesh K Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; BuG ReMeDEE consortium and Composite and Nanocomposite Advanced Manufacturing Centre/Biomaterials (CNAM/Bio), Rapid City, SD 57701, USA.
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Purohit A, Singh G, Yadav SK. Chimeric bi-functional enzyme possessing xylanase and deacetylase activity for hydrolysis of agro-biomass rich in acetylated xylan. Colloids Surf B Biointerfaces 2021; 204:111832. [PMID: 33984614 DOI: 10.1016/j.colsurfb.2021.111832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
Here, a chimeric bifunctional enzyme was developed for two activities xylanase and deacetylase. Chimeric enzyme was designed by combining the relevant amino acid stretches from two different parent sequences, such as polysaccharide/xylan deacetylase (ref id: MT682066) and xylanase (ref id WP_110897546.1). Five different hypothetical chimeras were developed and one of the best predicted chimeric protein GA_2(syn_SKYAP01) was synthesized. The GA_2(syn_SKYAP01) possessed the specific activity of 14.905 ± 0.8 U/mg for deacetylase and 100.87 ± 14.2 U/mg for xylanase. Optimum level of both the activities together was achieved at pH 5 and 60 °C. The chimeric protein was also found to be stable at higher temperature of 71°C. Functionality of the developed chimeric protein for both the activities was confirmed by the hydrolysis of commercial xylan into xylooligosaccharides and the release of acetic acid from glucose pentacetate and 7-amino cephalosporin. The designed bifunctional enzyme was found to be highly efficient.
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Affiliation(s)
- Anjali Purohit
- Center of Innovative and Applied Bioprocessing (CIAB), Sector-81 (Knowledge City), Mohali, 140306, PB, India
| | - Gurjant Singh
- Center of Innovative and Applied Bioprocessing (CIAB), Sector-81 (Knowledge City), Mohali, 140306, PB, India
| | - Sudesh Kumar Yadav
- Center of Innovative and Applied Bioprocessing (CIAB), Sector-81 (Knowledge City), Mohali, 140306, PB, India.
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Cao H, Sun L, Huang Y, Liu X, Yang D, Liu T, Jia X, Wen B, Gu T, Wang F, Xin F. Structural Insights into the Dual-Substrate Recognition and Catalytic Mechanisms of a Bifunctional Acetyl Ester–Xyloside Hydrolase from Caldicellulosiruptor lactoaceticus. ACS Catal 2019. [DOI: 10.1021/acscatal.8b03383] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Hao Cao
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lichao Sun
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ying Huang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xin Liu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Dong Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Tengfei Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China
| | - Xiaojing Jia
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Boting Wen
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tianyi Gu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fengzhong Wang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fengjiao Xin
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Yang Y, Zhu N, Yang J, Lin Y, Liu J, Wang R, Wang F, Yuan H. A novel bifunctional acetyl xylan esterase/arabinofuranosidase from Penicillium chrysogenum P33 enhances enzymatic hydrolysis of lignocellulose. Microb Cell Fact 2017; 16:166. [PMID: 28950907 PMCID: PMC5615437 DOI: 10.1186/s12934-017-0777-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/18/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Xylan, the major constituent of hemicellulose, is composed of β-(1,4)-linked xylopyranosyl units that for the backbone, with side chains formed by other chemical moieties such as arabinose, galactose, mannose, ferulic acid and acetyl groups. Acetyl xylan esterases and α-L-arabinofuranosidases are two important accessory enzymes that remove side chain residues from xylan backbones and may act in synergy with other xylanolytic enzymes. Compared with enzymes possessing a single catalytic activity, multifunctional enzymes can achieve lignocellulosic biomass hydrolysis using a less complex mixture of enzymes. RESULTS Here, we cloned an acetyl xylan esterase (PcAxe) from Penicillium chrysogenum P33 and expressed it in Pichia pastoris GS115. The optimal pH and temperature of the recombinant PcAxe (rPcAxe) for 4-nitrophenyl acetate were 7.0 and 40 °C, respectively. rPcAxe is stable across a broad pH range, retaining 100% enzyme activity om pH 6-9 after a 1 h incubation. The enzyme tolerates the presence of a wide range of metal ions. Sequence alignment revealed a GH62 domain exhibiting α-L-arabinofuranosidase activity with pH and temperature optima of pH 7.0 and 50 °C, in addition to the expected esterase domain. rPcAxe displayed significant synergy with a recombinant xylanase, with a degree of synergy of 1.35 for the hydrolysis of delignified corn stover. Release of glucose was increased by 51% from delignified corn stover when 2 mg of a commercial cellulase was replaced by an equivalent amount of rPcAxe, indicating superior hydrolytic efficiency. CONCLUSIONS The novel bifunctional enzyme PcAxe was identified in P. chrysogenum P33. rPcAxe includes a carbohydrate esterase domain and a glycosyl hydrolase family 62 domain. This is the first detailed report on a novel bifunctional enzyme possessing acetyl xylan esterase and α-L-arabinofuranosidase activities. These findings expand our current knowledge of glycoside hydrolases and pave the way for the discovery of similar novel enzymes.
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Affiliation(s)
- Yi Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ning Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jinshui Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yujian Lin
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiawen Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ruonan Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Fengqin Wang
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- National Energy R & D Center for Non-food Biomass, China Agricultural University, Beijing, China
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Multiple nucleophilic elbows leading to multiple active sites in a single module esterase from Sorangium cellulosum. J Struct Biol 2015; 190:314-27. [DOI: 10.1016/j.jsb.2015.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 03/25/2015] [Accepted: 04/10/2015] [Indexed: 11/17/2022]
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Identification of GH10 xylanases in strains 2 and Mz5 of Pseudobutyrivibrio xylanivorans. Folia Microbiol (Praha) 2014; 59:507-14. [PMID: 24942109 DOI: 10.1007/s12223-014-0329-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 06/11/2014] [Indexed: 11/27/2022]
Abstract
Genes encoding glycosyl hydrolase family 11 (GH11) xylanases and xylanases have been identified from Pseudobutyrivibrio xylanivorans. In contrast, little is known about the diversity and distribution of the GH10 xylanase in strains of P. xylanivorans. Xylanase and associated activities of P. xylanivorans have been characterized in detail in the type strain, Mz5. The aim of the present study was to identify GH10 xylanase genes in strains 2 and Mz5 of P. xylanivorans. In addition, we evaluated degradation and utilization of xylan by P. xylanivorans 2 isolated from rumen of Creole goats. After a 12-h culture, P. xylanivorans 2 was able to utilize up to 53% of the total pentose content present in birchwood xylan (BWX) and to utilize up to 62% of a ethanol-acetic acid-soluble fraction prepared from BWX. This is the first report describing the presence of GH10 xylanase-encoding genes in P. xylanivorans. Strain 2 and Mz5 contained xylanases which were related to GH10 xylanase of Butyrivibrio sp. Identifying xylanase-encoding genes and activity of these enzymes are a step toward understanding possible functional role of P. xylanivorans in the rumen ecosystem and contribute to providing an improved choice of enzymes for improving fiber digestion in ruminant animals, agricultural biomass utilization for biofuel production, and other industries.
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Grilli DJ, Cerón ME, Paez S, Egea V, Schnittger L, Cravero S, Escudero MS, Allegretti L, Arenas GN. Isolation of Pseudobutyrivibrio ruminis and Pseudobutyrivibrio xylanivorans from rumen of Creole goats fed native forage diet. Folia Microbiol (Praha) 2012; 58:367-73. [PMID: 23275250 DOI: 10.1007/s12223-012-0219-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 12/20/2012] [Indexed: 11/24/2022]
Abstract
We isolated and identified functional groups of bacteria in the rumen of Creole goats involved in ruminal fermentation of native forage shrubs. The functional bacterial groups were evaluated by comparing the total viable, total anaerobic, cellulolytic, hemicellulolytic, and amylolytic bacterial counts in the samples taken from fistulated goats fed native forage diet (Atriplex lampa and Prosopis flexuosa). Alfalfa hay and corn were used as control diet. The roll tubes method increased the possibility of isolating and 16S rDNA gene sequencing allowed definitive identification of bacterial species involved in the ruminal fermentation. The starch and fiber contents of the diets influenced the number of total anaerobic bacteria and fibrolytic and amylolytic functional groups. Pseudobutyrivibrio ruminis and Pseudobutyrivibrio xylanivorans were the main species isolated and identified. The identification of bacterial strains involved in the rumen fermentation helps to explain the ability of these animals to digest fiber plant cell wall contained in native forage species.
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Affiliation(s)
- D J Grilli
- Cátedra de Bacteriología, Facultad de Ciencias Veterinarias y Ambientales, Universidad Juan Agustín Maza, Av. Acceso Este Lateral Sur 2245, CP 5519, Mendoza, Argentina.
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Pai CK, Wu ZY, Chen MJ, Zeng YF, Chen JW, Duan CH, Li ML, Liu JR. Molecular cloning and characterization of a bifunctional xylanolytic enzyme from Neocallimastix patriciarum. Appl Microbiol Biotechnol 2009; 85:1451-62. [DOI: 10.1007/s00253-009-2175-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/29/2009] [Accepted: 07/29/2009] [Indexed: 11/24/2022]
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Bifunctional xylanases and their potential use in biotechnology. J Ind Microbiol Biotechnol 2008; 35:635-44. [DOI: 10.1007/s10295-008-0342-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Revised: 03/06/2008] [Accepted: 03/06/2008] [Indexed: 10/22/2022]
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Cepeljnik T, Lah B, Narat M, Marinsek-Logar R. Adaptation of adhesion test using Caco-2 cells for anaerobic bacterium Pseudobutyrivibrio xylanivorans, a probiotic candidate. Folia Microbiol (Praha) 2008; 52:367-73. [PMID: 18062185 DOI: 10.1007/bf02932091] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Pseudobutyrivibrio xylanivorans strain Mz5(T), an anaerobic bacterium (originating from the rumen of a Holstein-Friesian cow), has some attributes that make it a possible probiotic strain (very active hydrolases, bacteriocin and conjugated linoleic acid production). For the estimation of its adhesion ability, the adhesion test on Caco-2 cells was introduced and adapted. The adhesion was performed in an anaerobic glove box in standard 24-well plates at neutral pH for 30 min. The best method for separation of the adhered bacteria from Caco-2 cells appeared to be homogenization with an automatic pipette. The number of adhered bacteria was too small to be determined microscopically, so a new approach, i.e. detection of the apparent lag phase in liquid growth medium was tested. Under the selected assay conditions 1.04 bacterial cells from the late exponential phase adhered to one Caco-2 cell, which confirms the adhesion capability of P. xylanivorans Mz5(T). The adapted adhesion test using Caco-2 cells is suitable for estimation of adhesion capability of anaerobic bacteria.
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Affiliation(s)
- T Cepeljnik
- Zootechnical Department, Biotechnical Faculty, University of Ljubljana, 1230 Domzale, Slovenia
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Production of feed enzymes (phytase and plant cell wall hydrolyzing enzymes) byMucor indicus MTCC 6333: Purification and characterization of phytase. Folia Microbiol (Praha) 2007; 52:491-7. [DOI: 10.1007/bf02932109] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Grootaert C, Delcour JA, Courtin CM, Broekaert WF, Verstraete W, Van de Wiele T. Microbial metabolism and prebiotic potency of arabinoxylan oligosaccharides in the human intestine. Trends Food Sci Technol 2007. [DOI: 10.1016/j.tifs.2006.08.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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