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St John FJ, Bynum L, Tauscheck DA, Crooks C. Use of xylosidase 3C from Segatella baroniae to discriminate xylan non-reducing terminus substitution characteristics. BMC Res Notes 2024; 17:175. [PMID: 38915023 PMCID: PMC11197168 DOI: 10.1186/s13104-024-06835-3] [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: 09/15/2023] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
OBJECTIVE New characterized carbohydrate-active enzymes are needed for use as tools to discriminate complex carbohydrate structural features. Fungal glycoside hydrolase family 3 (GH3) β-xylosidases have been shown to be useful for the structural elucidation of glucuronic acid (GlcA) and arabinofuranose (Araf) substituted oligoxylosides. A homolog of these GH3 fungal enzymes from the bacterium Segatella baroniae (basonym Prevotella bryantii), Xyl3C, has been previously characterized, but those studies did not address important functional specificity features. In an interest to utilize this enzyme for laboratory methods intended to discriminate the structure of the non-reducing terminus of substituted xylooligosaccharides, we have further characterized this GH3 xylosidase. RESULTS In addition to verification of basic functional characteristics of this xylosidase we have determined its mode of action as it relates to non-reducing end xylose release from GlcA and Araf substituted oligoxylosides. Xyl3C cleaves xylose from the non-reducing terminus of β-1,4-xylan until occurrence of a penultimate substituted xylose. If this substitution is O2 linked, then Xyl3C removes the non-reducing xylose to leave the substituted xylose as the new non-reducing terminus. However, if the substitution is O3 linked, Xyl3C does not hydrolyze, thus leaving the substitution one-xylose (penultimate) from the non-reducing terminus. Hence, Xyl3C enables discrimination between O2 and O3 linked substitutions on the xylose penultimate to the non-reducing end. These findings are contrasted using a homologous enzyme also from S. baroniae, Xyl3B, which is found to yield a penultimate substituted nonreducing terminus regardless of which GlcA or Araf substitution exists.
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Affiliation(s)
- Franz J St John
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, One Gifford Pinchot Dr, Madison, WI, 53726, USA.
| | - Loreen Bynum
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, One Gifford Pinchot Dr, Madison, WI, 53726, USA
| | - Dante A Tauscheck
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, One Gifford Pinchot Dr, Madison, WI, 53726, USA
| | - Casey Crooks
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, One Gifford Pinchot Dr, Madison, WI, 53726, USA
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Šuchová K, Fathallah W, Puchart V. Characterization of a novel GH30 non-specific endoxylanase AcXyn30B from Acetivibrio clariflavus. Appl Microbiol Biotechnol 2024; 108:312. [PMID: 38683242 PMCID: PMC11058611 DOI: 10.1007/s00253-024-13155-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024]
Abstract
The xylanolytic enzymes Clocl_1795 and Clocl_2746 from glycoside hydrolase (GH) family 30 are highly abundant in the hemicellulolytic system of Acetivibrio clariflavus (Hungateiclostridium, Clostridium clariflavum). Clocl_1795 has been shown to be a xylobiohydrolase AcXbh30A releasing xylobiose from the non-reducing end of xylan and xylooligosaccharides. In this work, biochemical characterization of Clocl_2746 is presented. The protein, designated AcXyn30B, shows low sequence similarity to other GH30 members and phylogenetic analysis revealed that AcXyn30B and related proteins form a separate clade that is proposed to be a new subfamily GH30_12. AcXyn30B exhibits similar specific activity on glucuronoxylan, arabinoxylan, and aryl glycosides of linear xylooligosaccharides suggesting that it is a non-specific xylanase. From polymeric substrates, it releases the fragments of degrees of polymerization (DP) 2-6. Hydrolysis of different xylooligosaccharides indicates that AcXyn30B requires at least four occupied catalytic subsites for effective cleavage. The ability of the enzyme to hydrolyze a wide range of substrates is interesting for biotechnological applications. In addition to subfamilies GH30_7, GH30_8, and GH30_10, the newly proposed subfamily GH30_12 further widens the spectrum of GH30 subfamilies containing xylanolytic enzymes. KEY POINTS: Bacterial GH30 endoxylanase from A. clariflavus (AcXyn30B) has been characterized AcXyn30B is non-specific xylanase hydrolyzing various xylans and xylooligosaccharides Phylogenetic analysis placed AcXyn30B in a new GH30_12 subfamily.
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Affiliation(s)
- Katarína Šuchová
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia.
| | - Walid Fathallah
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
- Faculty of Science, Beni-Suef University, Beni-Suef, 625 11, Egypt
| | - Vladimír Puchart
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38, Bratislava, Slovakia
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Akram F, Fatima T, Ibrar R, Shabbir I, Shah FI, Haq IU. Trends in the development and current perspective of thermostable bacterial hemicellulases with their industrial endeavors: A review. Int J Biol Macromol 2024; 265:130993. [PMID: 38508567 DOI: 10.1016/j.ijbiomac.2024.130993] [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: 07/15/2023] [Revised: 03/12/2024] [Accepted: 03/17/2024] [Indexed: 03/22/2024]
Abstract
Hemicellulases are enzymes that hydrolyze hemicelluloses, common polysaccharides in nature. Thermophilic hemicellulases, derived from microbial strains, are extensively studied as natural biofuel sources due to the complex structure of hemicelluloses. Recent research aims to elucidate the catalytic principles, mechanisms and specificity of hemicellulases through investigations into their high-temperature stability and structural features, which have applications in biotechnology and industry. This review article targets to serve as a comprehensive resource, highlighting the significant progress in the field and emphasizing the vital role of thermophilic hemicellulases in eco-friendly catalysis. The primary goal is to improve the reliability of hemicellulase enzymes obtained from thermophilic bacterial strains. Additionally, with their ability to break down lignocellulosic materials, hemicellulases hold immense potential for biofuel production. Despite their potential, the commercial viability is hindered by their high enzyme costs, necessitating the development of efficient bioprocesses involving waste pretreatment with microbial consortia to overcome this challenge.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan.
| | - Taseer Fatima
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Ramesha Ibrar
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Ifrah Shabbir
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | | | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan; Pakistan Academy of Sciences, Islamabad, Pakistan
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Chen SK, Wang X, Guo YQ, Song XX, Yin JY, Nie SP. Exploring the partial degradation of polysaccharides: Structure, mechanism, bioactivities, and perspectives. Compr Rev Food Sci Food Saf 2023; 22:4831-4870. [PMID: 37755239 DOI: 10.1111/1541-4337.13244] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/22/2023] [Accepted: 09/04/2023] [Indexed: 09/28/2023]
Abstract
Polysaccharides are promising biomolecules with lowtoxicity and diverse bioactivities in food processing and clinical drug development. However, an essential prerequisite for their applications is the fine structure characterization. Due to the complexity of polysaccharide structure, partial degradation is a powerful tool for fine structure analysis, which can effectively provide valid information on the structure of backbone and branching glycosidic fragments of complex polysaccharides. This review aims to conclude current methods of partial degradation employed for polysaccharide structural characterization, discuss the molecular mechanisms, and describe the molecular structure and solution properties of degraded polysaccharides. In addition, the effects of polysaccharide degradation on the conformational relationships between the molecular structure and bioactivities, such as antioxidant, antitumor, and immunomodulatory activities, are also discussed. Finally, we summarize the prospects and current challenges for the partial degradation of polysaccharides. This review will be of great value for the scientific elucidation of polysaccharide fine structures and potential applications.
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Affiliation(s)
- Shi-Kang Chen
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province, China
| | - Xin Wang
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province, China
| | - Yu-Qing Guo
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province, China
| | - Xiao-Xiao Song
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province, China
| | - Jun-Yi Yin
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province, China
| | - Shao-Ping Nie
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province, China
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Nakamichi Y, Watanabe M, Fujii T, Inoue H, Morita T. Crystal structure of reducing-end xylose-releasing exoxylanase in subfamily 7 of glycoside hydrolase family 30. Proteins 2023; 91:1341-1350. [PMID: 37144255 DOI: 10.1002/prot.26505] [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: 03/14/2023] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/06/2023]
Abstract
TcXyn30A from Talaromyces cellulolyticus, which belongs to subfamily 7 of the glycoside hydrolase family 30 (GH30-7), releases xylose from the reducing end of xylan and xylooligosaccharides (XOSs), the so-called reducing-end xylose-releasing exoxylanase (ReX). In this study, the crystal structures of TcXyn30A with and without xylose at subsite +1 (the binding site of the xylose residue at the reducing end) were determined. This is the first report on the structure of ReX in the family GH30-7. TcXyn30A forms a dimer. The complex structure of TcXyn30A with xylose revealed that subsite +1 is located at the dimer interface. TcXyn30A recognizes xylose at subsite +1 composed of amino acid residues from each monomer and blocks substrate binding to subsite +2 by dimer formation. Thus, the dimeric conformation is responsible for ReX activity. The structural comparison between TcXyn30A and the homologous enzyme indicated that subsite -2 is composed of assembled three stacked Trp residues, Trp49, Trp333, and Trp334, allowing TcXyn30A to accommodate xylan and any branched XOSs decorated with a substitution such as α-1,2-linked 4-O-methyl-d-glucuronic acid or α-1,2- and/or -1,3-linked L-arabinofuranose. These findings provide an insight into the structural determinants for ReX activity of TcXyn30A.
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Affiliation(s)
- Yusuke Nakamichi
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Higashi-Hiroshima, Hiroshima, Japan
| | - Masahiro Watanabe
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Higashi-Hiroshima, Hiroshima, Japan
| | - Tatsuya Fujii
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Higashi-Hiroshima, Hiroshima, Japan
| | - Hiroyuki Inoue
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Higashi-Hiroshima, Hiroshima, Japan
| | - Tomotake Morita
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Higashi-Hiroshima, Hiroshima, Japan
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St John FJ, Crooks C, Kim Y, Tan K, Joachimiak A. The first crystal structure of a xylobiose-bound xylobiohydrolase with high functional specificity from the bacterial glycoside hydrolase 30 subfamily 10. FEBS Lett 2022; 596:2449-2464. [PMID: 35876256 DOI: 10.1002/1873-3468.14454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/05/2022] [Accepted: 07/09/2022] [Indexed: 11/05/2022]
Abstract
Xylobiose is a prebiotic sugar that has applications in functional foods. This report describes the first X-ray crystallographic structure models of apo and xylobiose bound forms of a xylobiohydrolase (XBH) from Acetivibrio clariflavus. This xylan active enzyme, a member of the recently described glycoside hydrolase family 30 (GH30) subfamily 10 phylogenetic clade has been shown to strictly release xylobiose as its primary hydrolysis product. Inspection of the apo-structure reveals a glycone region X2 binding slot. When X2 binds, the nonreducing xylose in the -2 subsite is highly coordinated with numerous hydrogen bond contacts while contacts in the -1 subsite mostly reflect interactions typical for GH30 and enzymes in clan A of the carbohydrate-active enzymes database (CAZy). This structure provides an explanation for the high functional specificity of this new bacterial GH30 XBH subfamily.
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Affiliation(s)
- Franz J St John
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, Madison, WI, 53726, USA
| | - Casey Crooks
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, Madison, WI, 53726, USA
| | - Youngchang Kim
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Il, 60439, USA
| | - Kemin Tan
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Il, 60439, USA
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Il, 60439, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
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Yeast GH30 Xylanase from Sugiyamaella lignohabitans Is a Glucuronoxylanase with Auxiliary Xylobiohydrolase Activity. Molecules 2022; 27:molecules27030751. [PMID: 35164030 PMCID: PMC8840591 DOI: 10.3390/molecules27030751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 02/01/2023] Open
Abstract
Xylanases are the enzymes that catalyze the breakdown of the main hemicellulose present in plant cell walls. They have attracted attention due to their biotechnological potential for the preparation of industrially interesting products from lignocellulose. While many xylanases have been characterized from bacteria and filamentous fungi, information on yeast xylanases is scarce and no yeast xylanase belonging to glycoside hydrolase (GH) family 30 has been described so far. Here, we cloned, expressed and characterized GH30 xylanase SlXyn30A from the yeast Sugiyamaella lignohabitans. The enzyme is active on glucuronoxylan (8.4 U/mg) and rhodymenan (linear β-1,4-1,3-xylan) (3.1 U/mg) while its activity on arabinoxylan is very low (0.03 U/mg). From glucuronoxylan SlXyn30A releases a series of acidic xylooligosaccharides of general formula MeGlcA2Xyln. These products, which are typical for GH30-specific glucuronoxylanases, are subsequently shortened at the non-reducing end, from which xylobiose moieties are liberated. Xylobiohydrolase activity was also observed during the hydrolysis of various xylooligosaccharides. SlXyn30A thus expands the group of glucuronoxylanases/xylobiohydrolases which has been hitherto represented only by several fungal GH30-7 members.
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Šuchová K, Puchart V, Spodsberg N, Mørkeberg Krogh KBR, Biely P. Catalytic Diversity of GH30 Xylanases. Molecules 2021; 26:molecules26154528. [PMID: 34361682 PMCID: PMC8347883 DOI: 10.3390/molecules26154528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/16/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Catalytic properties of GH30 xylanases belonging to subfamilies 7 and 8 were compared on glucuronoxylan, modified glucuronoxylans, arabinoxylan, rhodymenan, and xylotetraose. Most of the tested bacterial GH30-8 enzymes are specific glucuronoxylanases (EC 3.2.1.136) requiring for action the presence of free carboxyl group of MeGlcA side residues. These enzymes were not active on arabinoxylan, rhodymenan and xylotetraose, and conversion of MeGlcA to its methyl ester or its reduction to MeGlc led to a remarkable drop in their specific activity. However, some GH30-8 members are nonspecific xylanases effectively hydrolyzing all tested substrates. In terms of catalytic activities, the GH30-7 subfamily is much more diverse. In addition to specific glucuronoxylanases, the GH30-7 subfamily contains nonspecific endoxylanases and predominantly exo-acting enzymes. The activity of GH30-7 specific glucuronoxylanases also depend on the presence of the MeGlcA carboxyl, but not so strictly as in bacterial enzymes. The modification of the carboxyl group of glucuronoxylan had only weak effect on the action of predominantly exo-acting enzymes, as well as nonspecific xylanases. Rhodymenan and xylotetraose were the best substrates for exo-acting enzymes, while arabinoxylan represented hardly degradable substrate for almost all tested GH30-7 enzymes. The results expand current knowledge on the catalytic properties of this relatively novel group of xylanases.
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Affiliation(s)
- Katarína Šuchová
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovakia; (V.P.); (P.B.)
- Correspondence: ; Tel.: +421-25-941-0229
| | - Vladimír Puchart
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovakia; (V.P.); (P.B.)
| | - Nikolaj Spodsberg
- Novozymes A/S, Krogshøjvej 36, 2880 Bagsværd, Denmark; (N.S.); (K.B.R.M.K.)
| | | | - Peter Biely
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovakia; (V.P.); (P.B.)
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