1
|
Pentari C, Kosinas C, Nikolaivits E, Dimarogona M, Topakas E. Structural and molecular insights into a bifunctional glycoside hydrolase 30 xylanase specific to glucuronoxylan. Biotechnol Bioeng 2024; 121:2067-2078. [PMID: 38678481 DOI: 10.1002/bit.28731] [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: 02/20/2024] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024]
Abstract
Glycoside hydrolase (GH) 30 family xylanases are enzymes of biotechnological interest due to their capacity to degrade recalcitrant hemicelluloses, such as glucuronoxylan (GX). This study focuses on a subfamily 7 GH30, TtXyn30A from Thermothelomyces thermophilus, which acts on GX in an "endo" and "exo" mode, releasing methyl-glucuronic acid branched xylooligosaccharides (XOs) and xylobiose, respectively. The crystal structure of inactive TtXyn30A in complex with 23-(4-O-methyl-α-D-glucuronosyl)-xylotriose (UXX), along with biochemical analyses, corroborate the implication of E233, previously identified as alternative catalytic residue, in the hydrolysis of decorated xylan. At the -1 subsite, the xylose adopts a distorted conformation, indicative of the Michaelis complex of TtXyn30AEE with UXX trapped in the semi-functional active site. The most significant structural rearrangements upon substrate binding are observed at residues W127 and E233. The structures with neutral XOs, representing the "exo" function, clearly show the nonspecific binding at aglycon subsites, contrary to glycon sites, where the xylose molecules are accommodated via multiple interactions. Last, an unproductive ligand binding site is found at the interface between the catalytic and the secondary β-domain which is present in all GH30 enzymes. These findings improve current understanding of the mechanism of bifunctional GH30s, with potential applications in the field of enzyme engineering.
Collapse
Affiliation(s)
- Christina Pentari
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Christos Kosinas
- Laboratory of Structural Biology and Biotechnology, Department of Chemical Engineering, University of Patras, Patras, Greece
| | - Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Maria Dimarogona
- Laboratory of Structural Biology and Biotechnology, Department of Chemical Engineering, University of Patras, Patras, Greece
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| |
Collapse
|
2
|
Chang C, Guo Y, Tang K, Hu Y, Xu W, Chen W, McLaughlin N, Wang Z. Straw from Different Crop Species Recruits Different Communities of Lignocellulose-Degrading Microorganisms in Black Soil. Microorganisms 2024; 12:938. [PMID: 38792768 PMCID: PMC11123855 DOI: 10.3390/microorganisms12050938] [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: 04/07/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
The biological degradation of plant residues in the soil or on the soil surface is an integral part of the natural life cycle of annual plants and does not have adverse effects on the environment. Crop straw is characterized by a complex structure and exhibits stability and resistance to rapid microbial decomposition. In this study, we conducted a microcosm experiment to investigate the dynamic succession of the soil microbial community and the functional characteristics associated with lignocellulose-degrading pathways. Additionally, we aimed to identify lignocellulose-degrading microorganisms from the straw of three crop species prevalent in Northeast China: soybean (Glycine max Merr.), rice (Oryza sativa L.), and maize (Zea mays L.). Our findings revealed that both the type of straw and the degradation time influenced the bacterial and fungal community structure and composition. Metagenome sequencing results demonstrated that during degradation, different straw types assembled carbohydrate-active enzymes (CAZymes) and KEGG pathways in distinct manners, contributing to lignocellulose and hemicellulose degradation. Furthermore, isolation of lignocellulose-degrading microbes yielded 59 bacterial and 14 fungal strains contributing to straw degradation, with fungi generally exhibiting superior lignocellulose-degrading enzyme production compared to bacteria. Experiments were conducted to assess the potential synergistic effects of synthetic microbial communities (SynComs) comprising both fungi and bacteria. These SynComs resulted in a straw weight loss of 42% at 15 days post-inoculation, representing a 22% increase compared to conditions without any SynComs. In summary, our study provides novel ecological insights into crop straw degradation by microbes.
Collapse
Affiliation(s)
- Chunling Chang
- College of Life Science and Agroforestry, Qiqihar University, Qiqihar 161006, China; (C.C.); (Y.G.); (K.T.); (Y.H.); (W.X.); (W.C.)
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
- Heilongjiang Provincial Collaborative Innovation Center of Agrobiological Preparation Industrialization, Qiqihar 161006, China
| | - Yue Guo
- College of Life Science and Agroforestry, Qiqihar University, Qiqihar 161006, China; (C.C.); (Y.G.); (K.T.); (Y.H.); (W.X.); (W.C.)
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
- Heilongjiang Provincial Collaborative Innovation Center of Agrobiological Preparation Industrialization, Qiqihar 161006, China
| | - Kuanqiang Tang
- College of Life Science and Agroforestry, Qiqihar University, Qiqihar 161006, China; (C.C.); (Y.G.); (K.T.); (Y.H.); (W.X.); (W.C.)
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
- Heilongjiang Provincial Collaborative Innovation Center of Agrobiological Preparation Industrialization, Qiqihar 161006, China
| | - Yunlong Hu
- College of Life Science and Agroforestry, Qiqihar University, Qiqihar 161006, China; (C.C.); (Y.G.); (K.T.); (Y.H.); (W.X.); (W.C.)
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
- Heilongjiang Provincial Collaborative Innovation Center of Agrobiological Preparation Industrialization, Qiqihar 161006, China
| | - Weihui Xu
- College of Life Science and Agroforestry, Qiqihar University, Qiqihar 161006, China; (C.C.); (Y.G.); (K.T.); (Y.H.); (W.X.); (W.C.)
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
- Heilongjiang Provincial Collaborative Innovation Center of Agrobiological Preparation Industrialization, Qiqihar 161006, China
| | - Wenjing Chen
- College of Life Science and Agroforestry, Qiqihar University, Qiqihar 161006, China; (C.C.); (Y.G.); (K.T.); (Y.H.); (W.X.); (W.C.)
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
- Heilongjiang Provincial Collaborative Innovation Center of Agrobiological Preparation Industrialization, Qiqihar 161006, China
| | - Neil McLaughlin
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada;
| | - Zhigang Wang
- College of Life Science and Agroforestry, Qiqihar University, Qiqihar 161006, China; (C.C.); (Y.G.); (K.T.); (Y.H.); (W.X.); (W.C.)
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
- Heilongjiang Provincial Collaborative Innovation Center of Agrobiological Preparation Industrialization, Qiqihar 161006, China
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Zheng Y, Yan J, Cao C, Liu Y, Yu D, Liang X. Application of chromatography in purification and structural analysis of natural polysaccharides: A review. J Sep Sci 2023; 46:e2300368. [PMID: 37480171 DOI: 10.1002/jssc.202300368] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 07/23/2023]
Abstract
Polysaccharides are widely distributed in natural sources from monocytic microorganisms to higher animals, and are found in a variety of biological activities in recent decades. Natural polysaccharides have the characteristics of large molecular weight, diverse composition, and complex structure, so their purification and structural analysis are difficult issues in research. Chromatography as a powerful separation technique, plays an irreplaceable role in the separation and structural analysis of natural polysaccharides, especially in the purification of polysaccharides, the separation of hydrolysates, and the analysis of monosaccharide composition. The separation mechanisms and application of different chromatographic methods in the studies of polysaccharides were summarized in this review. Moreover, the advantages and drawbacks of various chromatography methods were discussed as well.
Collapse
Affiliation(s)
- Yi Zheng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- Ganjiang Chinese Medicine Innovation Center, Nanchang, China
| | - Jingyu Yan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- Ganjiang Chinese Medicine Innovation Center, Nanchang, China
| | - Cuiyan Cao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- Ganjiang Chinese Medicine Innovation Center, Nanchang, China
| | - Yanfang Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- Ganjiang Chinese Medicine Innovation Center, Nanchang, China
| | - Dongping Yu
- Ganjiang Chinese Medicine Innovation Center, Nanchang, China
| | - Xinmiao Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- Ganjiang Chinese Medicine Innovation Center, Nanchang, China
| |
Collapse
|
5
|
Mendonça M, Barroca M, Collins T. Endo-1,4-β-xylanase-containing glycoside hydrolase families: Characteristics, singularities and similarities. Biotechnol Adv 2023; 65:108148. [PMID: 37030552 DOI: 10.1016/j.biotechadv.2023.108148] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 04/02/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Endo-1,4-β-xylanases (EC 3.2.1.8) are O-glycoside hydrolases that cleave the internal β-1,4-D-xylosidic linkages of the complex plant polysaccharide xylan. They are produced by a vast array of organisms where they play critical roles in xylan saccharification and plant cell wall hydrolysis. They are also important industrial biocatalysts with widespread application. A large and ever growing number of xylanases with wildly different properties and functionalites are known and a better understanding of these would enable a more effective use in various applications. The Carbohydrate-Active enZYmes database (CAZy), which classifies evolutionarily related proteins into a glycoside hydrolase family-subfamily organisational scheme has proven powerful in understanding these enzymes. Nevertheless, ambiguity currently exists as to the number of glycoside hydrolase families and subfamilies harbouring catalytic domains with true endoxylanase activity and as to the specific characteristics of each of these families/subfamilies. This review seeks to clarify this, identifying 9 glycoside hydrolase families containing enzymes with endo-1,4-β-xylanase activity and discussing their properties, similarities, differences and biotechnological perspectives. In particular, substrate specificities and hydrolysis patterns and the structural determinants of these are detailed, with taxonomic aspects of source organisms being also presented. Shortcomings in current knowledge and research areas that require further clarification are highlighted and suggestions for future directions provided. This review seeks to motivate further research on these enzymes and especially of the lesser known endo-1,4-β-xylanase containing families. A better understanding of these enzymes will serve as a foundation for the knowledge-based development of process-fitted endo-1,4-β-xylanases and will accelerate their development for use with even the most recalcitrant of substrates in the biobased industries of the future.
Collapse
|
6
|
Arumapperuma T, Li J, Hornung B, Soler NM, Goddard-Borger ED, Terrapon N, Williams SJ. A subfamily classification to choreograph the diverse activities within glycoside hydrolase family 31. J Biol Chem 2023; 299:103038. [PMID: 36806678 PMCID: PMC10074150 DOI: 10.1016/j.jbc.2023.103038] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/01/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
The Carbohydrate-Active Enzyme classification groups enzymes that breakdown, assemble, or decorate glycans into protein families based on sequence similarity. The glycoside hydrolases (GH) are arranged into over 170 enzyme families, with some being very large and exhibiting distinct activities/specificities towards diverse substrates. Family GH31 is a large family that contains more than 20,000 sequences with a wide taxonomic diversity. Less than 1% of GH31 members are biochemically characterized and exhibit many different activities that include glycosidases, lyases, and transglycosidases. This diversity of activities limits our ability to predict the activities and roles of GH31 family members in their host organism and our ability to exploit these enzymes for practical purposes. Here, we established a subfamily classification using sequence similarity networks that was further validated by a structural analysis. While sequence similarity networks provide a sequence-based separation, we obtained good segregation between activities among the subfamilies. Our subclassification consists of 20 subfamilies with sixteen subfamilies containing at least one characterized member and eleven subfamilies that are monofunctional based on the available data. We also report the biochemical characterization of a member of the large subfamily 2 (GH31_2) that lacked any characterized members: RaGH31 from Rhodoferax aquaticus is an α-glucosidase with activity on a range of disaccharides including sucrose, trehalose, maltose, and nigerose. Our subclassification provides improved predictive power for the vast majority of uncharacterized proteins in family GH31 and highlights the remaining sequence space that remains to be functionally explored.
Collapse
Affiliation(s)
- Thimali Arumapperuma
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute and University of Melbourne, Parkville, Victoria, Australia
| | - Jinling Li
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute and University of Melbourne, Parkville, Victoria, Australia
| | - Bastian Hornung
- AFMB, UMR 7257 CNRS Aix-Marseille Univ., USC 1408 INRAE, Marseille, France
| | - Niccolay Madiedo Soler
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Ethan D Goddard-Borger
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Nicolas Terrapon
- AFMB, UMR 7257 CNRS Aix-Marseille Univ., USC 1408 INRAE, Marseille, France
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute and University of Melbourne, Parkville, Victoria, Australia.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Li X, Kouzounis D, Kabel MA, de Vries RP. GH10 and GH11 endoxylanases in Penicillium subrubescens: comparative characterization and synergy with GH51, GH54, GH62 α-L-arabinofuranosidases from the same fungus. N Biotechnol 2022; 70:84-92. [PMID: 35597447 DOI: 10.1016/j.nbt.2022.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/13/2022] [Accepted: 05/14/2022] [Indexed: 11/25/2022]
Abstract
Penicillium subrubescens has an expanded set of genes encoding putative endoxylanases (PsXLNs) compared to most other Penicillia and other fungi. In this study, all GH10 and GH11 PsXLNs were produced heterologously in Pichia pastoris and characterized. They were active towards beech wood xylan (BWX) and wheat flour arabinoxylan (WAX), and showed stability over a wide pH range. Additionally, PsXLNs released distinct oligosaccharides from WAX, and showed significant cooperative action with P. subrubescens α-L-arabinofuranosidases (PsABFs) from GH51 or GH54 for WAX degradation, giving insight into a more diverse XLN and ABF system for the efficient degradation of complex hemicelluloses. Homology modelling analysis pointed out differences in the catalytic center of PsXLNs, which are discussed in view of the different modes of action observed. These findings facilitate understanding of structural requirements for substrate recognition to contribute to recombinant XLN engineering for biotechnological applications.
Collapse
Affiliation(s)
- Xinxin Li
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Dimitrios Kouzounis
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Mirjam A Kabel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| |
Collapse
|