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Mukherjee S, Lodha TD, Madhuprakash J. Comprehensive Genome Analysis of Cellulose and Xylan-Active CAZymes from the Genus Paenibacillus: Special Emphasis on the Novel Xylanolytic Paenibacillus sp. LS1. Microbiol Spectr 2023; 11:e0502822. [PMID: 37071006 PMCID: PMC10269863 DOI: 10.1128/spectrum.05028-22] [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: 12/06/2022] [Accepted: 03/24/2023] [Indexed: 04/19/2023] Open
Abstract
Xylan is the most abundant hemicellulose in hardwood and graminaceous plants. It is a heteropolysaccharide comprising different moieties appended to the xylose units. Complete degradation of xylan requires an arsenal of xylanolytic enzymes that can remove the substitutions and mediate internal hydrolysis of the xylan backbone. Here, we describe the xylan degradation potential and underlying enzyme machinery of the strain, Paenibacillus sp. LS1. The strain LS1 was able to utilize both beechwood and corncob xylan as the sole source of carbon, with the former being the preferred substrate. Genome analysis revealed an extensive xylan-active CAZyme repertoire capable of mediating efficient degradation of the complex polymer. In addition to this, a putative xylooligosaccharide ABC transporter and homologues of the enzymes involved in the xylose isomerase pathway were identified. Further, we have validated the expression of selected xylan-active CAZymes, transporters, and metabolic enzymes during growth of the LS1 on xylan substrates using qRT-PCR. The genome comparison and genomic index (average nucleotide identity [ANI] and digital DNA-DNA hybridization) values revealed that strain LS1 is a novel species of the genus Paenibacillus. Lastly, comparative genome analysis of 238 genomes revealed the prevalence of xylan-active CAZymes over cellulose across the Paenibacillus genus. Taken together, our results indicate that Paenibacillus sp. LS1 is an efficient degrader of xylan polymers, with potential implications in the production of biofuels and other beneficial by-products from lignocellulosic biomass. IMPORTANCE Xylan is the most abundant hemicellulose in the lignocellulosic (plant) biomass that requires cooperative deconstruction by an arsenal of different xylanolytic enzymes to produce xylose and xylooligosaccharides. Microbial (particularly, bacterial) candidates that encode such enzymes are an asset to the biorefineries to mediate efficient and eco-friendly deconstruction of xylan to generate products of value. Although xylan degradation by a few Paenibacillus spp. is reported, a complete genus-wide understanding of the said trait is unavailable till date. Through comparative genome analysis, we showed the prevalence of xylan-active CAZymes across Paenibacillus spp., therefore making them an attractive option towards efficient xylan degradation. Additionally, we deciphered the xylan degradation potential of the strain Paenibacillus sp. LS1 through genome analysis, expression profiling, and biochemical studies. The ability of Paenibacillus sp. LS1 to degrade different xylan types obtained from different plant species, emphasizes its potential implication in lignocellulosic biorefineries.
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Affiliation(s)
- Saumashish Mukherjee
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India
| | | | - Jogi Madhuprakash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India
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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.
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Liu J, Zhu J, Xu Q, Shi R, Liu C, Sun D, Liu W. Functional identification of two novel carbohydrate-binding modules of glucuronoxylanase CrXyl30 and their contribution to the lignocellulose saccharification. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:40. [PMID: 36890582 PMCID: PMC9996879 DOI: 10.1186/s13068-023-02290-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/28/2023] [Indexed: 03/10/2023]
Abstract
BACKGROUND Glycoside hydrolase (GH) family 30 xylanases are a distinct group of xylanases, most of which have a highly specific catalytic activity for glucuronoxylan. Since GH30 xylanases do not normally carry carbohydrate-binding modules (CBMs), our knowledge of the function of their CBMs is lacking. RESULTS In this work, the CBM functions of CrXyl30 were investigated. CrXyl30 was a GH30 glucuronoxylanase containing tandem CBM13 (CrCBM13) and CBM2 (CrCBM2) at its C terminus, which was identified in a lignocellulolytic bacterial consortium previously. Both CBMs could bind insoluble and soluble xylan, with CrCBM13 having binding specificity for the xylan with L-arabinosyl substitutions, whereas CrCBM2 targeted L-arabinosyl side chains themselves. Such binding abilities of these two CBMs were completely different from other CBMs in their respective families. Phylogenetic analysis also suggested that both CrCBM13 and CrCBM2 belong to novel branches. Inspection of the simulated structure of CrCBM13 identified a pocket that just accommodates the side chain of 3(2)-alpha-L-arabinofuranosyl-xylotriose, which forms hydrogen bonds with three of the five amino acid residues involved in ligand interaction. The truncation of either CrCBM13 or CrCBM2 did not alter the substrate specificity and optimal reaction conditions of CrXyl30, whereas truncation of CrCBM2 decreased the kcat/Km value by 83% (± 0%). Moreover, the absence of CrCBM2 and CrCBM13 resulted in a 5% (± 1%) and a 7% (± 0%) decrease, respectively, in the amount of reducing sugar released by the synergistic hydrolysis of delignified corncob whose hemicellulose is arabinoglucuronoxylan, respectively. In addition, fusion of CrCBM2 with a GH10 xylanase enhanced its catalytic activity against the branched xylan and improved the synergistic hydrolysis efficiency by more than fivefold when delignified corncob was used as substrate. Such a strong stimulation of hydrolysis resulted from the enhancement of hemicellulose hydrolysis on the one hand, and the cellulose hydrolysis is also improved according to the lignocellulose conversion rate measured by HPLC. CONCLUSIONS This study identifies the functions of two novel CBMs in CrXyl30 and shows the good potential of such CBMs specific for branched ligands in the development of efficient enzyme preparations.
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Affiliation(s)
- Jiawen Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China
| | - Jingrong Zhu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China
| | - Qian Xu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China
| | - Rui Shi
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China
| | - Cong Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China.
| | - Di Sun
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China.
| | - Weijie Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu, China.
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Trovão F, Correia VG, Lourenço FM, Ribeiro DO, Carvalho AL, Palma AS, Pinheiro BA. The structure of a Bacteroides thetaiotaomicron carbohydrate-binding module provides new insight into the recognition of complex pectic polysaccharides by the human microbiome. J Struct Biol X 2023; 7:100084. [PMID: 36660365 PMCID: PMC9843283 DOI: 10.1016/j.yjsbx.2022.100084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/28/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023] Open
Abstract
The Bacteroides thetaiotaomicron has developed a consortium of enzymes capable of overcoming steric constraints and degrading, in a sequential manner, the complex rhamnogalacturonan II (RG-II) polysaccharide. BT0996 protein acts in the initial stages of the RG-II depolymerisation, where its two catalytic modules remove the terminal monosaccharides from RG-II side chains A and B. BT0996 is modular and has three putative carbohydrate-binding modules (CBMs) for which the roles in the RG-II degradation are unknown. Here, we present the characterisation of the module at the C-terminal domain, which we designated BT0996-C. The high-resolution structure obtained by X-ray crystallography reveals that the protein displays a typical β-sandwich fold with structural similarity to CBMs assigned to families 6 and 35. The distinctive features are: 1) the presence of several charged residues at the BT0996-C surface creating a large, broad positive lysine-rich patch that encompasses the putative binding site; and 2) the absence of the highly conserved binding-site signatures observed in CBMs from families 6 and 35, such as region A tryptophan and region C asparagine. These findings hint at a binding mode of BT0996-C not yet observed in its homologues. In line with this, carbohydrate microarrays and microscale thermophoresis show the ability of BT0996-C to bind α1-4-linked polygalacturonic acid, and that electrostatic interactions are essential for the recognition of the anionic polysaccharide. The results support the hypothesis that BT0996-C may have evolved to potentiate the action of BT0996 catalytic modules on the complex structure of RG-II by binding to the polygalacturonic acid backbone sequence.
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Affiliation(s)
- Filipa Trovão
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal,Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Viviana G. Correia
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal,Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Frederico M. Lourenço
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal,Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Diana O. Ribeiro
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal,Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Luísa Carvalho
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal,Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Angelina S. Palma
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal,Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal,Corresponding authors at: UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
| | - Benedita A. Pinheiro
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal,Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal,Corresponding authors at: UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
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Bioengineering and Molecular Biology of Miscanthus. ENERGIES 2022. [DOI: 10.3390/en15144941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Miscanthus is a perennial wild plant that is vital for the production of paper and roofing, as well as horticulture and the development of new high-yielding crops in temperate climates. Chromosome-level assembly of the ancient tetraploid genome of miscanthus chromosomes is reported to provide resources that can link its chromosomes to related diploid sorghum and complex polyploid sugarcane. Analysis of Miscanthus sinensis and Miscanthus sacchariflorus showed intense mixing and interspecific hybridization and documented the origin of a high-yielding triploid bioenergetic plant, Miscanthus × giganteus. The Miscanthus genome expands comparative genomics functions to better understand the main abilities of Andropogoneae herbs. Miscanthus × giganteus is widely regarded as a promising lignocellulosic biomass crop due to its high-biomass yield, which does not emit toxic compounds into the environment, and ability to grow in depleted lands. The high production cost of lignocellulosic bioethanol limits its commercialization. The main components that inhibit the enzymatic reactions of fermentation and saccharification are lignin in the cell wall and its by-products released during the pre-treatment stage. One approach to overcoming this barrier could be to genetically modify the genes involved in lignin biosynthesis, manipulating the lignin content and composition of miscanthus.
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Novel Nematode-Killing Protein-1 (Nkp-1) from a Marine Epiphytic Bacterium Pseudoalteromonas tunicata. Biomedicines 2021; 9:biomedicines9111586. [PMID: 34829814 PMCID: PMC8615270 DOI: 10.3390/biomedicines9111586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
Drug resistance among parasitic nematodes has resulted in an urgent need for the development of new therapies. However, the high re-discovery rate of anti-nematode compounds from terrestrial environments necessitates a new repository for future drug research. Marine epiphytes are hypothesised to produce nematicidal compounds as a defence against bacterivorous predators, thus representing a promising yet underexplored source for anti-nematode drug discovery. The marine epiphytic bacterium Pseudoalteromonas tunicata is known to produce several bioactive compounds. Screening heterologously expressed genomic libraries of P. tunicata against the nematode Caenorhabditis elegans, identified as an E. coli clone (HG8), shows fast-killing activity. Here we show that clone HG8 produces a novel nematode-killing protein-1 (Nkp-1) harbouring a predicted carbohydrate-binding domain with weak homology to known bacterial pore-forming toxins. We found bacteria expressing Nkp-1 were able to colonise the C. elegans intestine, with exposure to both live bacteria and protein extracts resulting in physical damage and necrosis, leading to nematode death within 24 h of exposure. Furthermore, this study revealed C. elegans dar (deformed anal region) and internal hatching may act as a nematode defence strategy against Nkp-1 toxicity. The characterisation of this novel protein and putative mode of action not only contributes to the development of novel anti-nematode applications in the future but reaffirms the potential of marine epiphytic bacteria as a new source of novel biomolecules.
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Crooks C, Bechle NJ, St John FJ. A New Subfamily of Glycoside Hydrolase Family 30 with Strict Xylobiohydrolase Function. Front Mol Biosci 2021; 8:714238. [PMID: 34557520 PMCID: PMC8453022 DOI: 10.3389/fmolb.2021.714238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
The Acetivibrio clariflavus (basonym: Clostridium clariflavum) glycoside hydrolase family 30 cellulosomal protein encoded by the Clocl_1795 gene was highly represented during growth on cellulosic substrates. In this report, the recombinantly expressed protein has been characterized and shown to be a non-reducing terminal (NRT)-specific xylobiohydrolase (AcXbh30A). Biochemical function, optimal biophysical parameters, and phylogeny were investigated. The findings indicate that AcXbh30A strictly cleaves xylobiose from the NRT up until an α-1,2-linked glucuronic acid (GA)-decorated xylose if the number of xyloses is even or otherwise a single xylose will remain resulting in a penultimate GA-substituted xylose. Unlike recently reported xylobiohydrolases, AcXbh30A has no other detectable hydrolysis products under our optimized reaction conditions. Sequence analysis indicates that AcXbh30A represents a new GH30 subfamily. This new xylobiohydrolase may be useful for commercial production of industrial quantities of xylobiose.
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Affiliation(s)
- Casey Crooks
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, Madison, WI, United States
| | - Nathan J Bechle
- Engineering Mechanics and Remote Sensing Laboratory, Forest Products Laboratory, USDA Forest Service, Madison, WI, United States
| | - Franz J St John
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, Madison, WI, United States
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Baker JT, Duarte ME, Holanda DM, Kim SW. Friend or Foe? Impacts of Dietary Xylans, Xylooligosaccharides, and Xylanases on Intestinal Health and Growth Performance of Monogastric Animals. Animals (Basel) 2021; 11:609. [PMID: 33652614 PMCID: PMC7996850 DOI: 10.3390/ani11030609] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/11/2021] [Accepted: 02/24/2021] [Indexed: 12/27/2022] Open
Abstract
This paper discusses the structural difference and role of xylan, procedures involved in the production of xylooligosaccharides (XOS), and their implementation into animal feeds. Xylan is non-starch polysaccharides that share a β-(1-4)-linked xylopyranose backbone as a common feature. Due to the myriad of residues that can be substituted on the polymers within the xylan family, more anti-nutritional factors are associated with certain types of xylan than others. XOS are sugar oligomers extracted from xylan-containing lignocellulosic materials, such as crop residues, wood, and herbaceous biomass, that possess prebiotic effects. XOS can also be produced in the intestine of monogastric animals to some extent when exogenous enzymes, such as xylanase, are added to the feed. Xylanase supplementation is a common practice within both swine and poultry production to reduce intestinal viscosity and improve digestive utilization of nutrients. The efficacy of xylanase supplementation varies widely due a number of factors, one of which being the presence of xylanase inhibitors present in common feedstuffs. The use of prebiotics in animal feeding is gaining popularity as producers look to accelerate growth rate, enhance intestinal health, and improve other production parameters in an attempt to provide a safe and sustainable food product. Available research on the impact of xylan, XOS, as well as xylanase on the growth and health of swine and poultry, is also summarized. The response to xylanase supplementation in swine and poultry feeds is highly variable and whether the benefits are a result of nutrient release from NSP, reduction in digesta viscosity, production of short chain xylooligosaccharides or a combination of these is still in question. XOS supplementation seems to benefit both swine and poultry at various stages of production, as well as varying levels of XOS purity and degree of polymerization; however, further research is needed to elucidate the ideal dosage, purity, and degree of polymerization needed to confer benefits on intestinal health and performance in each respective species.
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Affiliation(s)
| | | | | | - Sung Woo Kim
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695, USA; (J.T.B.); (M.E.D.); (D.M.H.)
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9
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Xylanases of glycoside hydrolase family 30 - An overview. Biotechnol Adv 2021; 47:107704. [PMID: 33548454 DOI: 10.1016/j.biotechadv.2021.107704] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/23/2021] [Accepted: 01/25/2021] [Indexed: 12/22/2022]
Abstract
Xylan is the most abundant hemicellulose in nature and as such it is a huge source of renewable carbon. Its bioconversion requires a battery of xylanolytic enzymes. Of them the most important are the endo-β-1,4-xylanases which depolymerize the polysaccharide into smaller fragments. Most of the xylanases are members of glycoside hydrolase (GH) families 10 and 11, although they are classified in some other GH families. The relatively new xylanases of GH30 are of special interest. Initially, they appeared to be specific glucuronoxylanases, however, other specificities were found later among prokaryotic and in particular eukaryotic enzymes. This review gives an overview of the substrate and product specificities observed for the GH30 xylanases characterized to date. An emphasis is given to the structure-activity relationship in order to explain how minor differences in catalytic centre and its vicinity can alter catalytic properties from the endoxylanase into the reducing end xylose releasing exoxylanase or into the non-reducing end xylobiohydrolase. Biotechnological potential of the GH30 xylanases is also considered.
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10
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A novel bacterial GH30 xylobiohydrolase from Hungateiclostridium clariflavum. Appl Microbiol Biotechnol 2020; 105:185-195. [PMID: 33215261 DOI: 10.1007/s00253-020-11023-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/23/2020] [Accepted: 11/12/2020] [Indexed: 10/23/2022]
Abstract
Typical bacterial GH30 xylanases are glucuronoxylanases requiring 4-O-methylglucuronic acid (MeGlcA) substitution of a xylan main chain for their action. They do not exhibit a significant activity on neutral xylooligosaccharides, arabinoxylan (AraX), or rhodymenan (Rho). In this work, the biochemical characterization of the bacterial Clocl_1795 xylanase from Hungateiclostridium (Clostridium) clariflavum DSM 19732 (HcXyn30A) is presented. Amino acid sequence analysis of HcXyn30A revealed that the enzyme does not contain amino acids known to be responsible for MeGlcA coordination in the -2b subsite of glucuronoxylanases. This suggested that the catalytic properties of HcXyn30A may differ from those of glucuronoxylanases. HcXyn30A shows similar specific activity on glucuronoxylan (GX) and Rho, while the specific activity on AraX is about 1000 times lower. HcXyn30A releases Xyl2 as the main product from the non-reducing end of different polymeric and oligomeric substrates. Catalytic properties of HcXyn30A resemble the properties of the fungal GH30 xylobiohydrolase from Acremonium alcalophilum, AaXyn30A. HcXyn30A is the first representative of a prokaryotic xylobiohydrolase. Its unique specificity broadens the catalytic diversity of bacterial GH30 xylanases. KEY POINTS: • Bacterial GH30 xylobiohydrolase from H. clariflavum (HcXyn30A) has been characterized. • HcXyn30A releases xylobiose from the non-reducing end of different substrates. • HcXyn30A is the first representative of bacterial xylobiohydrolase.
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Jiménez‐Ortega E, Valenzuela S, Ramírez‐Escudero M, Pastor FJ, Sanz‐Aparicio J. Structural analysis of the reducing‐end xylose‐releasing exo‐oligoxylanase Rex8A from
Paenibacillus barcinonensis
BP‐23 deciphers its molecular specificity. FEBS J 2020; 287:5362-5374. [DOI: 10.1111/febs.15332] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/27/2020] [Accepted: 04/09/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Elena Jiménez‐Ortega
- Macromolecular Crystallography and Structural Biology Department Institute of Physical‐Chemistry ‘Rocasolano’ CSIC Madrid Spain
| | - Susana Valenzuela
- Department of Microbiology Faculty of Biology University of Barcelona Spain
- Institute of Nanoscience and Nanotechnology (IN2UB) University of Barcelona Spain
| | - Mercedes Ramírez‐Escudero
- Macromolecular Crystallography and Structural Biology Department Institute of Physical‐Chemistry ‘Rocasolano’ CSIC Madrid Spain
| | - Francisco Javier Pastor
- Department of Microbiology Faculty of Biology University of Barcelona Spain
- Institute of Nanoscience and Nanotechnology (IN2UB) University of Barcelona Spain
| | - Julia Sanz‐Aparicio
- Macromolecular Crystallography and Structural Biology Department Institute of Physical‐Chemistry ‘Rocasolano’ CSIC Madrid Spain
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Hagiwara Y, Mihara Y, Sakagami K, Sagara R, Bat-Erdene U, Yatsunami R, Nakamura S. Isolation of four xylanases capable of hydrolyzing corn fiber xylan from Paenibacillus sp. H2C. Biosci Biotechnol Biochem 2020; 84:640-650. [DOI: 10.1080/09168451.2019.1693253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
ABSTRACT
Corn fibre xylan (CX) shows high resistance to enzymatic hydrolysis due to its densely decorated side chains. To find enzymes capable of hydrolyzing CX, we isolated a bacterial strain (named H2C) from soil, by enrichment culture using non-starch polysaccharides of corn as the sole carbon source. Analysis based on the 16S rRNA sequence placed strain H2C within genus Paenibacillus. Enzymes were purified from supernatant of culture broth of strain H2C based on solubilizing activities toward CX. Four enzymes, Xyn5A, Xyn10B, Xyn11A, and Xyn30A, were successfully identified, which belong to glycoside hydrolase (GH) families, 5, 10, 11, and 30, respectively. Phylogenetic analysis classified Xyn5A in subfamily 35 of GH family 5, a subfamily of unknown function. Their activities toward beechwood xylan and/or wheat arabinoxylan indicated that these enzymes are β-1,4-xylanases. They showed high solubilizing activities toward a feed material, corn dried distiller’s grains with solubles, compared to five previously characterized xylanases.
Abbreviations : CX: corn fibre xylan; DDGS: corn dried distiller’s grains with solubles
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Affiliation(s)
- Yusuke Hagiwara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- Process Development Laboratories, Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Yasuhiro Mihara
- Process Development Laboratories, Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Koichi Sakagami
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ryuta Sagara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Undramaa Bat-Erdene
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Rie Yatsunami
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Satoshi Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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13
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Zhan P, Ye J, Lin X, Zhang F, Lin D, Zhang Y, Tang K. Complete genome sequence of Echinicola rosea JL3085, a xylan and pectin decomposer. Mar Genomics 2019; 52:100722. [PMID: 31677976 DOI: 10.1016/j.margen.2019.100722] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/05/2019] [Accepted: 10/17/2019] [Indexed: 01/21/2023]
Abstract
Marine Bacteroidetes are well known for their functional specialization on the decomposition of polysaccharides which results from a great number of carbohydrate-active enzymes. Here we represent the complete genome of a Bacteroitedes member Echinicola rosea JL3085T that was isolated from surface seawater of the South China Sea. The genome is 6.06 Mbp in size with a GC content of 44.1% and comprises 4613 protein coding genes. A remarkable genomic feature is that the number of glycoside hydrolase genes in the genome of E. rosea JL3085T is high in comparison with most of the sequenced members of marine Bacteroitedes. E. rosea JL3085T genome harbored multi-gene polysaccharide utilization loci (PUL) systems involved in the degradation of pectin, xylan and arabinogalactan. The large diversity of hydrolytic enzymes supports the use of E. rosea JL3085T as a candidate for biotechnological applications in enzymatic conversion of plant polysaccharides.
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Affiliation(s)
- Peiwen Zhan
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Jianing Ye
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiaopei Lin
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Fan Zhang
- Department of Molecular Virology & Microbiology, Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Dan Lin
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
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14
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Sharma K, Fontes CMGA, Najmudin S, Goyal A. Molecular organization and protein stability of the Clostridium thermocellum glucuronoxylan endo-β-1,4-xylanase of family 30 glycoside hydrolase in solution. J Struct Biol 2019; 206:335-344. [PMID: 30959107 DOI: 10.1016/j.jsb.2019.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 11/19/2022]
Abstract
Glucuronoxylan-β-1,4-xylanohydrolase from Clostridium thermocellum (CtXynGH30) hydrolyzes β-1,4-xylosidic linkages in 4-O-Methyl-D-glucuronoxylan. CtXynGH30 comprises an N-terminal catalytic domain, CtXyn30A, joined by a typical linker sequence to a family 6 carbohydrate-binding module, termed CtCBM6. ITC, mass spectrometric and enzyme activity analyses of CtXyn30A:CtCBM6 (1:1 M ratio), CtXyn30A and CtXynGH30 showed that the linker peptide plays a key role in connecting and orienting CtXyn30A and CtCBM6 modules resulting in the enhanced activity of CtXynGH30. To visualize the disposition of the two protein domains of CtXynGH30, SAXS analysis revealed that CtXynGH30 is monomeric and has a boot-shaped molecular envelope in solution with a Dmax of 18 nm and Rg of 3.6 nm. Kratky plot displayed the protein in a fully folded and flexible state. The ab initio derived dummy atom model of CtXynGH30 superposed well with the modelled structure.
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Affiliation(s)
- Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Carlos M G A Fontes
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Shabir Najmudin
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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15
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Katsimpouras C, Dedes G, Thomaidis NS, Topakas E. A novel fungal GH30 xylanase with xylobiohydrolase auxiliary activity. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:120. [PMID: 31110561 PMCID: PMC6511221 DOI: 10.1186/s13068-019-1455-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/29/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND The main representatives of hemicellulose are xylans, usually decorated β-1,4-linked d-xylose polymers, which are hydrolyzed by xylanases. The efficient utilization and complete hydrolysis of xylans necessitate the understanding of the mode of action of xylan degrading enzymes. The glycoside hydrolase family 30 (GH30) xylanases comprise a less studied group of such enzymes, and differences regarding the substrate recognition have been reported between fungal and bacterial GH30 xylanases. Besides their role in the utilization of lignocellulosic biomass for bioenergy, such enzymes could be used for the tailored production of prebiotic xylooligosaccharides (XOS) due to their substrate specificity. RESULTS The expression of a putative GH30_7 xylanase from the fungus Thermothelomyces thermophila (synonyms Myceliophthora thermophila, Sporotrichum thermophile) in Pichia pastoris resulted in the production and isolation of a novel xylanase with unique catalytic properties. The novel enzyme designated TtXyn30A, exhibited an endo- mode of action similar to that of bacterial GH30 xylanases that require 4-O-methyl-d-glucuronic acid (MeGlcA) decorations, in contrast to most characterized fungal ones. However, TtXyn30A also exhibited an exo-acting catalytic behavior by releasing the disaccharide xylobiose from the non-reducing end of XOS. The hydrolysis products from beechwood glucuronoxylan were MeGlcA substituted XOS, and xylobiose. The major uronic XOS (UXOS) were the aldotriuronic and aldotetrauronic acid after longer incubation indicating the ability of TtXyn30A to cleave linear parts of xylan and UXOS as well. CONCLUSIONS Hereby, we reported the heterologous production and biochemical characterization of a novel fungal GH30 xylanase exhibiting endo- and exo-xylanase activity. To date, considering its novel catalytic properties, TtXyn30A shows differences with most characterized fungal and bacterial GH30 xylanases. The discovered xylobiohydrolase mode of action offers new insights into fungal enzymatic systems that are employed for the utilization of lignocellulosic biomass. The recombinant xylanase could be used for the production of X2 and UXOS from glucuronoxylan, which in turn would be utilized as prebiotics carrying manifold health benefits.
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Affiliation(s)
- Constantinos Katsimpouras
- Industrial Biotechnology & Biocatalysis Group, School of Chemical Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
| | - Grigorios Dedes
- Industrial Biotechnology & Biocatalysis Group, School of Chemical Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
| | - Nikolaos S. Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771 Athens, Greece
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, School of Chemical Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
- Biochemical and Chemical Process Engineering, Division of Sustainable Process Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, 97187 Luleå, Sweden
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16
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Dhillon A, Sharma K, Rajulapati V, Goyal A. The multi-ligand binding first family 35 Carbohydrate Binding Module (CBM35) of Clostridium thermocellum targets rhamnogalacturonan I. Arch Biochem Biophys 2018; 654:194-208. [PMID: 30080990 DOI: 10.1016/j.abb.2018.07.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/25/2018] [Accepted: 07/27/2018] [Indexed: 11/24/2022]
Abstract
Carbohydrate Binding Modules (CBMs) targeting cellulose, xylan and mannan have been reported, however, a CBM targeting rhamnogalacturonan I (RG I) has never been identified. We had studied earlier a rhamnogalacturonan lyase (CtRGL) from Clostridium thermocellum that was associated with a family 35 CBM, Rgl-CBM35. In this study we show that Rgl-CBM35 displays binding with β-d-glucuronic acid (β-D-GlcpA), Δ4,5-anhydro-d-galactopyranosyluronic acid (Δ4,5-GalpA), rhamnogalacturonan I, arabinan, galactan, glucuronoxylans and arabinoxylans. Rgl-CBM35 contains a conserved ligand binding site in the loops known for binding β-D-GlcpA and Δ4,5-GalpA moiety of unsaturated RG I and pectic-oligosaccharides. Mutagenesis revealed that Asn118 plays an important role in binding β-D-GlcpA, Δ4,5-GalpA, sugarbeet arabinan and potato galactan at its conserved ligand binding site present in surface exposed loops. EDTA-treated Rgl-CBM35 showed no affinity towards β-D-GlcpA and Δ4,5-GalpA underscoring Ca2+ mediated ligand recognition. Contrastingly, the EDTA-treated Rgl-CBM35 and its mutant N118A displayed affinity for sugarbeet arabinan and potato galactan. The curtailed affinity of Y37A/N118A and R69A/N118A double mutants towards sugarbeet arabinan emphasized the presence of a second ligand binding site. Rgl-CBM35 is the first CBM reported to primarily target RG I and also is the first member of family 35 CBM possessing at least two ligand binding sites.
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Affiliation(s)
- Arun Dhillon
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Vikky Rajulapati
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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17
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Nordberg Karlsson E, Schmitz E, Linares-Pastén JA, Adlercreutz P. Endo-xylanases as tools for production of substituted xylooligosaccharides with prebiotic properties. Appl Microbiol Biotechnol 2018; 102:9081-9088. [PMID: 30196329 PMCID: PMC6208967 DOI: 10.1007/s00253-018-9343-4] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/16/2018] [Accepted: 08/19/2018] [Indexed: 01/14/2023]
Abstract
Xylan has a main chain consisting of β-1,4-linked xylose residues with diverse substituents. Endoxylanases cleave the xylan chain at cleavage sites determined by the substitution pattern and thus give different oligosaccharide product patterns. Most known endoxylanases belong to glycoside hydrolase (GH) families 10 and 11. These enzymes work well on unsubstituted xylan but accept substituents in certain subsites. The GH11 enzymes are more restricted by substituents, but on the other hand, they are normally more active than the GH10 enzymes on insoluble substrates, because of their smaller size. GH5 endoxylanases accept arabinose substituents in several subsites and require it in the - 1 subsite. This specificity makes the GH5 endoxylanases very useful for degradation of highly arabinose-substituted xylans and for the selective production of arabinoxylooligosaccharides, without formation of unsubstituted xylooligosaccharides. The GH30 endoxylanases have a related type of specificity in that they require a uronic acid substituent in the - 2 subsite, which makes them very useful for the production of uronic acid substituted oligosaccharides. The ability of dietary xylooligosaccharides to function as prebiotics in humans is governed by their substitution patterns. Endoxylanases are thus excellent tools to tailor prebiotic oligosaccharides to stimulate various types of intestinal bacteria and to cause fermentation in different parts of the gastrointestinal tract. Continuously increasing knowledge on the function of the gut microbiota and discoveries of novel endoxylanases increase the possibilities to achieve health-promoting effects.
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Affiliation(s)
| | - Eva Schmitz
- Division of Biotechnology, Lund University, P.O.Box 124, 221 00, Lund, Sweden
| | | | - Patrick Adlercreutz
- Division of Biotechnology, Lund University, P.O.Box 124, 221 00, Lund, Sweden.
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18
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Linares-Pastén JA, Aronsson A, Karlsson EN. Structural Considerations on the Use of Endo-Xylanases for the Production of prebiotic Xylooligosaccharides from Biomass. Curr Protein Pept Sci 2018; 19:48-67. [PMID: 27670134 PMCID: PMC5738707 DOI: 10.2174/1389203717666160923155209] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 08/31/2016] [Accepted: 09/15/2016] [Indexed: 11/24/2022]
Abstract
Xylooligosaccharides (XOS) have gained increased interest as prebiotics during the last years. XOS and arabinoxylooligosaccharides (AXOS) can be produced from major fractions of biomass including agricultural by-products and other low cost raw materials. Endo-xylanases are key enzymes for the production of (A)XOS from xylan. As the xylan structure is broadly diverse due to different substitutions, diverse endo-xylanases have evolved for its degradation. In this review structural and functional aspects are discussed, focusing on the potential applications of endo-xylanases in the production of differently substituted (A)XOS as emerging prebiotics, as well as their implication in the processing of the raw materials. Endo-xylanases are found in at least eight different glycoside hydrolase families (GH), and can either have a retaining or an inverting catalytic mechanism. To date, it is mainly retaining endo-xylanases that are used in applications to produce (A)XOS. Enzymes from these GH-families (mainly GH10 and GH11, and the more recently investigated GH30) are taken as prototypes to discuss substrate preferences and main products obtained. Finally, the need of new and accessory enzymes (new specificities from new families or sources) to increase the yield of different types of (A)XOS is discussed, along with in vitro tests of produced oligosaccharides and production of enzymes in GRAS organisms to facilitate use in functional food manufacturing.
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Affiliation(s)
| | - Anna Aronsson
- Biotechnology, Department of Chemistry, Lund University, Lund, Sweden
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19
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Carbohydrate active enzyme domains from extreme thermophiles: components of a modular toolbox for lignocellulose degradation. Extremophiles 2017; 22:1-12. [PMID: 29110088 DOI: 10.1007/s00792-017-0974-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/24/2017] [Indexed: 02/06/2023]
Abstract
Lignocellulosic biomass is a promising feedstock for the manufacture of biodegradable and renewable bioproducts. However, the complex lignocellulosic polymeric structure of woody tissue is difficult to access without extensive industrial pre-treatment. Enzyme processing of partly depolymerised biomass is an established technology, and there is evidence that high temperature (extremely thermophilic) lignocellulose degrading enzymes [carbohydrate active enzymes (CAZymes)] may enhance processing efficiency. However, wild-type thermophilic CAZymes will not necessarily be functionally optimal under industrial pre-treatment conditions. With recent advances in synthetic biology, it is now potentially possible to build CAZyme constructs from individual protein domains, tailored to the conditions of specific industrial processes. In this review, we identify a 'toolbox' of thermostable CAZyme domains from extremely thermophilic organisms and highlight recent advances in CAZyme engineering which will allow for the rational design of CAZymes tailored to specific aspects of lignocellulose digestion.
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20
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Jones DR, Uddin MS, Gruninger RJ, Pham TTM, Thomas D, Boraston AB, Briggs J, Pluvinage B, McAllister TA, Forster RJ, Tsang A, Selinger LB, Abbott DW. Discovery and characterization of family 39 glycoside hydrolases from rumen anaerobic fungi with polyspecific activity on rare arabinosyl substrates. J Biol Chem 2017; 292:12606-12620. [PMID: 28588026 DOI: 10.1074/jbc.m117.789008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/30/2017] [Indexed: 11/06/2022] Open
Abstract
Enzyme activities that improve digestion of recalcitrant plant cell wall polysaccharides may offer solutions for sustainable industries. To this end, anaerobic fungi in the rumen have been identified as a promising source of novel carbohydrate active enzymes (CAZymes) that modify plant cell wall polysaccharides and other complex glycans. Many CAZymes share insufficient sequence identity to characterized proteins from other microbial ecosystems to infer their function; thus presenting challenges to their identification. In this study, four rumen fungal genes (nf2152, nf2215, nf2523, and pr2455) were identified that encode family 39 glycoside hydrolases (GH39s), and have conserved structural features with GH51s. Two recombinant proteins, NF2152 and NF2523, were characterized using a variety of biochemical and structural techniques, and were determined to have distinct catalytic activities. NF2152 releases a single product, β1,2-arabinobiose (Ara2) from sugar beet arabinan (SBA), and β1,2-Ara2 and α-1,2-galactoarabinose (Gal-Ara) from rye arabinoxylan (RAX). NF2523 exclusively releases α-1,2-Gal-Ara from RAX, which represents the first description of a galacto-(α-1,2)-arabinosidase. Both β-1,2-Ara2 and α-1,2-Gal-Ara are disaccharides not previously described within SBA and RAX. In this regard, the enzymes studied here may represent valuable new biocatalytic tools for investigating the structures of rare arabinosyl-containing glycans, and potentially for facilitating their modification in industrial applications.
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Affiliation(s)
- Darryl R Jones
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Muhammed Salah Uddin
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada; Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta T1K 6T5, Canada
| | - Robert J Gruninger
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Thi Thanh My Pham
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Dallas Thomas
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Alisdair B Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
| | - Jonathan Briggs
- School of Biology, Ridley Building 2, Newcastle University, Claremont Road, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Benjamin Pluvinage
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
| | - Tim A McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Robert J Forster
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - L Brent Selinger
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta T1K 6T5, Canada
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada; Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta T1K 6T5, Canada.
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21
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Grondin JM, Duan D, Kirlin AC, Abe KT, Chitayat S, Spencer HL, Spencer C, Campigotto A, Houliston S, Arrowsmith CH, Allingham JS, Boraston AB, Smith SP. Diverse modes of galacto-specific carbohydrate recognition by a family 31 glycoside hydrolase from Clostridium perfringens. PLoS One 2017; 12:e0171606. [PMID: 28158290 PMCID: PMC5291390 DOI: 10.1371/journal.pone.0171606] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/23/2017] [Indexed: 02/03/2023] Open
Abstract
Clostridium perfringens is a commensal member of the human gut microbiome and an opportunistic pathogen whose genome encodes a suite of putative large, multi-modular carbohydrate-active enzymes that appears to play a role in the interaction of the bacterium with mucin-based carbohydrates. Among the most complex of these is an enzyme that contains a presumed catalytic module belonging to glycoside hydrolase family 31 (GH31). This large enzyme, which based on its possession of a GH31 module is a predicted α-glucosidase, contains a variety of non-catalytic ancillary modules, including three CBM32 modules that to date have not been characterized. NMR-based experiments demonstrated a preference of each module for galacto-configured sugars, including the ability of all three CBM32s to recognize the common mucin monosaccharide GalNAc. X-ray crystal structures of the CpGH31 CBM32s, both in apo form and bound to GalNAc, revealed the finely-tuned molecular strategies employed by these sequentially variable CBM32s in coordinating a common ligand. The data highlight that sequence similarities to previously characterized CBMs alone are insufficient for identifying the molecular mechanism of ligand binding by individual CBMs. Furthermore, the overlapping ligand binding profiles of the three CBMs provide a fail-safe mechanism for the recognition of GalNAc among the dense eukaryotic carbohydrate networks of the colonic mucosa. These findings expand our understanding of ligand targeting by large, multi-modular carbohydrate-active enzymes, and offer unique insights into of the expanding ligand-binding preferences and binding site topologies observed in CBM32s.
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Affiliation(s)
- Julie M. Grondin
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Da Duan
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Alyssa C. Kirlin
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Kento T. Abe
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Seth Chitayat
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Holly L. Spencer
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Craig Spencer
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Alisha Campigotto
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Scott Houliston
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl H. Arrowsmith
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John S. Allingham
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Alisdair B. Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Steven P. Smith
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
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22
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Xylanase 30 A from Clostridium thermocellum functions as a glucuronoxylan xylanohydrolase. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2017.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Freire F, Verma A, Bule P, Alves VD, Fontes CMGA, Goyal A, Najmudin S. Conservation in the mechanism of glucuronoxylan hydrolysis revealed by the structure of glucuronoxylan xylanohydrolase (CtXyn30A) from Clostridium thermocellum. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:1162-1173. [PMID: 27841749 DOI: 10.1107/s2059798316014376] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/09/2016] [Indexed: 11/10/2022]
Abstract
Glucuronoxylan endo-β-1,4-xylanases cleave the xylan chain specifically at sites containing 4-O-methylglucuronic acid substitutions. These enzymes have recently received considerable attention owing to their importance in the cooperative hydrolysis of heteropolysaccharides. However, little is known about the hydrolysis of glucuronoxylans in extreme environments. Here, the structure of a thermostable family 30 glucuronoxylan endo-β-1,4-xylanase (CtXyn30A) from Clostridium thermocellum is reported. CtXyn30A is part of the cellulosome, a highly elaborate multi-enzyme complex secreted by the bacterium to efficiently deconstruct plant cell-wall carbohydrates. CtXyn30A preferably hydrolyses glucuronoxylans and displays maximum activity at pH 6.0 and 70°C. The structure of CtXyn30A displays a (β/α)8 TIM-barrel core with a side-associated β-sheet domain. Structural analysis of the CtXyn30A mutant E225A, solved in the presence of xylotetraose, revealed xylotetraose-cleavage oligosaccharides partially occupying subsites -3 to +2. The sugar ring at the +1 subsite is held in place by hydrophobic stacking interactions between Tyr139 and Tyr200 and hydrogen bonds to the OH group of Tyr227. Although family 30 glycoside hydrolases are retaining enzymes, the xylopyranosyl ring at the -1 subsite of CtXyn30A-E225A appears in the α-anomeric configuration. A set of residues were found to be strictly conserved in glucuronoxylan endo-β-1,4-xylanases and constitute the molecular determinants of the restricted specificity displayed by these enzymes. CtXyn30A is the first thermostable glucuronoxylan endo-β-1,4-xylanase described to date. This work reveals that substrate recognition by both thermophilic and mesophilic glucuronoxylan endo-β-1,4-xylanases is modulated by a conserved set of residues.
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Affiliation(s)
- Filipe Freire
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Anil Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Pedro Bule
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Victor D Alves
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Carlos M G A Fontes
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Arun Goyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Shabir Najmudin
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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The Glycoside Hydrolase Family 8 Reducing-End Xylose-Releasing Exo-oligoxylanase Rex8A from Paenibacillus barcinonensis BP-23 Is Active on Branched Xylooligosaccharides. Appl Environ Microbiol 2016; 82:5116-24. [PMID: 27316951 DOI: 10.1128/aem.01329-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 05/27/2016] [Indexed: 01/06/2023] Open
Abstract
UNLABELLED A GH8 family enzyme involved in xylan depolymerization has been characterized. The enzyme, Rex8A, is a reducing-end xylose-releasing exo-oligoxylanase (Rex) that efficiently hydrolyzes xylooligosaccharides and shows minor activity on polymeric xylan. Rex8A hydrolyzes xylooligomers of 3 to 6 xylose units to xylose and xylobiose in long-term incubations. Kinetic constants of Rex8A were determined on xylotriose, showing a Km of 1.64 ± 0.03 mM and a kcat value of 118.8 s(-1) Besides linear xylooligosaccharides, the enzyme hydrolyzed decorated xylooligomers. The catalytic activity on branched xylooligosaccharides, i.e., the release of xylose from the reducing end, is a newly described trait of xylose-releasing exo-oligoxylanases, as the exo-activity on these substrates has not been reported for the few of these enzymes characterized to date. Modeling of the three-dimensional (3D) structure of Rex8A shows an (α/α)6 barrel fold where the loops connecting the α-helices contour the active site. These loops, which show high sequence diversity among GH8 enzymes, shape a catalytic cleft with a -2 subsite that can accommodate methyl-glucuronic acid decorations. The hydrolytic ability of Rex8A on branched oligomers can be crucial for the complete depolymerization of highly substituted xylans, which is indispensable to accomplish biomass deconstruction and to generate efficient catalysts. IMPORTANCE A GH8 family enzyme involved in xylan depolymerization has been characterized. The Rex8A enzyme from Paenibacillus barcinonensis is involved in depolymerization of glucuronoxylan, a major component of the lignocellulosic substrates. The study shows that Rex8A is a reducing-end xylose-releasing exo-oligoxylanase that efficiently hydrolyzes xylose from neutral and acidic xylooligosaccharides generated by the action of other xylanases also secreted by the strain. The activity of a Rex enzyme on branched xylooligosaccharides has not been described to date. This report provides original and useful information on the properties of a new example of the rarely studied Rex enzymes. Depolymerization of highly substituted xylans is crucial for biomass valorization as a platform for generation of biofuels, chemicals, and solvents.
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Classification, mode of action and production strategy of xylanase and its application for biofuel production from water hyacinth. Int J Biol Macromol 2016; 82:1041-54. [DOI: 10.1016/j.ijbiomac.2015.10.086] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 01/07/2023]
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Marchetti R, Berrin JG, Couturier M, Ul Qader SA, Molinaro A, Silipo A. NMR analysis of the binding mode of two fungal endo-β-1,4-mannanases from GH5 and GH26 families. Org Biomol Chem 2016; 14:314-22. [DOI: 10.1039/c5ob01851j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A different mode of action among two endo-β-1,4 mannanases from Podospora anserina has been revealed through an accurate NMR analysis.
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Affiliation(s)
- Roberta Marchetti
- Department of Chemical Sciences
- Università di Napoli Federico II
- Complesso Universitario Monte S. Angelo
- Naples
- Italy
| | | | | | - Shah Ali Ul Qader
- Department of Chemical Sciences
- Università di Napoli Federico II
- Complesso Universitario Monte S. Angelo
- Naples
- Italy
| | - Antonio Molinaro
- Department of Chemical Sciences
- Università di Napoli Federico II
- Complesso Universitario Monte S. Angelo
- Naples
- Italy
| | - Alba Silipo
- Department of Chemical Sciences
- Università di Napoli Federico II
- Complesso Universitario Monte S. Angelo
- Naples
- Italy
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27
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Valls A, Diaz P, Pastor FIJ, Valenzuela SV. A newly discovered arabinoxylan-specific arabinofuranohydrolase. Synergistic action with xylanases from different glycosyl hydrolase families. Appl Microbiol Biotechnol 2015; 100:1743-1751. [DOI: 10.1007/s00253-015-7061-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 09/27/2015] [Accepted: 10/05/2015] [Indexed: 01/11/2023]
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The role of the glucuronoxylan carboxyl groups in the action of endoxylanases of three glycoside hydrolase families: A study with two substrate mutants. Biochim Biophys Acta Gen Subj 2015; 1850:2246-55. [PMID: 26172579 DOI: 10.1016/j.bbagen.2015.07.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/02/2015] [Accepted: 07/10/2015] [Indexed: 11/21/2022]
Abstract
BACKGROUND Bacterial appendage-dependent GH30 glucuronoxylan hydrolases recognize the substrate through an ionic interaction of a conserved positively charged arginine with the carboxyl group of 4-O-methyl-d-glucuronic acid. One of the options to verify this interaction is preparation of enzyme mutants. An alternative approach is a chemical modification of the substrate, glucuronoxylan, in which the free carboxyl group in all residues of MeGlcA is eliminated. METHODS In this work the carboxyl groups of 4-O-methyl-d-glucuronic acid residues of an alkali extracted beechwood xylan were esterified with methanol. A water-soluble fraction of the polysaccharide methyl ester was converted by NaBH4 reduction to the second soluble derivative, 4-O-methylglucoxylan. Specific activities of several endoxylanases (EXs) of GH families 10, 11 and 30 were determined on glucuronoxylan, and its two new uncharged derivatives. RESULTS Elimination of the free carboxyl group from the polysaccharide did not influence activities of GH10 EXs, but resulted in 50% decrease of specific activity of GH11 EXs, and led to more than 300-fold reduction of specific activity of Erwinia chrysanthemi GH30 xylanase. CONCLUSIONS These results confirm the crucial role of the interactions between GH30 xylanases and the MeGlcA carboxyl group for efficient cleavage of the polysaccharide. Analysis of the hydrolysis products by TLC and MS confirmed that all three types of xylanases hydrolyzed uncharged glucuronoxylans similarly as the original one. SIGNIFICANCE The uncharged glucuronoxylan derivatives will be useful to differentiate GH30 xylanases with various degree of selectivity for glucuronoxylan, including fungal enzymes without the conserved arginine.
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Sainz-Polo MA, González B, Menéndez M, Pastor FIJ, Sanz-Aparicio J. Exploring Multimodularity in Plant Cell Wall Deconstruction: STRUCTURAL AND FUNCTIONAL ANALYSIS OF Xyn10C CONTAINING THE CBM22-1-CBM22-2 TANDEM. J Biol Chem 2015; 290:17116-30. [PMID: 26001782 DOI: 10.1074/jbc.m115.659300] [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: 04/15/2015] [Indexed: 11/06/2022] Open
Abstract
Elucidating the molecular mechanisms regulating multimodularity is a challenging task. Paenibacillus barcinonensis Xyn10C is a 120-kDa modular enzyme that presents the CBM22/GH10/CBM9 architecture found in a subset of large xylanases. We report here the three-dimensional structure of the Xyn10C N-terminal region, containing the xylan-binding CBM22-1-CBM22-2 tandem (Xyn10C-XBD), which represents the first solved crystal structure of two contiguous CBM22 modules. Xyn10C-XBD is folded into two separate CBM22 modules linked by a flexible segment that endows the tandem with extraordinary plasticity. Each isolated domain has been expressed and crystallized, and their binding abilities have been investigated. Both domains contain the R(W/Y)YYE motif required for xylan binding. However, crystallographic analysis of CBM22-2 complexes shows Trp-308 as an additional binding determinant. The long loop containing Trp-308 creates a platform that possibly contributes to the recognition of precise decorations at subsite S2. CBM22-2 may thus define a subset of xylan-binding CBM22 modules directed to particular regions of the polysaccharide. Affinity electrophoresis reveals that Xyn10C-XBD binds arabinoxylans more tightly, which is more apparent when CBM22-2 is tested against highly substituted xylan. The crystal structure of the catalytic domain, also reported, shows the capacity of the active site to accommodate xylan substitutions at almost all subsites. The structural differences found at both Xyn10C-XBD domains are consistent with the isothermal titration calorimetry experiments showing two sites with different affinities in the tandem. On the basis of the distinct characteristics of CBM22, a delivery strategy of Xyn10C mediated by Xyn10C-XBD is proposed.
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Affiliation(s)
| | - Beatriz González
- From the Departamentos de Cristalografía y Biología Estructural y
| | - Margarita Menéndez
- Química Física Biólogica, Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006-Madrid and
| | - F I Javier Pastor
- the Departamento de Microbiología, Facultad de Biología, Universidad de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
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Molecular engineering of cycloisomaltooligosaccharide glucanotransferase from Bacillus circulans T-3040: structural determinants for the reaction product size and reactivity. Biochem J 2015; 467:259-70. [PMID: 25649478 DOI: 10.1042/bj20140860] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cycloisomaltooligosaccharide glucanotransferase (CITase) is a member of glycoside hydrolase family 66 and it produces cycloisomaltooligosaccharides (CIs). Small CIs (CI-7-9) and large CIs (CI-≥10) are designated as oligosaccharide-type CIs (oligo-CIs) and megalosaccharide-type CIs (megalo-CIs) respectively. CITase from Bacillus circulans T-3040 (BcCITase) produces mainly CI-8 with little megalo-CIs. It has two family 35 carbohydrate-binding modules (BcCBM35-1 and BcCBM35-2). BcCBM35-1 is inserted in a catalytic domain of BcCITase and BcCBM35-2 is located at the C-terminal region. Our previous studies suggested that BcCBM35-1 has two substrate-binding sites (B-1 and B-2) [Suzuki et al. (2014) J. Biol. Chem. 289, 12040-12051]. We implemented site-directed mutagenesis of BcCITase to explore the preference for product size on the basis of the 3D structure of BcCITase. Mutational studies provided evidence that B-1 and B-2 contribute to recruiting substrate and maintaining product size respectively. A mutant (mutant-R) with four mutations (F268V, D469Y, A513V and Y515S) produced three times as much megalo-CIs (CI-10-12) and 1.5 times as much total CIs (CI-7-12) as compared with the wild-type (WT) BcCITase. The 3D structure of the substrate-enzyme complex of mutant-R suggested that the modified product size specificity was attributable to the construction of novel substrate-binding sites in the B-2 site of BcCBM35-1 and reactivity was improved by mutation on subsite -3 on the catalytic domain.
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31
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Verma AK, Bule P, Ribeiro T, Brás JLA, Mukherjee J, Gupta MN, Fontes CMGA, Goyal A. The family 6 Carbohydrate Binding Module (CtCBM6) of glucuronoxylanase (CtXynGH30) of Clostridium thermocellum binds decorated and undecorated xylans through cleft A. Arch Biochem Biophys 2015; 575:8-21. [PMID: 25857803 DOI: 10.1016/j.abb.2015.03.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 02/24/2015] [Accepted: 03/17/2015] [Indexed: 10/23/2022]
Abstract
CtCBM6 of glucuronoxylan-xylanohydrolase (CtXynGH30) from Clostridium thermocellum was cloned, expressed and purified as a soluble ~14 kDa protein. Quantitative binding analysis with soluble polysaccharides by affinity electrophoresis and ITC revealed that CtCBM6 displays similar affinity towards decorated and undecorated xylans by binding wheat- and rye-arabinoxylans, beechwood-, birchwood- and oatspelt-xylan. Protein melting studies confirmed thermostable nature of CtCBM6 and that Ca(2+) ions did not affect its structure stability and binding affinity significantly. The CtCBM6 structure was modeled and refined and CD spectrum displayed 44% β-strands supporting the predicted structure. CtCBM6 displays a jelly roll β-sandwich fold presenting two potential carbohydrate binding clefts, A and B. The cleft A, is located between two loops connecting β4-β5 and β8-β9 strands. Tyr28 and Phe84 present on these loops make a planar hydrophobic binding surface to accommodate sugar ring of ligand. The cleft B, is located on concave surface of β-sandwich fold. Tyr34 and Tyr104 make a planar hydrophobic platform, which may be inaccessible to ligand due to hindrance by Pro68. Site-directed mutagenesis revealed Tyr28 and Phe84 in cleft A, playing a major role in ligand binding. The results suggest that CtCBM6 interacts with carbohydrates through cleft A, which recognizes equally well both decorated and un-decorated xylans.
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Affiliation(s)
- Anil Kumar Verma
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Pedro Bule
- CIISA-Faculdade de Medicina Veterinária, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Teresa Ribeiro
- CIISA-Faculdade de Medicina Veterinária, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Joana L A Brás
- CIISA-Faculdade de Medicina Veterinária, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Joyeeta Mukherjee
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Munishwar N Gupta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Carlos M G A Fontes
- CIISA-Faculdade de Medicina Veterinária, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Arun Goyal
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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