Modular Structures of Carbohydrate-Active Enzymes and Their Applications

A special issue of Catalysts (ISSN 2073-4344). This special issue belongs to the section "Biocatalysis".

Deadline for manuscript submissions: closed (20 February 2023) | Viewed by 10961

Special Issue Editors


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Guest Editor
Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
Interests: lignin conversion; biomass pretreatment and characterization; lignin and carbohydrate active enzyme
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Co-Guest Editor
Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
Interests: materials science; enzymology; bioresource technology
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Special Issue Information

Dear Colleagues, 

The bioconversion of lignocellulosic biomass into simple sugars for subsequent fermentation is an essential platform for the sustainable production of biofuels and biochemicals. However, the degradation of polysaccharides in biomass to sugar is difficult, and it has become a rate-limiting step in the industrial process.

The crystallinity and insoluble forms of polysaccharides appear to be a barrier for enzymatic hydrolysis. Several studies have shown that carbohydrate-active enzymes, i.e., cellulases and xylanases, have modular structures, making the enzymes more active on the insoluble substrate than a single-catalytic domain enzyme. The additional modules include carbohydrate-binding modules (CBMs), fibronectin-like domains, and other modules with unknown functions. The functions of CBMs are to bring the enzymes to the insoluble substrate, concentrate the enzyme on the substrate surfaces, and prolong the adsorption. Fibronectin-like domains have been reported to be involved in anchoring enzymes to the large substrates or stabilizing the entire protein structure, for example. These modules are linked with a catalytic module(s) via short-peptide linkers to make the enzyme(s) modular, and the linkers are glycosylated to prevent proteolytic cleavage. The linkers are also believed to promote polysaccharide binding during catalysis.

Interestingly, some microorganisms develop their sophisticated enzyme system to degrade the crystalline form of polysaccharides efficiently. For example, the multienzyme “cellulosome” has shown the efficient degradation of crystalline cellulose.  Additionally, it contains enzyme components that actively degrade other polysaccharides, including xylan, starch, pectin, and mannan. Cellulosomal enzymes have a specialized module called dockerin, which interacts with the cohesin on the scaffolding protein. The assembly of the enzymes into the complex leads to enzyme proximity and synergy among the enzymes. However, mimicking the complex formation of the naturally occurring cellulosome complex is difficult. The limitations include an efficient protein expression system, proper glycosylation, protein folding, and ways to choose enzymes and orders of the enzymes for construction.

This Special Issue focuses on the modular structure of carbohydrate-active enzymes, the architecture of the entire protein structures, and their biological functions during catalysis. We welcome the submission of research articles, reviews, and perspectives related, but not limited to, the following themes of interest:

  • Protein expression and development of hosts for expressing enzymes
  • Enzymology of carbohydrates active enzymes and the cellulosome system
  • Application of CBMs in protein purification, biomass characterization, or biomarker/reporter
  • Application of carbohydrate-active enzymes in agriculture, food, feed, and the biofuel/chemical industry
  • Modular structures and substrate–enzyme interactions
  • Techniques for increasing enzymatic activity and stability
  • Computational tools for designing enzymes
  • Effects of pretreatment methods on biomass structure and enzymactic acitivity

Dr. Paripok Phitsuwan
Dr. Ken-Lin Chang
Guest Editors

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Keywords

  • plant biomass
  • lignocellulose
  • biorefinery
  • circular bioeconomy
  • cellulose
  • hemicellulose
  • lignin
  • green solvent
  • gene manipulation
  • enzyme kinetics
  • molecular docking
  • protein assembly
  • protein
  • hydrolysis
  • polysaccharide degradation
  • binding interaction

Published Papers (5 papers)

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Research

13 pages, 2184 KiB  
Article
Conversion of Sugarcane Trash to Nanocrystalline Cellulose and its Life Cycle Assessment
by Agung Wibowo, Nutchapon Chiarasumran, Anusith Thanapimmetha, Maythee Saisriyoot, Penjit Srinophakun, Nopparat Suriyachai and Verawat Champreda
Catalysts 2022, 12(10), 1215; https://0-doi-org.brum.beds.ac.uk/10.3390/catal12101215 - 12 Oct 2022
Cited by 3 | Viewed by 1451
Abstract
Sugarcane trash (SCT) is a promising, underutilized raw material for producing value-added bio-based materials. Nanocrystalline cellulose (NCC) production conditions were obtained from the experiment. On the other hand, bioethanol production conditions were retrieved from the secondary data. This study compared the environmental impact [...] Read more.
Sugarcane trash (SCT) is a promising, underutilized raw material for producing value-added bio-based materials. Nanocrystalline cellulose (NCC) production conditions were obtained from the experiment. On the other hand, bioethanol production conditions were retrieved from the secondary data. This study compared the environmental impact of SCT in NCC production to that of bioethanol. For NCC production, SCT was subjected to organosolv pretreatment (140, 160, or 180 °C) in a mixed solvent system (methyl isobutyl ketone (MIBK), ethanol, and water), bleached, and then hydrolyzed with different concentrations of sulfuric acid (50 and 58%) for varying times. Organosolv pretreatment at 180 °C removed 98.24 and 81.15% of the hemicellulose and lignin, respectively, resulting in 73.51 and 79.72% cellulose purity and recovery. In addition, bleaching increased the cellulose purity to 95.42%. Field Emission Transmission Electron Microscopy (FE-TEM) analysis showed that NCC’s small 2:1 elliptical particles were found at the hydrolysis of 50% H2SO4 for 45 min. The X-ray diffraction (XRD) pattern revealed 70% crystalline index values for NCC obtained from 50% H2SO4 with 45 min retention times. Then, the optimum conditions of NCC production were used for LCA analysis (Sigmapro software). The analysis included global warming, marine ecotoxicity, fresh water, and human carcinogenic toxicity. NCC production’s electricity consumption (freeze-dried step) was the highest environmental impact on LCA analysis. Full article
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10 pages, 1977 KiB  
Article
Effects of Site-Directed Mutations on the Communicability between Local Segments and Binding Pocket Distortion of Engineered GH11 Xylanases Visualized through Network Topology Analysis
by Thana Sutthibutpong, Auwal Muhammad, Nuttawat Sawang and Pongsak Khunrae
Catalysts 2022, 12(10), 1165; https://0-doi-org.brum.beds.ac.uk/10.3390/catal12101165 - 03 Oct 2022
Cited by 1 | Viewed by 1343
Abstract
Mutations occurred within the binding pocket of enzymes directly modified the interaction network between an enzyme and its substrate. However, some mutations affecting the catalytic efficiency occurred far from the binding pocket and the explanation regarding mechanisms underlying the transmission of the mechanical [...] Read more.
Mutations occurred within the binding pocket of enzymes directly modified the interaction network between an enzyme and its substrate. However, some mutations affecting the catalytic efficiency occurred far from the binding pocket and the explanation regarding mechanisms underlying the transmission of the mechanical signal from the mutated site to the binding pocket was lacking. In this study, network topology analysis was used to characterize and visualize the changes of interaction networks caused by site-directed mutations on a GH11 xylanase from our previous study. For each structure, coordinates from molecular dynamics (MD) trajectory were obtained to create networks of representative atoms from all protein and xylooligosaccharide substrate residues, in which edges were defined between pairs of residues within a cutoff distance. Then, communicability matrices were extracted from the network to provide information on the mechanical signal transmission from the number of possible paths between any residue pairs or local protein segments. The analysis of subgraph centrality and communicability clearly showed that site-direct mutagenesis at non-reducing or reducing ends caused binding pocket distortion close to the opposite ends and created denser interaction networks. However, site-direct mutagenesis at both ends cancelled the binding pocket distortion, while enhancing the thermostability. Therefore, the network topology analysis tool on the atomistic simulations of engineered proteins could play some roles in protein design for the minimization to the correction of binding pocket tilting, which could affect the functionality and efficacy of enzymes. Full article
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19 pages, 6452 KiB  
Article
Agri-Biodegradable Mulch Films Derived from Lignin in Empty Fruit Bunches
by Kittitat Sirivechphongkul, Nutchapon Chiarasumran, Maythee Saisriyoot, Anusith Thanapimmetha, Penjit Srinophakun, Kesinee Iamsaard and Yao-Tung Lin
Catalysts 2022, 12(10), 1150; https://0-doi-org.brum.beds.ac.uk/10.3390/catal12101150 - 01 Oct 2022
Cited by 10 | Viewed by 2175
Abstract
Mulch films increase soil temperature, maintain soil moisture, improve water and fertilizer absorption, and reduce weed growth. This work studied a mulching film made using polyvinyl alcohol (PVA) and lignin extracted from empty fruit bunches (EFBs). The mulch films were investigated for opaqueness, [...] Read more.
Mulch films increase soil temperature, maintain soil moisture, improve water and fertilizer absorption, and reduce weed growth. This work studied a mulching film made using polyvinyl alcohol (PVA) and lignin extracted from empty fruit bunches (EFBs). The mulch films were investigated for opaqueness, biodegradation, water-solubility, absorption, and mechanical properties. Life cycle assessment (LCA) and cost estimate analysis were conducted. The composite mulch film-PVA solution was blended with 6% EFB lignin in dimethyl sulfoxide (DMSO) solution using five different amounts (0, 20, 40, 60, or 80 wt% lignin). The results showed that increasing the amount of lignin increased the film’s water solubility, moisture content, and biodegradability. At the same time, water absorption tended to decrease. Consequently, the light transmittance of the film was reduced, which had a positive effect on preventing soil weed growth. Tests of the mechanical properties showed that 60% lignin in the PVA film had the highest tensile strength (16.293 MPa). According to the LCA studies and cost estimation, the lignin-mixed PVA film had the lowest impact and was cheaper than the commercial mulching film. The results suggested that it is possible to blend polyvinyl alcohol polymer with lignin to improve biodegradability up to 25.47% by soil burial and 32% by water solubility. Full article
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19 pages, 7019 KiB  
Article
In-Depth Characterization of Debranching Type I Pullulanase from Priestia koreensis HL12 as Potential Biocatalyst for Starch Saccharification and Modification
by Daran Prongjit, Hataikarn Lekakarn, Benjarat Bunterngsook, Katesuda Aiewviriyasakul, Wipawee Sritusnee, Nattapol Arunrattanamook and Verawat Champreda
Catalysts 2022, 12(9), 1014; https://0-doi-org.brum.beds.ac.uk/10.3390/catal12091014 - 07 Sep 2022
Cited by 3 | Viewed by 2103
Abstract
Pullulanase is an effective starch debranching enzyme widely used in starch saccharification and modification. In this work, the biochemical characteristics and potential application of a new type I pullulanase from Priestia koreensis HL12 (HL12Pul) were evaluated and reported for the first time. Through [...] Read more.
Pullulanase is an effective starch debranching enzyme widely used in starch saccharification and modification. In this work, the biochemical characteristics and potential application of a new type I pullulanase from Priestia koreensis HL12 (HL12Pul) were evaluated and reported for the first time. Through in-depth evolutionary analysis, HL12Pul was classified as type I pullulanase belonging to glycoside hydrolase family 13, subfamily 14 (GH13_14). HL12Pul comprises multi-domains architecture, including two carbohydrate-binding domains, CBM68 and CBM48, at the N-terminus, the TIM barrel structure of glycoside hydrolase family 13 (GH13) and C-domain. Based on sequence analysis and experimental cleavage profile, HL12Pul specifically hydrolyzes only α-1,6 glycosidic linkage-rich substrates. The enzyme optimally works at 40 °C, pH 6.0, with the maximum specific activity of 181.14 ± 3.55 U/mg protein and catalytic efficiency (kcat/Km) of 49.39 mL/mg·s toward pullulan. In addition, HL12Pul worked in synergy with raw starch-degrading α-amylase, promoting raw cassava starch hydrolysis and increasing the sugar yield by 2.9-fold in comparison to the α-amylase alone in a short reaction time. Furthermore, HL12Pul effectively produces type III-resistant starch (RSIII) from cassava starch with a production yield of 70%. These indicate that HL12Pul has the potential as a biocatalyst for starch saccharification and modification. Full article
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19 pages, 4531 KiB  
Article
Functional Characterization of Recombinant Raw Starch Degrading α-Amylase from Roseateles terrae HL11 and Its Application on Cassava Pulp Saccharification
by Daran Prongjit, Hataikarn Lekakarn, Benjarat Bunterngsook, Katesuda Aiewviriyasakul, Wipawee Sritusnee and Verawat Champreda
Catalysts 2022, 12(6), 647; https://0-doi-org.brum.beds.ac.uk/10.3390/catal12060647 - 13 Jun 2022
Cited by 4 | Viewed by 2765
Abstract
Exploring new raw starch-hydrolyzing α-amylases and understanding their biochemical characteristics are important for the utilization of starch-rich materials in bio-industry. In this work, the biochemical characteristics of a novel raw starch-degrading α-amylase (HL11 Amy) from Roseateles terrae HL11 was firstly reported. Evolutionary analysis [...] Read more.
Exploring new raw starch-hydrolyzing α-amylases and understanding their biochemical characteristics are important for the utilization of starch-rich materials in bio-industry. In this work, the biochemical characteristics of a novel raw starch-degrading α-amylase (HL11 Amy) from Roseateles terrae HL11 was firstly reported. Evolutionary analysis revealed that HL11Amy was classified into glycoside hydrolase family 13 subfamily 32 (GH13_32). It contains four protein domains consisting of domain A, domain B, domain C and carbohydrate-binding module 20 (CMB20). The enzyme optimally worked at 50 °C, pH 4.0 with a specific activity of 6270 U/mg protein and 1030 raw starch-degrading (RSD) U/mg protein against soluble starch. Remarkably, HL11Amy exhibited activity toward both raw and gelatinized forms of various substrates, with the highest catalytic efficiency (kcat/Km) on starch from rice, followed by potato and cassava, respectively. HL11Amy effectively hydrolyzed cassava pulp (CP) hydrolysis, with a reducing sugar yield of 736 and 183 mg/g starch from gelatinized and raw CP, equivalent to 72% and 18% conversion based on starch content in the substrate, respectively. These demonstrated that HL11Amy represents a promising raw starch-degrading enzyme with potential applications in starch modification and cassava pulp saccharification. Full article
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