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Novel Enzymes for Natural Polymer Degradation

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (31 January 2022) | Viewed by 12393

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Special Issue Editors

Dr. Maria Dimarogona

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Guest Editor

Department of Chemical Engineering, University of Patras, Patras, Greece
Interests: X-ray crystallography; protein structure; industrial biocatalysts; LPMOs; protein engineering

Dr. Mats Sandgren

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Guest Editor

Department of Chemistry and Biotechnology, Swdish University of Agricultural, Uppsala, Sweden

Special Issue Information

Dear Colleagues,

The Special Issue of Molecules on “Novel Enzymes for Natural Polymer Degradation” aims to explore the most recent developments in the enzymatic conversion of various natural polysaccharides, polyesters, proteins and the related production of added-value products. Over the past few years, significant progress in the enzymology of microbial degradation of natural polymers such as lignocellulose has been achieved. Thus, the discovery of new types of enzymes—both oxidative and hydrolytic—poses new challenges and possibilities for the production of efficient enzyme cocktails for industrial use.

This Special Issue will include overview and original papers addressing but not restricted to the topics listed below:

Studies on the kinetics and mechanism of novel enzymes active on natural polymers;
Structural studies of these enzymes, alone or in complex with substrate analogues;
Enzyme engineering for improved function;
Bioproduction of value-added compounds;
Combination of different enzymes for the formulation of enzymatic cocktails with improved efficiency;
Enzymatic functionalization of biopolymers

Guest Editors

Dr. Maria Dimarogona

Dr. Mats Sandgren

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

Lignocellulose
Oxidoreductases
Natural polymers
Carbohydrate-active enzymes
Lytic Polysaccharide monooxygenases
Synergism
Structure-function relations
Polymer functionalization
Enzyme engineering

Published Papers (6 papers)

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Research

20 pages, 2033 KiB

Open AccessArticle

Enzymatic Conversion of Different Qualities of Refined Softwood Hemicellulose Recovered from Spent Sulfite Liquor

by Abhishek Bhattacharya, Samuel Butler, Basel Al-Rudainy, Ola Wallberg and Henrik Stålbrand

Molecules 2022, 27(10), 3207; https://doi.org/10.3390/molecules27103207 - 17 May 2022

Cited by 3 | Viewed by 2140

Abstract

Spent sulfite liquor (SSL) from softwood processing is rich in hemicellulose (acetyl galactoglucomannan, AcGGM), lignin, and lignin-derived compounds. We investigated the effect of sequential AcGGM purification on the enzymatic bioconversion of AcGGM. SSL was processed through three consecutive purification steps (membrane filtration, precipitation, and adsorption) to obtain AcGGM with increasing purity. Significant reduction (~99%) in lignin content and modest loss (~18%) of polysaccharides was observed during purification from the least pure preparation (UFR), obtained by membrane filtration, compared to the purest preparation (AD), obtained by adsorption. AcGGM (~14.5 kDa) was the major polysaccharide in the preparations; its enzymatic hydrolysis was assessed by reducing sugar and high-performance anion-exchange chromatography analysis. The hydrolysis of the UFR preparation with Viscozyme L or Trichoderma reesei β-mannanase TrMan5A (1 mg/mL) resulted in less than ~50% bioconversion of AcGGM. The AcGGM in the AD preparation was hydrolyzed to a higher degree (~67% with TrMan5A and 80% with Viscozyme L) and showed the highest conversion rate. This indicates that SSL contains enzyme-inhibitory compounds (e.g., lignin and lignin-derived compounds such as lignosulfonates) which were successfully removed. Full article

(This article belongs to the Special Issue Novel Enzymes for Natural Polymer Degradation)

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14 pages, 2801 KiB

Open AccessArticle

Impact of Modular Architecture on Activity of Glycoside Hydrolase Family 5 Subfamily 8 Mannanases

by Marie Sofie Møller

Molecules 2022, 27(6), 1915; https://doi.org/10.3390/molecules27061915 - 16 Mar 2022

Cited by 4 | Viewed by 1920

Abstract

Glycoside hydrolase family 5 subfamily 8 (GH5_8) mannanases belong to Firmicutes, Actinomycetia, and Proteobacteria. The presence or absence of carbohydrate-binding modules (CBMs) present a striking difference. While various GH5_8 mannanases need a CBM for binding galactomannans, removal of the CBM did not affect activity of some, whereas it in other cases reduced the catalytic efficiency due to increased K_M. Here, monomodular GH5_8 mannanases from Eubacterium siraeum (EsGH5_8) and Xanthomonas citri pv. aurantifolii (XcGH5_8) were produced and characterized to clarify if GH5_8 mannanases from Firmicutes and Proteobacteria without CBM(s) possess distinct properties. EsGH5_8 showed a remarkably high temperature optimum of 55 °C, while XcGH5_8 had an optimum at 30 °C. Both enzymes were highly active on carob galactomannan and konjac glucomannan. Notably, EsGH5_8 was equally active on both substrates, whereas XcGH5_8 preferred galactomannan. The K_M values were comparable with those of catalytic domains of truncated GH5_8s, while the turn-over numbers (k_cat) were in the higher end. Notably, XcGH5_8 bound to but did not degrade insoluble ivory nut mannan. The findings support the hypothesis that GH5_8 mannanases with CBMs target insoluble mannans found in plant cell walls and seeds, while monomodular GH5_8 members have soluble mannans and mannooligosaccharides as primary substrates. Full article

(This article belongs to the Special Issue Novel Enzymes for Natural Polymer Degradation)

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13 pages, 2161 KiB

Open AccessArticle

Crab-Eating Monkey Acidic Chitinase (CHIA) Efficiently Degrades Chitin and Chitosan under Acidic and High-Temperature Conditions

by Maiko Uehara, Chinatsu Takasaki, Satoshi Wakita, Yasusato Sugahara, Eri Tabata, Vaclav Matoska, Peter O. Bauer and Fumitaka Oyama

Molecules 2022, 27(2), 409; https://doi.org/10.3390/molecules27020409 - 09 Jan 2022

Cited by 1 | Viewed by 1495

Abstract

Chitooligosaccharides, the degradation products of chitin and chitosan, possess anti-bacterial, anti-tumor, and anti-inflammatory activities. The enzymatic production of chitooligosaccharides may increase the interest in their potential biomedical or agricultural usability in terms of the safety and simplicity of the manufacturing process. Crab-eating monkey acidic chitinase (CHIA) is an enzyme with robust activity in various environments. Here, we report the efficient degradation of chitin and chitosan by monkey CHIA under acidic and high-temperature conditions. Monkey CHIA hydrolyzed α-chitin at 50 °C, producing N-acetyl-d-glucosamine (GlcNAc) dimers more efficiently than at 37 °C. Moreover, the degradation rate increased with a longer incubation time (up to 72 h) without the inactivation of the enzyme. Five substrates (α-chitin, colloidal chitin, P-chitin, block-type, and random-type chitosan substrates) were exposed to monkey CHIS at pH 2.0 or pH 5.0 at 50 °C. P-chitin and random-type chitosan appeared to be the best sources of GlcNAc dimers and broad-scale chitooligosaccharides, respectively. In addition, the pattern of the products from the block-type chitosan was different between pH conditions (pH 2.0 and pH 5.0). Thus, monkey CHIA can degrade chitin and chitosan efficiently without inactivation under high-temperature or low pH conditions. Our results show that certain chitooligosaccharides are enriched by using different substrates under different conditions. Therefore, the reaction conditions can be adjusted to obtain desired oligomers. Crab-eating monkey CHIA can potentially become an efficient tool in producing chitooligosaccharide sets for agricultural and biomedical purposes. Full article

(This article belongs to the Special Issue Novel Enzymes for Natural Polymer Degradation)

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14 pages, 2014 KiB

Open AccessArticle

Unraveling Synergism between Various GH Family Xylanases and Debranching Enzymes during Hetero-Xylan Degradation

by Samkelo Malgas, Mpho S. Mafa, Brian N. Mathibe and Brett I. Pletschke

Molecules 2021, 26(22), 6770; https://doi.org/10.3390/molecules26226770 - 09 Nov 2021

Cited by 6 | Viewed by 2171

Abstract

Enzymes classified with the same Enzyme Commission (EC) that are allotted in different glycoside hydrolase (GH) families can display different mechanisms of action and substrate specificities. Therefore, the combination of different enzyme classes may not yield synergism during biomass hydrolysis, as the GH family allocation of the enzymes influences their behavior. As a result, it is important to understand which GH family combinations are compatible to gain knowledge on how to efficiently depolymerize biomass into fermentable sugars. We evaluated GH10 (Xyn10D and XT6) and GH11 (XynA and Xyn2A) β-xylanase performance alone and in combination with various GH family α-l-arabinofuranosidases (GH43 AXH-d and GH51 Abf51A) and α-d-glucuronidases (GH4 Agu4B and GH67 AguA) during xylan depolymerization. No synergistic enhancement in reducing sugar, xylose and glucuronic acid released from beechwood xylan was observed when xylanases were supplemented with either one of the glucuronidases, except between Xyn2A and AguA (1.1-fold reducing sugar increase). However, overall sugar release was significantly improved (≥1.1-fold reducing sugar increase) when xylanases were supplemented with either one of the arabinofuranosidases during wheat arabinoxylan degradation. Synergism appeared to result from the xylanases liberating xylo-oligomers, which are the preferred substrates of the terminal arabinofuranosyl-substituent debranching enzyme, Abf51A, allowing the exolytic β-xylosidase, SXA, to have access to the generated unbranched xylo-oligomers. Here, it was shown that arabinofuranosidases are key enzymes in the efficient saccharification of hetero-xylan into xylose. This study demonstrated that consideration of GH family affiliations of the carbohydrate-active enzymes (CAZymes) used to formulate synergistic enzyme cocktails is crucial for achieving efficient biomass saccharification. Full article

(This article belongs to the Special Issue Novel Enzymes for Natural Polymer Degradation)

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13 pages, 4205 KiB

Open AccessArticle

Non-Specific GH30_7 Endo-β-1,4-xylanase from Talaromyces leycettanus

by Katarína Šuchová, Nikolaj Spodsberg, Kristian B. R. Mørkeberg Krogh, Peter Biely and Vladimír Puchart

Molecules 2021, 26(15), 4614; https://doi.org/10.3390/molecules26154614 - 30 Jul 2021

Cited by 7 | Viewed by 2122

Abstract

This study describes the catalytic properties of a GH30_7 xylanase produced by the fungus Talaromyces leycettanus. The enzyme is an ando-β-1,4-xylanase, showing similar specific activity towards glucuronoxylan, arabinoxylan, and rhodymenan (linear β-1,3-β-1,4-xylan). The heteroxylans are hydrolyzed to a mixture of linear as well as branched β-1,4-xylooligosaccharides that are shorter than the products generated by GH10 and GH11 xylanases. In the rhodymenan hydrolyzate, the linear β-1,4-xylooligosaccharides are accompanied with a series of mixed linkage homologues. Initial hydrolysis of glucuronoxylan resembles the action of other GH30_7 and GH30_8 glucuronoxylanases, resulting in a series of aldouronic acids of a general formula MeGlcA²Xyl_n. Due to the significant non-specific endoxylanase activity of the enzyme, these acidic products are further attacked in the unbranched regions, finally yielding MeGlcA²Xyl_2-3. The accommodation of a substituted xylosyl residue in the −2 subsite also applies in arabinoxylan depolymerization. Moreover, the xylose residue may be arabinosylated at both positions 2 and 3, without negatively affecting the main chain cleavage. The catalytic properties of the enzyme, particularly the great tolerance of the side-chain substituents, make the enzyme attractive for biotechnological applications. The enzyme is also another example of extraordinarily great catalytic diversity among eukaryotic GH30_7 xylanases. Full article

(This article belongs to the Special Issue Novel Enzymes for Natural Polymer Degradation)

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14 pages, 4096 KiB

Open AccessArticle

Catalytic Diversity of GH30 Xylanases

by Katarína Šuchová, Vladimír Puchart, Nikolaj Spodsberg, Kristian B. R. Mørkeberg Krogh and Peter Biely

Molecules 2021, 26(15), 4528; https://doi.org/10.3390/molecules26154528 - 27 Jul 2021

Cited by 1 | Viewed by 1694

Abstract

Catalytic properties of GH30 xylanases belonging to subfamilies 7 and 8 were compared on glucuronoxylan, modified glucuronoxylans, arabinoxylan, rhodymenan, and xylotetraose. Most of the tested bacterial GH30-8 enzymes are specific glucuronoxylanases (EC 3.2.1.136) requiring for action the presence of free carboxyl group of MeGlcA side residues. These enzymes were not active on arabinoxylan, rhodymenan and xylotetraose, and conversion of MeGlcA to its methyl ester or its reduction to MeGlc led to a remarkable drop in their specific activity. However, some GH30-8 members are nonspecific xylanases effectively hydrolyzing all tested substrates. In terms of catalytic activities, the GH30-7 subfamily is much more diverse. In addition to specific glucuronoxylanases, the GH30-7 subfamily contains nonspecific endoxylanases and predominantly exo-acting enzymes. The activity of GH30-7 specific glucuronoxylanases also depend on the presence of the MeGlcA carboxyl, but not so strictly as in bacterial enzymes. The modification of the carboxyl group of glucuronoxylan had only weak effect on the action of predominantly exo-acting enzymes, as well as nonspecific xylanases. Rhodymenan and xylotetraose were the best substrates for exo-acting enzymes, while arabinoxylan represented hardly degradable substrate for almost all tested GH30-7 enzymes. The results expand current knowledge on the catalytic properties of this relatively novel group of xylanases. Full article

(This article belongs to the Special Issue Novel Enzymes for Natural Polymer Degradation)

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