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Deng Q, Sun X, Gao D, Wang Y, Liu Y, Li N, Wang Z, Liu M, Wang J, Wang Q. Characterization of Two Novel Rumen-Derived Exo-Polygalacturonases: Catalysis and Molecular Simulations. Microorganisms 2023; 11:microorganisms11030760. [PMID: 36985333 PMCID: PMC10059216 DOI: 10.3390/microorganisms11030760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Pectinases are a series of enzymes that degrade pectin and have been used extensively in the food, feed, and textile industries. The ruminant animal microbiome is an excellent source for mining novel pectinases. Two polygalacturonase genes, IDSPga28-4 and IDSPga28-16, from rumen fluid cDNA, were cloned and heterologously expressed. Recombinant IDSPGA28-4 and IDSPGA28-16 were stable from pH 4.0 to 6.0, with activities of 31.2 ± 1.5 and 330.4 ± 12.4 U/mg, respectively, against polygalacturonic acid. Hydrolysis product analysis and molecular dynamics simulation revealed that IDSPGA28-4 was a typical processive exo-polygalacturonase and cleaved galacturonic acid monomers from polygalacturonic acid. IDSPGA28-16 cleaved galacturonic acid only from substrates with a degree of polymerization greater than two, suggesting a unique mode of action. IDSPGA28-4 increased the light transmittance of grape juice from 1.6 to 36.3%, and IDSPGA28-16 increased the light transmittance of apple juice from 1.9 to 60.6%, indicating potential application in the beverage industry, particularly for fruit juice clarification.
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Affiliation(s)
- Qian Deng
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaobao Sun
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Deying Gao
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuting Wang
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yu Liu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Nuo Li
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhengguang Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Mingqi Liu
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Jiakun Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qian Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Correspondence: ; Tel.: +86-0571-88982389
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Distinct roles of carbohydrate-binding modules in multidomain β-1,3-1,4-glucanase on polysaccharide degradation. Appl Microbiol Biotechnol 2023; 107:1751-1764. [PMID: 36800030 DOI: 10.1007/s00253-023-12416-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 02/18/2023]
Abstract
Lam16A is a novel GH16 β-1,3-1,4-lichenase isolated from the genus Caldicellulosiruptor which can utilize untreated carbohydrate components of plant cell walls. Its catalytic module has been characterized that the six carbohydrate-binding modules (CBMs) were queued in the C-terminus, but their roles were still unclear. Here, full-length and CBM-truncated mutants of Lam16A were purified and characterized through heterologous expression in Escherichia coli. The profiles of these proteins, including the enzyme activity, degrading efficiency, substrate-binding affinity, and thermostability, were explored. Full-length Lam16A with six CBMs showed excellent thermostability and the highest activity against barley β-glucan and laminarin with optimum pH of 6.5. The CBMs stimulated degrading ability of the catalytic module, especially against β-1,3(4)-glucan-based polysaccharides. The released products from β-1,3-1,4-glucan by Lam16A or its truncated mutants revealed an endo-type glycoside hydrolase. Lam16As exhibited strong binding affinities to the insoluble polysaccharides, especially Lam16A-1CBM. The degradation of yeast cell walls by Lam16A enzyme solution relative to the control reduced the absorbance values at OD800 by ~ 85% ± 1.2, enabling the release of up to ~ 0.057 ± 0.0039 µg/mL of the cytoplasmic protein into the supernatant, lowering the viability of the cells by ~ 70.3% ± 6.9, thus causing significant damage in the cell wall structure. Taken together, CBMs could influence the substrate specificity, thermal stability, and binding affinity of β-1,3-1,4-glucanase. These results demonstrate the great potential of these enzymes to promote the bioavailability of β-1,3-glucan oligosaccharides for health benefits. KEY POINTS: • Carbohydrate-binding modules strongly influenced the enzyme activity and binding affinity, and further impacted glycoside hydrolase activity. • Lam16A enzymes have sufficient ability to hydrolyze β-1,3-1,4-glucan-based polysaccharides. • Lam16As provide a powerful tool to promote the bioavailability of β-1,3-glucan oligosaccharides.
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Long C, Qi XL, Venema K. Chemical and nutritional characteristics, and microbial degradation of rapeseed meal recalcitrant carbohydrates: A review. Front Nutr 2022; 9:948302. [PMID: 36245487 PMCID: PMC9554435 DOI: 10.3389/fnut.2022.948302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Approximately 35% of rapeseed meal (RSM) dry matter (DM) are carbohydrates, half of which are water-soluble carbohydrates. The cell wall of rapeseed meal contains arabinan, galactomannan, homogalacturonan, rhamnogalacturonan I, type II arabinogalactan, glucuronoxylan, XXGG-type and XXXG-type xyloglucan, and cellulose. Glycoside hydrolases including in the degradation of RSM carbohydrates are α-L-Arabinofuranosidases (EC 3.2.1.55), endo-α-1,5-L-arabinanases (EC 3.2.1.99), Endo-1,4-β-mannanase (EC 3.2.1.78), β-mannosidase (EC 3.2.1.25), α-galactosidase (EC 3.2.1.22), reducing-end-disaccharide-lyase (pectate disaccharide-lyase) (EC 4.2.2.9), (1 → 4)-6-O-methyl-α-D-galacturonan lyase (pectin lyase) (EC 4.2.2.10), (1 → 4)-α-D-galacturonan reducing-end-trisaccharide-lyase (pectate trisaccharide-lyase) (EC 4.2.2.22), α-1,4-D-galacturonan lyase (pectate lyase) (EC 4.2.2.2), (1 → 4)-α-D-galacturonan glycanohydrolase (endo-polygalacturonase) (EC 3.2.1.15), Rhamnogalacturonan hydrolase, Rhamnogalacturonan lyase (EC 4.2.2.23), Exo-β-1,3-galactanase (EC 3.2.1.145), endo-β-1,6-galactanase (EC 3.2.1.164), Endo-β-1,4-glucanase (EC 3.2.1.4), α-xylosidase (EC 3.2.1.177), β-glucosidase (EC 3.2.1.21) endo-β-1,4-glucanase (EC 3.2.1.4), exo-β-1,4-glucanase (EC 3.2.1.91), and β-glucosidase (EC 3.2.1.21). In conclusion, this review summarizes the chemical and nutritional compositions of RSM, and the microbial degradation of RSM cell wall carbohydrates which are important to allow to develop strategies to improve recalcitrant RSM carbohydrate degradation by the gut microbiota, and eventually to improve animal feed digestibility, feed efficiency, and animal performance.
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Affiliation(s)
- Cheng Long
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
- Faculty of Science and Engineering, Centre for Healthy Eating and Food Innovation, Maastricht University - Campus Venlo, Venlo, Netherlands
| | - Xiao-Long Qi
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Koen Venema
- Faculty of Science and Engineering, Centre for Healthy Eating and Food Innovation, Maastricht University - Campus Venlo, Venlo, Netherlands
- *Correspondence: Koen Venema
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Suzuki H, Morishima T, Handa A, Tsukagoshi H, Kato M, Shimizu M. Biochemical Characterization of a Pectate Lyase AnPL9 from Aspergillus nidulans. Appl Biochem Biotechnol 2022; 194:5627-5643. [PMID: 35802235 DOI: 10.1007/s12010-022-04036-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2022] [Indexed: 11/26/2022]
Abstract
Pectinolytic enzymes have diverse industrial applications. Among these, pectate lyases act on the internal α-1,4-linkage of the pectate backbone, playing a critical role in pectin degradation. While most pectate lyases characterized thus far are of bacterial origin, fungi can also be excellent sources of pectinolytic enzymes. In this study, we performed biochemical characterization of the pectate lyase AnPL9 belonging to the polysaccharide lyase family 9 (PL9) from the filamentous fungus Aspergillus nidulans. Recombinant AnPL9 was produced using a Pichia pastoris expression system and purified. AnPL9 exhibited high activity on homogalacturonan (HG), pectin from citrus peel, pectin from apple, and the HG region in rhamnogalacturonan-I. Although digalacturonic acid and trigalacturonic acid were not degraded by AnPL9, tetragalacturonic acid was converted to 4,5-unsaturated digalacturonic acid and digalacturonic acid. These results indicate that AnPL9 degrades HG oligosaccharides with a degree of polymerization > 4. Furthermore, AnPL9 was stable within a neutral-to-alkaline pH range (pH 6.0-11.0). Our findings suggest that AnPL9 is a candidate pectate lyase for biotechnological applications in the food, paper, and textile industries. This is the first report on a fungal pectate lyase belonging to the PL9 family.
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Affiliation(s)
- Hiromitsu Suzuki
- Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-0073, Japan
| | - Toshiki Morishima
- Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-0073, Japan
| | - Atsuya Handa
- Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-0073, Japan
| | | | - Masashi Kato
- Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-0073, Japan
| | - Motoyuki Shimizu
- Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-0073, Japan.
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Endo A, Tanno H, Kadowaki R, Fujii T, Tochio T. Extracellular fructooligosaccharide degradation in Anaerostipes hadrus for co-metabolism with non-fructooligosaccharide utilizers. Biochem Biophys Res Commun 2022; 613:81-86. [DOI: 10.1016/j.bbrc.2022.04.134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 04/28/2022] [Indexed: 12/23/2022]
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Ge Z, Kuang Z, Chen J, Chen J, Liu T, She Z, Lu Y. Comparative genomics analysis of Bacillus velezensis LOH112 isolated from a nonagenarian provides insights into its biocontrol and probiotic traits. Gene 2022; 835:146644. [PMID: 35680027 DOI: 10.1016/j.gene.2022.146644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/28/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022]
Abstract
Bacillus velezensis has recently received increasing attention as a biological fungicide and a potential probiotic agent because of its broad spectrum of antibacterial and antifungal activities. Here, we evaluated the beneficial traits of a newly isolated B. velezensis strain LOH112 using comprehensive bioinformatics and comparative genomic analyses and in vitro experimental approaches. Whole genome sequencing and assembly results showed that the genome of LOH112 consists of a circular chromosome and a circular plasmid, which encodes proteins involved in important biological processes such as sporulation, quorum sensing, and antibiotic synthesis. LOH112 contains 13 secondary metabolism gene clusters responsible for the production of antimicrobial compounds. In vitro experiments showed that LOH112 effectively inhibits several fungi and Gram-positive pathogenic bacteria, hydrolyzes protein and cellulose, and is capable of forming strong adhesive biofilms. Furthermore, comparative genomics revealed that LOH112 contains 34 strain-specific orthologous gene clusters, including two caseinolytic protease P (clpP) genes responsible for proteomic homeostasis. Selective pressure analysis indicated that the transmembrane transporter and ATP-dependent alanine/valine adenylase genes were strongly positively selected, which may endow LOH112 with better biocontrol ability and potential probiotic properties. Collectively, these results not only provide insights into a deeper understanding of the genomic characterization of LOH112 but also imply the potential application of LOH112 as biocontrol and probiotic agents.
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Affiliation(s)
- Zhenhuang Ge
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhiqi Kuang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China
| | - Jiahao Chen
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China
| | - Junyi Chen
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China
| | - Tianhao Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhigang She
- School of Chemistry, Sun Yat-sen University, Guangzhou 510275, China
| | - Yongjun Lu
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Run Ze Laboratory for Gastrointestinal Microbiome Study, Sun Yat-sen University, Guangzhou 510275, China.
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Zhou Z, Wang X. Rational design and structure-based engineering of alkaline pectate lyase from Paenibacillus sp. 0602 to improve thermostability. BMC Biotechnol 2021; 21:32. [PMID: 33941157 PMCID: PMC8091735 DOI: 10.1186/s12896-021-00693-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ramie degumming is often carried out at high temperatures; therefore, thermostable alkaline pectate lyase (PL) is beneficial for ramie degumming for industrial applications. Thermostable PLs are usually obtained by exploring new enzymes or reconstructing existing enzyme by rational design. Here, we improved the thermostability of an alkaline pectate lyase (PelN) from Paenibacillus sp. 0602 with rational design and structure-based engineering. RESULTS From 26 mutants, two mutants of G241A and G241V showed a higher thermostability compared with the wild-type PL. The mutant K93I showed increasing specific activity at 45 °C. Subsequently, we obtained combinational mutations (K93I/G241A) and found that their thermostability and specific activity improved simultaneously. The K93I/G241A mutant showed a half-life time of 15.9 min longer at 60 °C and a melting temperature of 1.6 °C higher than those of the wild PL. The optimum temperature decreased remarkably from 67.5 °C to 60 °C, accompanied by a 57% decrease in Km compared with the Km value of the wild-type strain. Finally, we found that the intramolecular interaction in PelN was the source in the improvements of molecular properties by comparing the model structures. Rational design of PelN was performed by stabilizing the α-helices with high conservation and increasing the stability of the overall structure of the protein. Two engineering strategies were applied by decreasing the mutation energy calculated by Discovery Studio and predicting the free energy in the process of protein folding by the PoPMuSiC algorithm. CONCLUSIONS The results demonstrated that the K93I/G241A mutant was more suitable for industrial production than the wild-type enzyme. Furthermore, the two forementioned strategies could be extended to reveal engineering of other kinds of industrial enzymes.
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Affiliation(s)
- Zhanping Zhou
- Tianjin Sinonocy Biological Technology Co. Ltd., Tianjin, 300308, China
| | - Xiao Wang
- Nanfang College of Sun Yat-Sen University, Guangzhou, 510970, China.
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