Biochemical and Molecular Characterizations of a Novel pH- and Temperature-Stable Pectate Lyase from Bacillus amyloliquefaciens S6 for Industrial Application

Bekli, Seda; Aktaş, Büşra; Gencer, Donus; Aslım, Belma

doi:10.1007/s12033-019-00194-2

Cited by 24 publications

(10 citation statements)

References 61 publications

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“…Pectate lyase ( Table 4 ) has been reported in Caldicellulosiruptor bescii ( 81 ), genus Bacillus: Bacillus subtilis, B. licheniformis, B. cereus, B. circulans, B. pasteurii, B . amyloliquefaciens , and B. pumilus ( 86 , 87 ), Paenibacillus sp. ( 88 ), Clostridium cellulovorans ( 89 ), Streptomyces thermocarboxydus ( 90 ), Bacteroides thetaiotaomicron ( 82 ), Bacteroides ovatus ( 83 ), Eubacterium eligens, Faecalibacterium prausnitzii ( 85 ), and Monoglobus pectinilyticus ( 41 ).…”

Section: Microbial Degradation Of Rsm Cell Wall Carbohydratesmentioning

confidence: 99%

Chemical and nutritional characteristics, and microbial degradation of rapeseed meal recalcitrant carbohydrates: A review

Cheng

Venema

2022

Front. Nutr.

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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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Section: Microbial Degradation Of Rsm Cell Wall Carbohydratesmentioning

confidence: 99%

Chemical and nutritional characteristics, and microbial degradation of rapeseed meal recalcitrant carbohydrates: A review

Cheng

Venema

2022

Front. Nutr.

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“…2B). Many reports indicated that polysaccharide lyase activities are mostly Ca 2ϩ dependent; for example, recombinant pectate lyase (recPEL S6) from Bacillus amyloliquefaciens S6 showed maximal activity at 0.5 mM CaCl 2 (8). In this study, after CbPLs and their catalytic domains were purified from E. coli, the detection of lyase activities was not possible in Ca 2ϩ -free buffer.…”

Section: Resultsmentioning

confidence: 85%

“…Its maximum activities were observed at pH 10.5 and 70°C, and it showed the highest degumming efficiency reported to date (7). A pectate lyase, PelS6, from the B. amyloliquefaciens S6 strain displayed highly thermostability and survival at a wide range of pHs, which could be suitable for juice clarity (8). To identify thermostable and highly active enzymes, the number of studies investigating thermophilic microorganisms such as those from the genera Thermotoga and Caldicellulosiruptor has been growing recently (9)(10)(11)(12)(13)(14).…”

mentioning

confidence: 99%

Exploration of Two Pectate Lyases from Caldicellulosiruptor bescii Reveals that the CBM66 Module Has a Crucial Role in Pectic Biomass Degradation

Hamouda

Ali

et al. 2020

Appl Environ Microbiol

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Pectin deconstruction is the initial step in breaking the recalcitrance of plant biomass by using selected microorganisms that encode for pectinolytic enzymes. Pectate lyases that cleave α-1,4-galacturonosidic linkage of pectin are widely used in industries, such as paper making and fruit softening. However, reports on pectate lyases with good thermostability are few. Here, two pectate lyases (CbPL3 and CbPL9) from a hyperthermophilic bacterium Caldicellulosiruptor bescii, respectively, belonged to family 3 and family 9 polysaccharide lyases, were investigated. Biochemical properties on two CbPLs were shown similarly under optimized conditions of 80°C–85°C and pH 8–9. However, the degradation products from pectin and polygalacturonic acids (pGA) were different. A family-66 carbohydrate-binding module (CbCBM66), located in the N-terminus of two CbPLs, shares 100% amino acid identity. CbCBM66-truncated mutant of CbPL9 showed lower activities than the wild-type, whereas the CbPL3 with CbCBM66 knock-out portion was reported with enhanced activities, thereby revealing the different effect of CbCBM66. Prediction by I-TASSAR server revealed CbCBM66 is structurally close to BsCBM66 from Bacillus subtilis, however, COFACTOR and COACH programs speculated that the substrate-binding sites between CbCBM66 and BsCBM66 are different. Furthermore, substrate-binding assay indicated that the catalytic domains in two CbPLs had strong affinities on pectate-related substrates, but CbCBM66 showed weak interaction with a number of lignocellulosic carbohydrates. Finally, scanning electron microscope (SEM) analysis and total reducing sugar assay showed that the two enzymes could improve the saccharification of switchgrass. The two CbPLs are impressive sources for degradation of plant biomass. Importance Thermophilic proteins could be implemented in diverse industrial applications. We sought to characterize two pectate lyases, CbPL3 and CbPL9, from a thermophilic bacterium Caldicellulosiruptor bescii. The two enzymes share high optimum temperature, low optimum pH, and good thermostability at evaluated temperature. A family-66 carbohydrate binding module (CbCBM66) was identified in two CbPLs with sharing 100% amino acid identity. Deletion of CbCBM66 dramatically decreased the activity of CbPL9, but increase the activity and thermostability of CbPL3, suggesting the different roles of CbCBM66 in two enzymes. Moreover, the degradation products by two CbPLs were different. These results revealed these enzymes could represent a potential pectate lyase for applications in paper and textile industries.

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“…In this study, however, fragment replacement did not improve the thermostability of PGLA but rather its enzymatic activity. The enzymatic activity of PGLA-rep4 was higher than that of the other four previously reported bacterial pectin lyases (Table 1 ): the pectin lyase pel4J4 with a total activity of 204.4 U/mL (Cheng et al 2019 ), the pectin lyase reported by Yuan et al ( 2019 ) with a specific enzyme activity of 298.5 U/mg, the pectate lyase studied by Zhou et al ( 2017b ) with a total activity of 85.2 U/mL after 24 h incubation in shake flasks with TB medium and a specific activity after purification of 320 U/mg, and the pectin lyase studied by Bekli et al ( 2019 ) with the specific enzyme activity of 49.6 U/mg after purification. In addition, the relative activity of PGLA-rep4 in the range of pH 4–10 was still more than 70% after being stored at 50 °C for 7 h, indicating good pH stability.…”

Section: Discussionmentioning

confidence: 99%

Modification and application of highly active alkaline pectin lyase

Wei

et al. 2022

AMB Expr

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Alkaline pectate lyase has developmental prospects in the textile, pulp, paper, and food industries. In this study, we selected BacPelA, the pectin lyase with the highest expression activity from Bacillus clausii, modified and expressed in Escherichia coli BL21(DE3). Through fragment replacement, the catalytic activity of the enzyme was significantly improved. The optimum pH and temperature of the modified pectin lyase (PGLA-rep4) were 11.0 and 70 °C, respectively. It also exhibited a superior ability to cleave methylated pectin. The enzyme activity of PGLA-rep4, measured at 235 nm with 0.2% apple pectin as the substrate, was 554.0 U/mL, and the specific enzyme activity after purification using a nickel column was 822.9 U/mg. After approximately 20 ns of molecular dynamics simulation, the structure of the pectin lyase PGLA-rep4 tended to be stable. The root mean square fluctuation (RMSF) values at the key catalytically active site, LYS168, were higher than those of the wildtype PGLA. In addition, PGLA-rep4 was relatively stable in the presence of metal ions. PGLA-rep4 has good enzymatic properties and activities and maintains a high pH and temperature. This study provides a successful strategy for enhancing the catalytic activity of PGLA-rep4, making it the ultimate candidate for degumming and various uses in the pulp, paper, and textile industries.

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Biochemical and Molecular Characterizations of a Novel pH- and Temperature-Stable Pectate Lyase from Bacillus amyloliquefaciens S6 for Industrial Application

Cited by 24 publications

References 61 publications

Chemical and nutritional characteristics, and microbial degradation of rapeseed meal recalcitrant carbohydrates: A review

Chemical and nutritional characteristics, and microbial degradation of rapeseed meal recalcitrant carbohydrates: A review

Exploration of Two Pectate Lyases from Caldicellulosiruptor bescii Reveals that the CBM66 Module Has a Crucial Role in Pectic Biomass Degradation

Modification and application of highly active alkaline pectin lyase

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