A pH-stable, detergent and chelator resistant type I pullulanase from Bacillus pseudofirmus 703 with high catalytic efficiency

N-terminal domain truncation yielded a unique dimer of polysaccharide hydrolase with enhanced enzymatic activity, stability and calcium ion independence

Domain engineering, including domain truncation, fusion, or swapping, has become a common strategy to improve properties of enzymes, especially glycosyl hydrolases. However, there are few reports explaining the mechanism of increased activity from a protein structure perspective. Amy703 is an alkaline amylase with a unique N-terminal domain. Prior studies have shown that N-Amy, a mutant without an N-terminal domain, exhibits improved activity, stability, and calcium ion independence. In this study, we have used X-ray crystallography to determine the crystal structure of N-Amy and used AlphaFold2 to model the Amy703 structure, respectively. We further used size exclusion chromatography to show that Amy703 existed as a monomer, whereas N-Amy formed a unique dimer. It was found that the N-terminus of one monomer of N-Amy was inserted into the catalytic domain of its symmetrical subunit, resulting in the expansion of the catalytic pocket. This also significantly increased the pKa of the hydrogen donor Glu350, thereby enhancing substrate binding affinity and contributing to increased N-Amy activity. Meanwhile, two calcium ions were found to bind to N-Amy at different binding sites, which also contributed to the stability of protein. Therefore, this study provided new structural insights into the mechanisms of various glycosyl hydrolases.

Isolation, characterization, and cloning of thermostable pullulanase from Geobacillus stearothermophilus ADM-11

This study aimed to identify thermo-stable pullulanase-producing bacteria in soil samples of potato fields and food-producing companies. Pullulan agar medium was used to screen 17 bacterial strains, which were incubated at 65 °C. The isolate with the maximum activity (375U/ml) was selected and recognized as Geobacillus stearothermophilus ADM-11 by morphological, biochemical characterization, and 16S rRNA gene sequencing. The pullulanase production required optimum pH of 7 and temperature of 75 °C, respectively. The electrophoresis of purified pullulanase on SDS-polyacrylamide gel revealed 83 kDa of a molecular weight that is active at 70 °C and pH 7.0. It was also stable at 90 °C but its activity was decreased by 10 % at 100 °C. The action of pullulanase was increased and stabilized by Ca+2 among the metal ions. Beta and gamma-cyclodextrins inhibited enzyme activity while ethylenediaminetetraacetate (EDTA) and phenylmethylsulfonyl fluoride (PMSF) have no significant effect on pullulanase activity. A full-length pullulanase gene was amplified from G. stearothermophilus ADM-11 using genomic DNA 2.1 kb of PCR product which was then purified and ligated in the cloning vector pTZ57R using the TA cloning technique. Colony PCR confirmed cloning on the positive clones after the pullulanase gene had been ligated and subjected to restriction digestion. It revealed 74 % similarity with the reported pullulanase gene from Geobacillus sp. 44C. The thermostability of pullulanase and its ability to degrade raw pullulan may therefore have wide-scale applications in starch processing, the detergent business, and new biotechnological applications.

Production, characterization, and application of novel fungal pullulanase for fruit juice processing

The present study aimed to produce, characterize, and apply pullulanase from Aspergillus flavus (BHU-46) for fruit juice processing, assessing its enzymatic properties and impact on juice quality. Pullulanase was produced via solid-state fermentation using wheat bran as the substrate. Purification and characterization included specific activity, molecular weight, pH and temperature optima, and substrate specificity. The enzyme was immobilized in sodium alginate beads and used for clarifying mosambi, apple, and mango juices. Parameters such as yield, clarity, reducing sugar, total soluble solids (TSS), total phenol, and enzymatic browning were evaluated pre-and post-treatment. The purified pullulanase had a specific activity of 652.2 U/mg and a molecular weight of 135 kDa. Optimal pH values were 6.5 and 10, with maximum activity at 50 °C. Pullulanase showed a high affinity for pullulan and starch, indicating Pullulanase type II classification. Immobilized pullulanase improved yield, clarity, reducing sugar, TSS, and total phenol in fruit juices. The highest yield and clarity were observed in mosambi juice. Additionally, the enzyme reduced enzymatic browning, increasing the lightness of the juice. This study provides a significant contribution to the juice processing industry and represents the first report on the application of pullulanase for fruit juice processing.

Characterization of a novel detergent-resistant type I pullulanase from Bacillus megaterium Y103 and its application in laundry detergent

This study aims to find a moderate pullulanase for detergent industry. The pulY103B gene (2217 bp) from Bacillus megaterium Y103 was cloned and expressed in Escherichia coli. PulY103B contained four conserved regions of glycoside hydrolase family (GH) 13 and the typical sequence of type I pullulanase. The optimal reaction conditions of PulY103B were pH 6.5 and 40 °C. In addition, it remained stable below 40 °C and over 80% of activity was retained at pH ranging from 6.0 to 8.5. The best substrate for the enzyme was pullulan. Furthermore, it exhibited activity toward wheat starch (36.5%) and soluble starch (33.4%) but had no activity toward amylose and glycogen. Maltotriose and maltohexaose were major pullulan hydrolysis products. Soluble starch and amylopectin were mainly hydrolyzed into maltotetraose. These results indicated that PulY103B is a novel type I pullulanase with transglycosylation activity via formation of α-1,4-glucosidic linkages. Moreover, PulY103B was strongly stimulated by nonionic detergents [viz, Tween 20 (10%), Tween 80 (1%), Triton X-100 (20%)] and commercial liquid detergents (3.0 g/L). Wash performance tests demonstrated that the mixture of PulY103B and detergent removed starch-based stains better than using detergent alone (p < 0.05). Therefore, this pullulanase has big potential as a detergent additive.

In-Depth Characterization of Debranching Type I Pullulanase from Priestia koreensis HL12 as Potential Biocatalyst for Starch Saccharification and Modification

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.

Microbial starch debranching enzymes: Developments and applications

Starch debranching enzymes (SDBEs) hydrolyze the α-1,6 glycosidic bonds in polysaccharides such as starch, amylopectin, pullulan and glycogen. SDBEs are also important enzymes for the preparation of sugar syrup, resistant starch and cyclodextrin. As the synergistic catalysis of SDBEs and other starch-acting hydrolases can effectively improve the raw material utilization and production efficiency during starch processing steps such as saccharification and modification, they have attracted substantial research interest in the past decades. The substrate specificities of the two major members of SDBEs, pullulanases and isoamylases, are quite different. Pullulanases generally require at least two α-1,4 linked glucose units existing on both sugar chains linked by the α-1,6 bond, while isoamylases require at least three units of α-1,4 linked glucose. SDBEs mainly belong to glycoside hydrolase (GH) family 13 and 57. Except for GH57 type II pullulanse, GH13 pullulanases and isoamylases share plenty of similarities in sequence and structure of the core catalytic domains. However, the N-terminal domains, which might be one of the determinants contributing to the substrate binding of SDBEs, are distinct in different enzymes. In order to overcome the current defects of SDBEs in catalytic efficiency, thermostability and expression level, great efforts have been made to develop effective enzyme engineering and fermentation strategies. Herein, the diverse biochemical properties and distinct features in the sequence and structure of pullulanase and isoamylase from different sources are summarized. Up-to-date developments in the enzyme engineering, heterologous production and industrial applications of SDBEs is also reviewed. Finally, research perspective which could help understanding and broadening the applications of SDBEs are provided.

Biotechnology and bioengineering of pullulanase: state of the art and perspectives

Pullulanase (EC 3.2.1.41) is a starch-debranching enzyme in the α-amylase family and specifically cleaves α-1,6-glycosidic linkages in starch-type polysaccharides, such as pullulan, β-limited dextrin, glycogen, and amylopectin. It plays a key role in debranching and hydrolyzing starch completely, thus bring improved product quality, increased productivity, and reduced production cost in producing resistant starch, sugar syrup, and beer. Plenty of researches have been made with respects to the discovery of either thermophilic or mesophilic pullulanases, however, few examples meet the demand of industrial application. This review presents the progress made in the recent years from the first aspect of characteristics of pullulanases. The heterologous expression of pullulanases in different microbial hosts and the methods used to improve the expression effectiveness and the regulation of enzyme production are also described. Then, the function evolution of pullulanases from a protein engineering view is discussed. In addition, the immobilization strategy using novel materials is introduced to improve the recyclability of pullulanases. At the same time, we indicate the trends in the future research to facilitate the industrial application of pullulanases.

A novel cold-active type I pullulanase from a hot-spring metagenome for effective debranching and production of resistant starch

Pullulanase is a potent enzyme for starch debranching. In this study, a novel type I pullulanase (Pul_M) was identified from the metagenome of a thermal aquatic habitat that exhibits optimal activity of debranching at 40 °C temperature and pH 6.0 to 7.0. More than 50% enzymatic activity was detected at the low temperature of 4 °C, determining it a cold-active type I pullulanase. It was able to efficiently catalyze the hydrolysis of α-1,6-glycosidic linkages in pullulan, with a specific activity of 177 U mg^-1. The results determined Pul_M to be a potential starch debranching biocatalyst, causing a significant increase of about 80% in the apparent amylose content of potato starch. Retrogradation of the debranched starch resulted in the formation of resistant starch 3. The yield of resistant starch was estimated to be about 45%. The resistant starch exhibited higher crystallinity, enhanced heat-stability, and resistance to α-amylase digestion, as compared to native starch.

Consolidated bioprocessing of raw starch to ethanol by Saccharomyces cerevisiae: Achievements and challenges

Recent advances in amylolytic strain engineering for starch-to-ethanol conversion have provided a platform for the development of raw starch consolidated bioprocessing (CBP) technologies. Several proof-of-concept studies identified improved enzyme combinations, alternative feedstocks and novel host strains for evaluation and application under fermentation conditions. However, further research efforts are required before this technology can be scaled up to an industrial level. In this review, different CBP approaches are defined and discussed, also highlighting the role of auxiliary enzymes for a supplemented CBP process. Various achievements in the development of amylolytic Saccharomyces cerevisiae strains for CBP of raw starch and the remaining challenges that need to be tackled/pursued to bring yeast raw starch CBP to industrial realization, are described. Looking towards the future, it provides potential solutions to develop more cost-effective processes that include cheaper substrates, integration of the 1G and 2G economies and implementing a biorefinery concept where high-value products are also derived from starchy substrates.

Optimizing the DO-stat protocol for enhanced production of thermostable pullulanase in Escherichia coli by using oxygen control strategies

Production of a thermostable pullulanase by DO-stat fed-batch fermentation of recombinant Escherichia coli BL 21 was investigated in a 5 L of fermentor. The effect of three oxygen control strategies, glucose feedback, shifting fermentor pressure, and adding oxygen-enriched air, on cell growth and pullulanase expression were examined. The oxygen-transfer capacity was found to be enhanced with increasing fermentor pressure and oxygen ratio in oxygen-enriched air, but the cell growth and pullulanase production were restrained under high fermentor pressure. The highest cell density and pullulanase activity reached 55.1 g/L and 412 U/mL, respectively, in the case by adding oxygen-enriched air, which was suggested as an effective approach to enhance both cell growth and pullulanase production. PRACTICAL APPLICATIONS: This thermostable pullulanase displayed optimal activity at 90°C and pH 5.4, which could be applied for one-step saccharification of starch biomass. The optimization of the DO-stat fed-batch fermentation in high cell density level would provide a research basis for its industrialization.

Current prospective in using cold-active enzymes as eco-friendly detergent additive

Advanced developments in the field of enzyme technology have increased the use of enzymes in industrial applications, especially in detergents. Enzymes as detergent additives have been extensively studied and the demand is considerably increasing due to its distinct properties and potential applications. Enzymes from microorganisms colonized at various geographical locations ranging from extreme hot to cold are explored for compatibility studies as detergent additives. Especially psychrophiles growing at cold conditions have cold-active enzymes with high catalytic activity and their stability under extreme conditions makes it as an appropriate eco-friendly and cost-effective additive in detergents. Adequate number of reports are available on cold-active enzymes such as proteases, lipases, amylases, and cellulases with high efficiency and exceptional features. These enzymes with increased thermostability and alkaline stability have become the premier choice as detergent additives. Modern approaches in genomics and proteomics paved the way to understand the compatibility of cold-active enzymes as detergent additives in broader dimensions. The molecular techniques such as gene coding, amino acid sequencing, and protein engineering studies helped to solve the mysteries related to alkaline stability of these enzymes and their chemical compatibility with oxidizing agents. The present review provides an overview of cold-active enzymes used as detergent additives and molecular approaches that resulted in development of these enzymes as commercial hit in detergent industries. The scope and challenges in using cold-active enzymes as eco-friendly and sustainable detergent additive are also discussed.

A new cold-active and alkaline pectate lyase from Antarctic bacterium with high catalytic efficiency

Cold-active enzymes have become attractive biocatalysts in biotechnological applications for their ability to retain high catalytic activity below 30 °C, which allows energy reduction and cost saving. Here, a 1041 bp gene pel1 encoding a 34.7 KDa pectate lyase was cloned from a facultatively psychrophilic Antarctic bacterium Massilia eurypsychrophila and heterologously expressed in Escherichia coli. PEL1 presented the highest 66% identity to the reported mesophilic pectate lyase PL_Xc. The purified PEL1 exhibits the optimum temperature and pH of 30 °C and 10 toward polygalacturonic acid, respectively. PEL1 is a cold-active enzyme that can retain 60% and 25% relative activity at 10 °C and 0 °C, respectively, while it loses most of activity at 40 °C for 10 min. PEL1 has the highest specific activity (78.75 U mg^-1) than all other reported cold-active pectinase, making it a better choice for use in industry. Based on the detailed sequence and structure comparison between PEL1 and PL_Xc and mutation analysis, more flexible structure and some loop regions may contribute to the cold activity and thermal instability of PEL1. Our investigations of the cold-active mechanism of PEL1 might guide the rational design of PEL1 and other related enzymes.

Industrially produced pullulanases with thermostability: Discovery, engineering, and heterologous expression

Pullulanases (EC 3.2.1.41) are well-known starch-debranching enzymes widely used to hydrolyze α-1,6-glucosidic linkages in starch, pullulan, amylopectin, and other oligosaccharides, with application potentials in food, brewing, and pharmaceutical industries. Although extensive studies are done to discover and express pullulanases, only few are available with desirable characteristics for industrial applications. This raises the challenge to mine new enzyme sources, engineer proteins based on sequence/structure, and regulate expressions. We review here the identification of extremophilic and mesophilic microbes as sources of industrial pullulanases with desirable characteristics, including acid-resistance, thermostability, and psychrotrophism. We present current advances in site-directed mutagenesis and sequence/structure-guided protein engineering of pullulanases. In addition, we discuss heterologous expression of pullulanases in prokaryotic and eukaryotic microbial systems, and address the effectiveness of the expression elements and their regulation of enzyme production. Finally, we indicate future research needs to develop desired industrial pullulanases.