Magnesium ions increase the activity of Bacillus deramificans pullulanase expressed by Brevibacillus choshinensis

Evaluation of antibody variants using a ribosome display and Brevibacillus choshinensis secretion system

In antibody engineering, the development of rapid and efficient strategies for improving affinity is highly necessary. In this study, we aimed to establish a method to efficiently enrich and analyze high-affinity antibody variants by combining protein synthesis using recombinant elements (PURE) ribosome display with next-generation sequencing (NGS) and Brevibacillus choshinensis secretion system using the NZ-1 antibody, which targets the PA tag peptide (GVAMPGAEDDVV) as a model antibody. From the mutated scFab library designed based on the structure, we performed a single-round of PURE ribosome display selection and analyzed the data by NGS to obtain high-affinity scFab candidates with high enrichment factor and high read counts. Subsequently, the most promising candidate was produced as a Fab in the B. choshinensis secretion system, and the purified Fab had an affinity (KD = 1.6 × 10-9 M) similar to the wild type. Overall, this study highlights the potential of the integrated PURE ribosome display with NGS analysis and the B. choshinensis secretion system for the rapid identification and analysis of high-affinity antibody variants.

Activation of microbial community and enhancement of quality by inoculating Zygosaccharomyces rouxii during the post-fermentation stage of Doubanjiang

The prolonged post-fermentation stage of Doubanjiang imparts unique flavors but may reduce microbial vitality and increase contamination, affecting quality. This study investigated the effect of Zygosaccharomyces rouxii inoculation during post-fermentation. Results showed a 46.7% increase in amino nitrogen and a significant rise in volatile compounds like phenethyl alcohol, 3-methyl-1-butanol, and ethyl octanoate. The relative abundances of Staphylococcus and Pantoea increased among bacteria, while Pichia, Wickerhamiella, and Zygosaccharomyces increased among fungi. Redundancy analysis showed a positive correlation between these genera and the main volatiles. Microbial ecological network analysis showed that inoculating Z. rouxii increased nodes and edges, resulting in tighter inter-module connections and enhanced robustness. Key genera included Zygosaccharomyces, Staphylococcus, Kazachstania, and Weissella. Metaproteomic results demonstrated that upregulated proteins were predominantly enriched in pathways related to flavor formation, while downregulated proteins were associated with ribosome and DNA synthesis-related pathways. PICRUSt2 analysis results showed higher expression of enzymes related to volatiles in innoculated samples. Inoculating Z. rouxii during the post-fermentation could boost core microorganisms, curb foodborne pathogens, stabilize the microbial community, and enhance Doubanjiang quality.

Pullulanase: unleashing the power of enzyme with a promising future in the food industry

Pullulanases are the most important industrial group of enzymes in family 13 glycosyl hydrolases. They hydrolyze either α-1,6 and α-1,4 or both glycosidic bonds in pullulan as well as other carbohydrates to produce glucose, maltose, and maltotriose syrups, which have important uses in food and other related sectors. However, very less reports are available on pullulanase production from native strains because of low yield issues. In line with the increasing demands for pullulanase, it has become important to search for novel pullulanase-producing microorganisms with high yields. Moreover, high production costs and low yield are major limitations in the industrial production of pullulanase enzymes. The production cost of pullulanase by using the solid-state fermentation (SSF) process can be minimized by selecting agro-industrial waste. This review summarizes the types, sources, production strategies, and potential applications of pullulanase in different food and other related industries. Researchers should focus on fungal strains producing pullulanase for better yield and low production costs by using agro-waste. It will prove a better enzyme in different food processing industries and will surely reduce the cost of products.

Study on the mechanism of efficient extracellular expression of toxic streptomyces phospholipase D in Brevibacillus choshinensis under Mg2+ stress

Background

Phospholipase D (PLD) has significant advantages in the food and medicine industries due to its unique transphosphatidylation. However, the high heterologous expression of PLD is limited by its cytotoxicity. The present study sought to develop an efficient and extracellular expression system of PLD in the non-pathogenic Brevibacillus choshinensis (B. choshinensis).

Results

The extracellular PLD was effectively expressed by the strong promoter (P2) under Mg2+ stress, with the highest activity of 10 U/mL. The inductively coupled plasma–mass spectrometry (ICP-MS) results elucidated that the over-expression of PLD by P2 promoter without Mg2+ stress induced the ionic homeostasis perturbation caused by the highly enhanced Ca2+ influx, leading to cell injury or death. Under Mg2+ stress, Ca2+ influx was significantly inhibited, and the strengths of P2 promoter and HWP gene expression were weakened. The study results revealed that the mechanism of Mg2+ induced cell growth protection and PLD expression might be related to the lowered strength of PLD expression by P2 promoter repression to meet with the secretion efficiency of B. choshinensis, and the redistribution of intracellular ions accompanied by decreased Ca2+ influx.

Conclusions

The PLD production was highly improved under Mg2+ stress. By ICP-MS and qPCR analysis combined with other results, the mechanism of the efficient extracellular PLD expression under Mg2+ stress was demonstrated. The relatively low-speed PLD expression during cell growth alleviated cell growth inhibition and profoundly improved PLD production. These results provided a potential approach for the large-scale production of extracellular PLD and novel insights into PLD function.

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.

An Acylase from Shewanella Putrefaciens Presents a Vibrio Parahaemolyticus Acylhomoserine Lactone-Degrading Activity and Exhibits Temperature-, Ph- and Metal-Dependences

Shewanella putrefaciens supernatant was found to increase the virulence factors of Vibrio parahaemolyticus by efficiently degrading its acylhomoserine lactone (AHL). To further reveal the regulation mechanism and its key degrading enzyme, a potential AHL-degrading enzyme acylase (Aac) from S. putrefaciens was cloned, and the influences of temperature, pH, protein modifiers, and metals on Aac were tested. Aac was significantly influenced by temperature and pH, and exhibited the highest AHL-degrading activity at temperatures of 37 °C and pH of 8. Mg2+ and Fe2+ can further increase the AHL-degrading activity. 10 mM EDTA inhibited its activity possibly by chelating the co-factors (metals) required for Aac activity. Tryptophan and arginine were identified as key components for Aac activity that are critical to its AHL-degrading activity. This study provides useful information on Aac and for V. parahaemolyticus control.

Available strategies for improved expression of recombinant proteins in Brevibacillus expression system: a review

Brevibacillus offers great potential as a recombinant protein expression host because of its exceptional abilities to synthesize and excrete proteins and its low extracellular protease activity. Despite these strengths, effective recombinant expression strategies are still the key to achieving high-level expression of recombinant proteins in Brevibacillus due to individual differences among strains and target proteins. Many strategies have been developed to improve recombinant protein expression in Brevibacillus. This review begins by introducing the processes used to establish and apply the Brevibacillus expression system, and then critically discusses the strategies available for improving recombinant protein expression in Brevibacillus, including optimization of the host and the expression vector, co-expression of a fusion partner or foldase, and optimization of the fermentation process. Finally, the prospects for further improvement of recombinant protein expression based on Brevibacillus are also discussed. This review is intended to provide a strategic reference for scientists wanting to improve the expression of a specific recombinant protein in Brevibacillus or other expression systems.

Cell-free biology using remote-controlled digital microfluidics for individual droplet control

Cell-free biology for diverse protein expression and biodetection in vitro has developed rapidly in recent years because of its more open and controllable reaction environment. However, complex liquid handling schemes are troublesome, especially when scaling up to perform multiple different reactions simultaneously. Digital microfluidic (DMF) technology can operate a single droplet by controlling its movement, mixing, separation, and some other actions, and is a suitable scaffold for cell-free reactions with higher efficiency. In this paper, a commercial DMF board, OpenDrop, was used, and DMF technology via remote real-time control inspired by the Internet of Things (IoT) was developed for detecting glucose enzyme catalytic cell-free reactions and verifying the feasibility of programmed cell-free protein expression. A cell-free biological reaction process which can be remote-controlled visually with excellent interactivity, controllability and flexibility was achieved. As proof-of-concept research, this work proposed a new control interface for single-drop cell-free biological reactions. It is much like the "droplet operation desktop" concept, used for remote-controllable operations and distributions of cell-free biology for efficient biological screening and protein synthesis in complex reaction networks, with expanded operability and less artificial interference.

Production of recombinant beta-amylase of Bacillus aryabhattai

In this study, the effects of carbon source, nitrogen source, and metal ions on cell growth and Bacillus aryabhattai β-amylase production in recombinant Brevibacillus choshinensis were investigated. The optimal medium for β-amylase production, containing glucose (7.5 g·L^-1), pig bone peptone (40.0 g·L^-1), Mg²⁺ (0.05 mol·L^-1), and trace metal elements, was determined through single-factor experiments in shake flasks. When cultured in the optimized medium, the β-amylase yield reached 925.4 U mL^-1, which was 7.2-fold higher than that obtained in the initial medium. Besides, a modified feeding strategy was proposed and applied in a 3-L fermentor fed with glucose, which achieved a dry cell weight of 15.4 g L^-1. Through this cultivation approached 30 °C with 0 g·L^-1 initial glucose concentration, the maximum β-amylase activity reached 5371.8 U mL^-1, which was 41.7-fold higher than that obtained with the initial medium in shake flask.

Enhanced Expression of Pullulanase in Bacillus subtilis by New Strong Promoters Mined From Transcriptome Data, Both Alone and in Combination

Pullulanase plays an important role as a starch hydrolysis enzyme in the production of bio-fuels and animal feed, and in the food industry. Compared to the methods currently used for pullulanase production, synthesis by Bacillus subtilis would be safer and easier. However, the current yield of pullulanase from B. subtilis is low to meet industrial requirements. Therefore, it is necessary to improve the yield of pullulanase by B. subtilis. In this study, we mined 10 highly active promoters from B. subtilis based on transcriptome and bioinformatic data. Individual promoters and combinations of promoters were used to improve the yield of pullulanase in B. subtilis BS001. Four recombinant strains with new promoters (Phag, PtufA, PsodA, and PfusA) had higher enzyme activity than the control (PamyE). The strain containing PsodA+fusA (163 U/mL) and the strain containing PsodA+fusA+amyE (336 U/mL) had the highest activity among the analyzed dual- and triple-promoter construct stains in shake flask, which were 2.29 and 4.73 times higher than that of the strain with PamyE, respectively. Moreover, the activity of the strain containing PsodA+fusA+amyE showed a maximum activity of 1,555 U/mL, which was 21.9 times higher than that of the flask-grown PamyE strain in a 50-liter fermenter. Our work showed that these four strong promoters mined from transcriptome data and their combinations could reliably increase the yield of pullulanase in quantities suitable for industrial applications.