Overexpression of an endogenous raw starch digesting mesophilic α-amylase gene in Bacillus amyloliquefaciens Z3 by in vitro methylation protocol

Novel Strain of Paenibacillus phyllosphaerae CS-148 for the Direct Hydrolysis of Raw Starch into Glucose: Isolation and Fermentation Optimization

The conventional process for converting starch to glucose is energy-intensive. To lower the cost of this process, a novel strain of Paenibacillus phyllosphaerae CS-148 was isolated and identified, which could directly hydrolyze raw starch into glucose and accumulate glucose in the fermentation broth. The effects of different organic and inorganic nitrogen sources, the culture temperature, the initial pH, and the agitation speed on the yield of glucose were optimized through the one-factor-at-a-time method. Nine factors were screened by Plackett-Burman design, and three factors (raw corncob starch, yeast extract and (NH4)2SO4) had significant effects on glucose yield. Three significant factors were further optimized using Box-Behnken design. Under the optimized fermentation conditions (raw corncob starch 40.4 g/L, yeast extract 4.27 g/L, (NH4)2SO4 4.39 g/L, KH2PO4 2 g/L, MgSO4`7H2O 2 g/L, FeSO4`7H2O 0.02 g/L, NaCl 2 g/L, KCl 0.5 g/L, inoculums volume 4%, temperature 35 °C, agitation rate 150 rpm, and initial pH 7.0), the maximum glucose yield reached 17.32 ± 0.46 g/L, which is 1.33-fold compared to that by initial fermentation conditions. The maximum conversion rate and glucose productivity were 0.43 ± 0.01 g glucose/g raw corn starch and 0.22 ± 0.01 g/(L·h), respectively. These results implied that P. phyllosphaerae CS-148 could be used in the food industry or fermentation industry at a low cost.

Bacillus amyloliquefaciens LM-1 Affects Multiple Cell Biological Processes in Magnaporthe oryzae to Suppress Rice Blast

Magnaporthe oryzae, one of the most destructive rice pathogens, causes significant losses during the rice harvest every year. Bacillus amyloliquefaciens has been explored in many crops as a potential biocontrol agent. However, the mechanisms of B. amyloliquefaciens controled rice blast are not fully understood. Here, a biocontrol strain LM-1, isolated from a contaminated medium, was identified as B. amyloliquefaciens using morphological observation, physiological and biochemical tests, and 16S rDNA sequencing. LM-1 inhibited the growth and pathogenicity of M. oryzae and Bipolaris oryzae (Breda de Haan) Shoem. The mycelia of M. oryzae co-cultured with LM-1 were enlarged and broken by fluorescence microscopy using calcofluor white. LM-1 inhibited the mycelia of M. oryzae from producing conidia. Genes itu, srf, and fenB were detected in LM-1. Furthermore, the supernatant of LM-1 interfered with the appressorium formation of M. oryzae, blocked conidial cell death, and reduced autophagy degradation but did not affect the normal germination of rice seeds and seeding growth. Additionally, we observed hypersensitivity reactions, reactive oxygen species, and iron accumulation reduction in rice cells inoculated with supernatant. Our study reveals that LM-1 has a control effect on rice blast and affects cell wall integrity, sporulation, appressorium formation, cell death, and autophagy.

CRISPR-dCpf1 mediated whole genome crRNA inhibition library for high-throughput screening of growth characteristic genes in Bacillus amyloliquefaciens LB1ba02

Bacillus amyloliquefaciens LB1ba02 is generally recognized as food safe (GRAS) microbial host and important enzyme-producing strain in the industry. However, autolysis affects the growth of bacteria, further affecting the yield of target products. Besides, the restriction-modification system, existed in B. amyloliquefaciens LB1ba02, results in a low transformation efficiency, which further leads to a lack of high-throughput screening tools. Here, we constructed a genome-wide crRNA inhibition library based on the CRISPR/dCpf1 system and high-throughput screening of related genes affecting the cell growth and autolysis using flow cytometry in B. amyloliquefaciens LB1ba02. The whole genome crRNA library was first validated for resistance to the toxic chemical 5-fluorouracil, and then used for validation of essential genes. In addition, seven gene loci (oppD, flil, tuaA, prmA, sigO, hslU, and GE03231) that affect the growth characteristics of LB1ba02 were screened. Among them, the Opp system had the greatest impact on growth. When the expression of operon oppA-oppB-oppC-oppD-oppF was inhibited, the cell growth difference was most significant. Inhibition of other sites could also promote rapid growth of bacteria to varying degrees; however, inhibition of GE03231 site accelerated cell autolysis. Therefore, the whole genome crRNA inhibition library is well suited for B. amyloliquefaciens LB1ba02 and can be further applied to high-throughput mining of other functional genes.

Structural and Functional Properties of Porous Corn Starch Obtained by Treating Raw Starch with AmyM

Porous starch is attracting considerable attention for its high surface area and shielding ability, properties which are useful in many food applications. In this study, native corn starch with 15, 25, and 45% degrees of hydrolysis (DH-15, DH-25, and DH-45) were prepared using a special raw starch-digesting amylase, AmyM, and their structural and functional properties were evaluated. DH-15, DH-25, and DH-45 exhibited porous surface morphologies, diverse pore size distributions and pore areas, and their adsorptive capacities were significantly enhanced by improved molecular interactions. Structural measures showed that the relative crystallinity decreased as the DH increased, while the depolymerization of starch double helix chains promoted interactions involving disordered chains, followed by chain rearrangement and the formation of sub-microcrystalline structures. In addition, DH-15, DH-25, and DH-45 displayed lower hydrolysis rates, and DH-45 showed a decreased C∞ value of 18.9% with higher resistant starch (RS) content and lower glucose release. Our results indicate that AmyM-mediated hydrolysis is an efficient pathway for the preparation of porous starches with different functionalities which can be used for a range of applications.

Activity-Based Screening of Soil Samples from Nyingchi, Tibet, for Amylase-Producing Bacteria and Other Multifunctional Enzyme Capacities

Despite the interest in Tibetan soil as a promising source of functional enzymes with potential biotechnological applications, few studies have considered the screening and identification of amylase producing bacteria from Tibetan soil. Amylase has many applications in the food and feed industries, textile and biofuel production, and biomedical engineering. The area of amylase with specific properties is attracting growing attention because of its better application to various industrial conditions. This study aims to screen and identify amylase-producing strains from soil samples collected in Nyingchi, Tibet, and then explore whether the bacterial isolates are superior for unique enzymes. In this paper, a total of 127 amylase producing bacteria were isolated by activity-based screening of six Tibetan soil samples. The 16S rRNA gene survey then identified four major phyla, namely, firmicutes, bacteroidetes, proteobacteria, and actinobacteria, which were differentiated into twelve genera with a dominance of Bacillus (67.72%), followed by Pseudomonas (8.66%). Microbial diversity analysis revealed that the amylase-producing bacterial community of the Kadinggou forest soil sample showed the best variety (the Simpson index was 0.69 and the Shannon index was 0.85). The amylase activity assay of the bacterial isolates showed a mean of 0.66 U/mL at 28°C and pH 5.2. Based on the effect of temperatures and pHs on amylase activity, several bacterial isolates can produce thermophilic (50°C), psychrophilic (10°C), acidophilic (pH 4.2), and alkaliphilic (pH 10.2) amylases. Furthermore, four bacterial isolates were screened for amylase, protease, and esterase activities, which indicated multifunctional enzyme capacities. The present study is expected to contribute to our understanding of Tibetan microbial resources and their potential for scientific research and industrial applications.

Development and application of a CRISPR-dCpf1 assisted multiplex gene regulation system in Bacillus amyloliquefaciens LB1ba02

Bacillus amyloliquefaciens LB1ba02 is generally recognized as food safe (GRAS) microbial host and important enzyme-producing strain in the industry. However, the restriction-modification system, existed in B. amyloliquefaciens LB1ba02, results in a low transformation efficiency, which makes its CRISPR tool development lagging far behind other Bacillus species. Here, we adapted a nuclease-deficient mutant dCpf1 (D917A) of Cpf1 and developed a CRISPR/dCpf1 assisted multiplex gene regulation system for the first time in B. amyloliquefaciens LB1ba02. A 73.9-fold inhibition efficiency and an optimal 1.8-fold activation effect at the - 327 bp site upstream of the TSS were observed in this system. In addition, this system achieved the simultaneous activation of the expression of three genes (secE, secDF, and prsA) by designing a crRNA array. On this basis, we constructed a crRNA activation library for the proteins involved in the Sec pathway, and screened 7 proteins that could promote the secretion of extracellular proteins. Among them, the most significant effect was observed when the expression of molecular motor transporter SecA was activated. Not only that, we constructed crRNA arrays to activate the expression of two or three proteins in combination. The results showed that the secretion efficiency of fluorescent protein GFP was further increased and an optimal 9.8-fold effect was observed when SecA and CsaA were simultaneously activated in shake flask fermentation. Therefore, the CRISPR/dCpf1-ω transcription regulation system can be applied well in a restriction-modification system strain and this system provides another CRISPR-based regulation tool for researchers who are committed to the development of genetic engineering and metabolic circuits in B. amyloliquefaciens.

Enhanced extracellular raw starch-degrading α-amylase production in Bacillus subtilis by promoter engineering and translation initiation efficiency optimization

Background

A raw starch-degrading α-amylase from Pontibacillus sp. ZY (AmyZ1), previously screened by our laboratory, showed a promising application potential for starch-processing industries. However, the AmyZ1 secretory production still under investigation, which seriously restricts its application in the starch-processing industry. On the other hand, Bacillus subtilis is widely used to achieve the extracellular expression of target proteins.

Results

AmyZ1 secretory production was achieved in B. subtilis and was enhanced by promoter engineering and translation initiation efficiency optimization. First, based on the different phase-dependent promoters, the dual-promoter P_spoVG–P_spoVG142 was constructed by combining dual-promoter engineering and promoter modification. The corresponding strain BZd34 showed an extracellular AmyZ1 activity of 1437.6 U/mL during shake flask cultivation, which was 3.11-fold higher than that of the original strain BZ1 (P_groE). Then, based on translation initiation efficiency optimization, the best strain BZd343 containing optimized 5'-proximal coding sequence (opt3) produced the highest extracellular α-amylase activity of 1691.1 U/mL, which was 3.65-fold higher than that of the strain BZ1. Finally, cultivation of BZd343 in 3-L fermenter exhibited an extracellular AmyZ1 activity of 14,012 U/mL at 48 h, with productivity of 291.9 U/mL·h.

Conclusions

This is the first report of recombinant expression of AmyZ1 in B. subtilis and the expression level of AmyZ1 represents the highest raw starch-degrading α-amylase level in B. subtilis to date. The high-level expression of AmyZ1 in this work provides a foundation for its industrial production. The strategies used in this study also provide a strategic reference for improving the secretory expression of other enzymes in B. subtilis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01855-9.

Development of a Microalgae-Based Continuous Starch-to-Hydrogen Conversion Approach

Eukaryotic algae represent a highly heterogeneous group in terms of organization, lifestyle, and metabolic capabilities. Unicellular green microalgae are capable of biohydrogen production through direct and indirect photolysis as well as dark fermentation. Most algae hydrogen studies focus on axenic algal cultures, although these are difficult and expensive to maintain for continuous operation. Moreover, the complex interplays and metabolic fluxes between algae and bacteria in natural ecosystems provide a number of clear biological and technological benefits to large-scale functional algae-based systems. Two green algae species from the Chlamydomonas and Chlorella genera were used to engineer stable synthetic communities by incorporating a starch-degrading bacterium from the Bacillus genus into the inter-kingdom consortium. Continuous photoheterotrophic biohydrogen production was achieved by elaborating an appropriate algal–bacterial ratio and fine-tuning the culture conditions for the synthetic consortia. Medium with starch as only carbon source served as a simple model of cheap substrate for algal hydrogen generation. The engineered pairwise algal–bacterial associations showed increased biomass and biohydrogen yield compared to the axenic control conditions. Chlorella sp. MACC-360 produced a significantly higher amount of hydrogen when both the bacterium partner and starch were added to the media compared to the axenic algae. Continuous, elevated algal hydrogen production was achieved in media supplemented with 8 g L−1 starch as sole carbon source when carefully selected initial cell number values were used for the Chlorella sp. MACC-360–B. amlyloliquefaciens co-cultures.

Amylases from thermophilic bacteria: structure and function relationship

Amylases hydrolyze starch to diverse products including dextrins and progressively smaller polymers of glucose units. Thermally stable amylases account for nearly 25% of the enzyme market. This review highlights the structural attributes of the α-amylases from thermophilic bacteria. Heterologous expression of amylases in suitable hosts is discussed in detail. Further, specific value maximization approaches, such as protein engineering and immobilization of the amylases are discussed in order to improve its suitability for varied applications on a commercial scale. The review also takes into account of the immobilization of the amylases on nanomaterials to increase the stability and reusability of the enzymes. The function-based metagenomics would provide opportunities for searching amylases with novel characteristics. The review is expected to explore novel amylases for future potential applications.

Prebiotic, Probiotic, Antimicrobial, and Functional Food Applications of Bacillus amyloliquefaciens

Bacillus amyloliquefaciens belongs to the genus Bacillus and family Baciliaceae. It is ubiquitously found in food, plants, animals, soil, and in different environments. In this review, the application of B. amyloliquefaciens in probiotic and prebiotic microbes in fermentation, synthesis, and hydrolysis of food compounds is discussed as well as further insights into its potential application and gaps. B. amyloliquefaciens is also a potential microbe in the synthesis of bioactive compounds including peptides and exopolysaccharides. In addition, it can synthesize antimicrobial compounds (e.g., Fengycin, and Bacillomycin Lb), which makes its novelty in the food sector greater. Moreover, it imparts and improves the functional, sensory, and shelf life of the end products. The hydrolysis of complex compounds including insoluble proteins, carbohydrates, fibers, hemicellulose, and lignans also shows that B. amyloliquefaciens is a multifunctional and potential microbe which can be applied in the food industry and in functional food processing.