Transcriptomic analysis of gene expression of menaquinone-7 in Bacillus subtilis natto toward different oxygen supply

Maggot Kinase and Natural Thrombolytic Proteins

Thrombolytic enzymes constitute a class of proteases with antithrombotic functions. Derived from natural products and abundant in nature, certain thrombolytic enzymes, such as urokinase, earthworm kinase, and streptokinase, have been widely used in the clinical treatment of vascular embolic diseases. Fly maggots, characterized by their easy growth and low cost, are a traditional Chinese medicine recorded in the Compendium of Materia Medica. These maggots can also be used as raw material for the extraction and preparation of thrombolytic enzymes (maggot kinase). In this review, we assembled global research reports on natural thrombolytic enzymes through a literature search and reviewed the functions and structures of natural thrombolytic enzymes to provide a reference for natural thrombophilic drug screening and development.

Enhancing menaquinone-7 biosynthesis through strengthening precursor supply and product secretion

Menaquinone-7 (MK-7) is an important class of vitamin K2 that is essential in human health and can prevent osteoporosis and cardiovascular disease. However, due to the complex synthesis pathway, the synthesis efficiency is low. The main objective of this study was to explore the effect of enhanced supply of precursors in Bacillus natto. Three precursors of pyruvate, shikimic acid, and sodium glutamate were chosen to investigate the effect of enhanced supply of precursors on MK-7 synthesis. Then, the optimal concentrations, different combinations, and different adding times were systematically studied, respectively. Results showed that the combination of shikimic acid and sodium glutamate could boost MK-7 production by 2 times, reaching 50 mg/L of MK-7 titer and 0.52 mg/(L·h) of MK-7 productivity. Furthermore, adding shikimic acid and sodium glutamate initially and feeding pyruvate at 48 h and 72 h increased MK-7 production to 58 mg/L. At the same time, the expression of the three related genes was also significantly upregulated. Subsequently, a new fermentation strategy combining the precursors enhancement and product secretion was proposed to enhance MK-7 yield and MK-7 productivity to 63 mg/L and 0.45 mg/(L·h). This study proposed a new fermentation regulation strategy for the enhancement of vitamin K2 biosynthesis.

Enhancing menaquinone-7 biosynthesis by adaptive evolution of Bacillus natto through chemical modulator

Menaquinone-7 (MK-7) is a kind of vitamin K2 playing an important role in the treatment and prevention of cardiovascular disease, osteoporosis and arterial calcification. The purpose of this study is to establish an adaptive evolution strategy based on a chemical modulator to improve MK-7 biosynthesis in Bacillus natto. The inhibitor of 5-enolpyruvylshikimate-3-phosphate synthase (EPSP synthase), glyphosate, was chosen as the chemical modulator to perform the experiments. The final strain ALE-25-40, which was obtained after 40 cycles in 25 mmol/L glyphosate, showed a maximal MK-7 titer of 62 mg/L and MK-7 productivity of 0.42 mg/(L h), representing 2.5 and 3 times the original strain, respectively. Moreover, ALE-25-40 generated fewer spores and showed a higher NADH and redox potential. Furthermore, the mechanism related to the improved performance of ALE-25-40 was investigated by comparative transcriptomics analysis. Genes related to the sporation formation were down-regulated. In addition, several genes related to NADH formation were also up-regulated. This strategy proposed here may provide a new and alternative directive for the industrial production of vitamin K2.

Effects of Alkali Stress on the Growth and Menaquinone-7 Metabolism of Bacillus subtilis natto

Menaquinone-7 (MK-7) is an important vitamin K₂, synthesized from the menaquinone parent ring and seven isoprene side chains. Presently, the synthesis of MK-7 stimulated by environmental stress primarily focuses on oxygen stress, while the effect of alkali stress is rarely studied. Therefore, this study researched the effects of alkali stress on the fermentation performance and gene expression of Bacillus subtilis natto. The organism’s growth characteristics, biomass, sporogenesis, MK-7 biosynthesis, and gene expression were analyzed. After a pH 8.5 stress adaptation treatment for 0.5 h and subsequent fermentation at pH 8.5, which promoted the growth of the strain and inhibited the spore formation rate. In addition, biomass was significantly increased (P < 0.05). The conversion rate of glycerol to MK-7 was 1.68 times higher than that of the control group, and the yield of MK-7 increased to 2.10 times. Transcriptomic analysis showed that the MK-7 high-yielding strain had enhanced carbon source utilization, increased glycerol and pyruvate metabolism, enhanced the Embden-Meyerhof pathway (EMP), tricarboxylic acid (TCA) circulation flux, and terpenoid biosynthesis pathway, and promoted the accumulation of acetyl-CoA, the side-chain precursor of isoprene. At the same time, the up-regulation of transketolase increased the metabolic flux of the pentose phosphate (HMP) pathway, which was conducive to the accumulation of D-erythrose 4-phosphate, the precursor of the menadione parent ring. This study’s results contribute to a better understanding of the effects of environmental stress on MK-7 fermentation by Bacillus subtilis natto and the molecular regulatory mechanism of MK-7 biosynthesis.

Transcriptome analysis revealing molecular mechanisms of enhanced pigment yield by succinic acid and fluconazole

This study aimed to elucidate the molecular mechanisms through which succinic acid and fluconazole stimulate Monascus pigment biosynthesis under liquid fermentation conditions. The pigment yield was significantly improved by adding 0.35 g·L^-1 succinic acid or 1.5 g·L^-1 fluconazole. Transcriptome sequencing and RT-qPCR confirmation were performed to reveal transcriptome changes. The results indicated that the addition of succinic acid significantly decreased mRNA expression of genes involved in fatty acid biosynthesis while increasing expression of genes involved in pyruvate metabolism. Fluconazole significantly down-regulated transcripts involved in branched-chain amino acid metabolism, fatty acid metabolism, glycolysis/gluconeogenesis, and pyruvate metabolism, as well as the generation of acetyl-CoA for pigment biosynthesis. On the other hand, nitrogen metabolism and lysine degradation pathways were significantly enriched, which could stimulate the generation of acetyl-CoA. Therefore, the mechanism for enhancing pigment yield may be attributed to the competitive regulation of metabolic pathways toward acetyl-CoA biosynthesis. Additionally, up-regulation of some different key genes in the presence of fluconazole or succinic acid was involved in improving pigment production. This study deepens the theoretical understanding for enhancing pigment biosynthesis and provides a few potential approaches for improving pigment yield.

Site-directed mutagenesis of the quorum-sensing transcriptional regulator SinR affects the biosynthesis of menaquinone in Bacillus subtilis

Background

Menaquinone (MK-7) is a highly valuable vitamin K₂ produced by Bacillus subtilis. Common static metabolic engineering approaches for promoting the production of MK-7 have been studied previously. However, these approaches caused an accumulation of toxic substances and reduced product yield. Hence, dynamic regulation by the quorum sensing (QS) system is a promising method for achieving a balance between product synthesis and cell growth.

Results

In this study, the QS transcriptional regulator SinR, which plays a significant role in biofilm formation and MK production simultaneously, was selected, and its site-directed mutants were constructed. Among these mutants, sinR knock out strain (KO-SinR) increased the biofilm biomass by 2.8-fold compared to the wild-type. SinR^quad maximized the yield of MK-7 (102.56 ± 2.84 mg/L). To decipher the mechanism of how this mutant regulates MK-7 synthesis and to find additional potential regulators that enhance MK-7 synthesis, RNA-seq was used to analyze expression changes in the QS system, biofilm formation, and MK-7 synthesis pathway. The results showed that the expressions of tapA, tasA and epsE were up-regulated 9.79-, 0.95-, and 4.42-fold, respectively. Therefore, SinR^quad formed more wrinkly and smoother biofilms than BS168. The upregulated expressions of glpF, glpk, and glpD in this biofilm morphology facilitated the flow of glycerol through the biofilm. In addition, NADH dehydrogenases especially sdhA, sdhB, sdhC and glpD, increased 1.01-, 3.93-, 1.87-, and 1.11-fold, respectively. The increased expression levels of NADH dehydrogenases indicated that more electrons were produced for the electron transport system. Electrical hyperpolarization stimulated the synthesis of the electron transport chain components, such as cytochrome c and MK, to ensure the efficiency of electron transfer. Wrinkly and smooth biofilms formed a network of interconnected channels with a low resistance to liquid flow, which was beneficial for the uptake of glycerol, and facilitated the metabolic flux of four modules of the MK-7 synthesis pathway.

Conclusions

In this study, we report for the first time that SinR^quad has significant effects on MK-7 synthesis by forming wrinkly and smooth biofilms, upregulating the expression level of most NADH dehydrogenases, and providing higher membrane potential to stimulate the accumulation of the components in the electron transport system.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01603-5.