A high-efficient strategy for combinatorial engineering paralogous gene family: A case study on histidine kinases in Clostridium

Elucidating the Biosynthesis and Function of an Autoinducing Peptide in Clostridium acetobutylicum

Clostridia produce autoinducing peptides (AIPs) regulated by the accessory gene regulator (Agr) quorum sensing system, playing a critical role in intercellular communication. However, the biosynthetic pathway and regulatory functions of clostridial AIPs remain inadequately characterized. In this study, we employed chemical quantification, genetic investigations, and in vitro reconstitution experiments to elucidate the native Ca-AIP in Clostridium acetobutylicum, a prominent industrial producer of acetone, butanol, and ethanol. Our findings identified a signal peptidase (Cac1760) and two CAAX metalloproteases (Cac0077 and Cac2478) as key players in N-terminal cleavage, while AgrB was found to be essential for C-terminal processing during Ca-AIP biosynthesis. Notably, overexpression of agrBD led to a 4.4-fold enhancement in Ca-AIP formation, which corresponded with an increase in butanol production from 12.5 to 14.9 g/L, while preserving vegetative cell morphology. The direct involvement of Ca-AIP in both butanol production and maintenance of cell morphology was further validated through exogenous supplementation. Collectively, these results provide novel insights into the biosynthesis of AIPs and propose a promising strategy for optimizing microbial processes in industrial applications.

Metabolically Engineered Escherichia coli for Conversion of D-Fructose to D-Allulose via Phosphorylation-Dephosphorylation

D-Allulose is an ultra-low calorie sweetener with broad market prospects. As an alternative to Izumoring, phosphorylation-dephosphorylation is a promising method for D-allulose synthesis due to its high conversion of substrate, which has been preliminarily attempted in enzymatic systems. However, in vitro phosphorylation-dephosphorylation requires polyphosphate as a phosphate donor and cannot completely deplete the substrate, which may limit its application in industry. Here, we designed and constructed a metabolic pathway in Escherichia coli for producing D-allulose from D-fructose via in vivo phosphorylation-dephosphorylation. PtsG-F and Mak were used to replace the fructose phosphotransferase systems (PTS) for uptake and phosphorylation of D-fructose to fructose-6-phosphate, which was then converted to D-allulose by AlsE and A6PP. The D-allulose titer reached 0.35 g/L and the yield was 0.16 g/g. Further block of the carbon flux into the Embden-Meyerhof-Parnas (EMP) pathway and introduction of an ATP regeneration system obviously improved fermentation performance, increasing the titer and yield of D-allulose to 1.23 g/L and 0.68 g/g, respectively. The E. coli cell factory cultured in M9 medium with glycerol as a carbon source achieved a D-allulose titer of ≈1.59 g/L and a yield of ≈0.72 g/g on D-fructose.

Citrulline deiminase pathway provides ATP and boosts growth of Clostridium carboxidivorans P7

BACKGROUND

Clostridium carboxidivorans P7 is capable of producing ethanol and butanol from inexpensive and non-food feedstock, such as syngas. Achieving improved ethanol and butanol production in the strain for industrial application depends on the energetics and biomass, especially ATP availability.

RESULTS

This study found that exogenous addition of citrulline promoted accumulation of ATP, increased specific growth rate, and reduced the doubling time of C. carboxidivorans P7. In heterotrophic fermentation experiments, the addition of citrulline increased intracellular ATP by 3.39-fold, significantly enhancing the production of total alcohol (ethanol + butanol) by 20%. Moreover, in the syngas fermentation experiments, the addition of citrulline improved the level of intracellular ATP and the biomass by 80.5% and 31.6%, respectively, resulting in an 18.6% and 60.3% increase in ethanol and the alcohol/acid production ratio, respectively.

CONCLUSIONS

This is the first report that citrulline could promote the growth of C. carboxidivorans P7 and increase the level of intracellular ATP, which is of great significance for the use of C. carboxidivorans P7 to synthesize biofuels.