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Engineering Clostridium for improved solvent production: recent progress and perspective
Clostridia are Gram-positive, spore-forming, obligate anaerobic bacteria that can produce solvents such as acetone, ethanol, and butanol, which can be used as biofuels or building block chemicals. Many successful attempts have been made to improve solvent yield and titer from sugars through metabolic engineering of solventogenic and acidogenic clostridia. More recently, cellulolytic and acetogenic clostridia have also attracted high interests for their ability to utilize low-cost renewable substrates such as cellulose and syngas. Process engineering such as in situ butanol recovery and consolidated bioprocessing (CBP) has been developed for improved solvent titer and productivity. This review focuses on metabolic and process engineering strategies for solvent production from sugars, lignocellulosic biomass, and syngas by various clostridia, including conventional solventogenic
Clostridium acetobutylicum
, engineered acidogens such as
C. tyrobutyricum
and
C. cellulovorans
, and carboxydotrophic acetogens such as
C. carboxidivorans
and
C. ljungdahlii
.
Journal Article
Recent advances in n-butanol and butyrate production using engineered Clostridium tyrobutyricum
Acidogenic clostridia naturally producing acetic and butyric acids has attracted high interest as a novel host for butyrate and n-butanol production. Among them, Clostridium tyrobutyricum is a hyper butyrate-producing bacterium, which re-assimilates acetate for butyrate biosynthesis by butyryl-CoA/acetate CoA transferase (CoAT), rather than the phosphotransbutyrylase-butyrate kinase (PTB-BK) pathway widely found in clostridia and other microbial species. To date, C. tyrobutyricum has been engineered to overexpress a heterologous alcohol/aldehyde dehydrogenase, which converts butyryl-CoA to n-butanol. Compared to conventional solventogenic clostridia, which produce acetone, ethanol, and butanol in a biphasic fermentation process, the engineered C. tyrobutyricum with a high metabolic flux toward butyryl-CoA produced n-butanol at a high yield of > 0.30 g/g and titer of > 20 g/L in glucose fermentation. With no acetone production and a high C4/C2 ratio, butanol was the only major fermentation product by the recombinant C. tyrobutyricum, allowing simplified downstream processing for product purification. In this review, novel metabolic engineering strategies to improve n-butanol and butyrate production by C. tyrobutyricum from various substrates, including glucose, xylose, galactose, sucrose, and cellulosic hydrolysates containing the mixture of glucose and xylose, are discussed. Compared to other recombinant hosts such as Clostridium acetobutylicum and Escherichia coli, the engineered C. tyrobutyricum strains with higher butyrate and butanol titers, yields and productivities are the most promising hosts for potential industrial applications.
Journal Article
Engineering Clostridium acetobutylicum with a histidine kinase knockout for enhanced n-butanol tolerance and production
Clostridium acetobutylicum JB200, a mutant strain of C. acetobutylicum ATCC 55025 obtained through strain evolution in a fibrous bed bioreactor, had high butanol tolerance and produced up to ~21 g/L butanol from glucose in batch fermentation, an improvement of ~67 % over the parental strain (~12.6 g/L). Comparative genomic analysis revealed a single-base deletion in the cac3319 gene leading to C-terminal truncation in its encoding histidine kinase (HK) in JB200. To study the effects of cac3319 mutation on cell growth and fermentation, the cac3319 gene in ATCC 55025 was disrupted using the ClosTron group II intron-based gene inactivation system. Compared to ATCC 55025, the cac3319 HK knockout mutant, HKKO, produced 44.4 % more butanol (18.2 ± 1.3 vs. 12.6 ± 0.2 g/L) with a 90 % higher productivity (0.38 ± 0.03 vs. 0.20 ± 0.02 g/L h) due to increased butanol tolerance, confirming, for the first time, that cac3319 plays an important role in regulating solvent production and tolerance in C. acetobutylicum. This work also provides a novel metabolic engineering strategy for generating high-butanol-tolerant and high-butanol-producing strains for industrial applications.
Journal Article
Dirac surface states in intrinsic magnetic topological insulators EuSn2As2 and MnBi2nTe3n+1
In magnetic topological insulators (TIs), the interplay between magnetic order and nontrivial topology can induce fascinating topological quantum phenomena, such as the quantum anomalous Hall effect, chiral Majorana fermions, and axion electrodynamics. Recently, a great deal of attention has been focused on the intrinsic magnetic TIs, where disorder effects can be eliminated to a large extent, which is expected to facilitate the emergence of topological quantum phenomena. Despite intensive efforts, experimental evidence of the topological surface states (SSs) remains elusive. Here, by combining first-principles calculations and angle-resolved photoemission spectroscopy (ARPES) experiments, we reveal thatEuSn2As2is an antiferromagnetic TI with the observation of Dirac SSs consistent with our prediction. We also observe nearly gapless Dirac SSs in antiferromagnetic TIsMnBi2nTe3n+1(n=1and 2), which are absent in previous ARPES results. These results provide clear evidence for nontrivial topology of these intrinsic magnetic TIs. Furthermore, we find that the topological SSs show no observable changes across the magnetic transition within the experimental resolution, indicating that the magnetic order has a quite small effect on the topological SSs, which can be attributed to weak hybridization between the localized magnetic moments, from either4for3dorbitals, and the topological electronic states. This finding provides insights for further research that the correlations between magnetism and topological states need to be strengthened to induce larger gaps in the topological SSs, which will facilitate the realization of topological quantum phenomena at higher temperatures.
Journal Article
Chiral fermion reversal in chiral crystals
In materials chiral fermions such as Weyl fermions are characterized by nonzero chiral charges, which are singular points of Berry curvature in momentum space. Recently, new types of chiral fermions beyond Weyl fermions have been discovered in structurally chiral crystals CoSi, RhSi and PtAl. Here, we have synthesized RhSn single crystals, which have opposite structural chirality to the CoSi crystals we previously studied. Using angle-resolved photoemission spectroscopy, we show that the bulk electronic structures of RhSn are consistent with the band calculations and observe evident surface Fermi arcs and helical surface bands, confirming the existence of chiral fermions in RhSn. It is noteworthy that the helical surface bands of the RhSn and CoSi crystals have opposite handedness, meaning that the chiral fermions are reversed in the crystals of opposite structural chirality. Our discovery establishes a direct connection between chiral fermions in momentum space and chiral lattices in real space.
Exotic chiral fermions beyond Weyl fermions have recently been discovered in a series of chiral crystals such as CoSi. Here, the authors report the evidences of chiral fermions in RhSn with opposite handedness compared to those observed in CoSi, where the structural chirality is also opposite.
Journal Article
A novel β-galactosidase from Klebsiella oxytoca ZJUH1705 for efficient production of galacto-oligosaccharides from lactose
Galacto-oligosaccharides (GOS), which can be produced by enzymatic transgalactosylation of lactose with β-galactosidases, have attracted much attention in recent years because of their prebiotic functions and wide uses in infant formula, infant foods, livestock feed, and pet food industries. In this study, a novel β-galactosidase-producing Klebsiella oxytoca ZJUH1705, identified by its 16S rRNA sequence (GenBank accession no. MH981243), was isolated. Two β-galactosidase genes, bga 1 encoding a 2058-bp fragment (GenBank accession no. MH986613) and bga 2 encoding a 3108-bp fragment (GenBank accession no. MN182756), were cloned from K. oxytoca ZJUH1705 and expressed in E. coli. The purified β-gal 1 and β-gal 2 had the specific activity of 217.56 U mg−1 and 57.9 U mg−1, respectively, at the optimal pH of 7.0. The reaction kinetic parameters Km, Vmax, and Kcat with oNPG as the substrate at 40 °C were 5.62 mM, 167.1 μmol mg−1 min−1, and 218.1 s−1, respectively, for β-gal 1 and 3.91 mM, 14.6 μmol mg−1 min−1, and 28.9 s−1, respectively, for β-gal 2. Although β-gal 1 had a higher enzyme activity for lactose hydrolysis, only β-gal 2 had a high transgalactosylation capacity. Using β-gal 2 with the addition ratio of ~ 2.5 U g−1 lactose, a high GOS yield of 45.5 ± 2.3% (w/w−1) was obtained from lactose (40% w/w−1 or 480 g L−1) in a phosphate buffer (100 mM, pH 7.0) at 40 °C in 48 h. Thus, the β-gal 2 from K. oxytoca ZJUH1705 would be a promising biocatalyst for GOS production from lactose.Key Points• A novel bacterial β-galactosidase producer was isolated and identified.• β-Galactosidases were cloned and expressed in heterologous strain and characterized.• Both enzymes have hydrolytic activity but only one have transglycosilation activity.• The developed process with β-gal 2 could provide an alternative for GOS production.
Journal Article
An Efficient ECG Denoising Method Based on Empirical Mode Decomposition, Sample Entropy, and Improved Threshold Function
The electrocardiogram (ECG) signal can easily be affected by various types of noises while being recorded, which decreases the accuracy of subsequent diagnosis. Therefore, the efficient denoising of ECG signals has become an important research topic. In the paper, we proposed an efficient ECG denoising approach based on empirical mode decomposition (EMD), sample entropy, and improved threshold function. This method can better remove the noise of ECG signals and provide better diagnosis service for the computer-based automatic medical system. The proposed work includes three stages of analysis: (1) EMD is used to decompose the signal into finite intrinsic mode functions (IMFs), and according to the sample entropy of each order of IMF following EMD, the order of IMFs denoised is determined; (2) the new threshold function is adopted to denoise these IMFs after the order of IMFs denoised is determined; and (3) the signal is reconstructed and smoothed. The proposed method solves the shortcoming of discarding the first-order IMF directly in traditional EMD denoising and proposes a new threshold denoising function to improve the traditional soft and hard threshold functions. We further conduct simulation experiments of ECG signals from the MIT-BIH database, in which three types of noise are simulated: white Gaussian noise, electromyogram (EMG), and power line interference. The experimental results show that the proposed method is robust to a variety of noise types. Moreover, we analyze the effectiveness of the proposed method under different input SNR with reference to improving SNR (SNRimp) and mean square error (MSE), then compare the denoising algorithm proposed in this paper with previous ECG signal denoising techniques. The results demonstrate that the proposed method has a higher SNRimp and a lower MSE. Qualitative and quantitative studies demonstrate that the proposed algorithm is a good ECG signal denoising method.
Journal Article
Improved Production of 2,3-Butanediol in Bacillus amyloliquefaciens by Over-Expression of Glyceraldehyde-3-Phosphate Dehydrogenase and 2,3-butanediol Dehydrogenase
Previously, a safe strain, Bacillus amyloliquefaciens B10-127 was identified as an excellent candidate for industrial-scale microbial fermentation of 2,3-butanediol (2,3-BD). However, B. amyloliquefaciens fermentation yields large quantities of acetoin, lactate and succinate as by-products, and the 2,3-BD yield remains prohibitively low for commercial production.
In the 2,3-butanediol metabolic pathway, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyzes the conversion of 3-phosphate glyceraldehyde to 1,3-bisphosphoglycerate, with concomitant reduction of NAD(+) to NADH. In the same pathway, 2,3-BD dehydrogenase (BDH) catalyzes the conversion of acetoin to 2,3-BD with concomitant oxidation of NADH to NAD(+). In this study, to improve 2,3-BD production, we first over-produced NAD(+)-dependent GAPDH and NADH-dependent BDH in B. amyloliquefaciens. Excess GAPDH reduced the fermentation time, increased the 2,3-BD yield by 12.7%, and decreased the acetoin titer by 44.3%. However, the process also enhanced lactate and succinate production. Excess BDH increased the 2,3-BD yield by 16.6% while decreasing acetoin, lactate and succinate production, but prolonged the fermentation time. When BDH and GAPDH were co-overproduced in B. amyloliquefaciens, the fermentation time was reduced. Furthermore, in the NADH-dependent pathways, the molar yield of 2,3-BD was increased by 22.7%, while those of acetoin, lactate and succinate were reduced by 80.8%, 33.3% and 39.5%, relative to the parent strain. In fed-batch fermentations, the 2,3-BD concentration was maximized at 132.9 g/l after 45 h, with a productivity of 2.95 g/l·h.
Co-overexpression of bdh and gapA genes proved an effective method for enhancing 2,3-BD production and inhibiting the accumulation of unwanted by-products (acetoin, lactate and succinate). To our knowledge, we have attained the highest 2,3-BD fermentation yield thus far reported for safe microorganisms.
Journal Article
A Potential Probiotic for Diarrhea: Clostridium tyrobutyricum Protects Against LPS-Induced Epithelial Dysfunction via IL-22 Produced By Th17 Cells in the Ileum
Probiotics are clinically used for diarrhea and inflammatory bowel diseases in both humans and animals. Previous studies have shown that Clostridium tyrobutyricum (Ct) protects against intestinal dysfunction, while its regulatory function in the gut needs further investigation and the related mechanisms are still not fully elucidated. This study aims to further verify the protective function of Ct and reveal its underlying mechanisms in alleviating diarrhea and intestinal inflammation. Ct inhibited LPS-induced diarrhea and intestinal inflammation in the ileum. IL-22 was identified and the protective role of Ct in the ileum presented an IL-22-dependent manner according to the transcriptomic analysis and in vivo interference mice experiments. The flow cytometric analysis of immune cells in the ileum showed that Ct enhanced the proportions of Th17 cells in response to LPS. The results of in situ hybridization further verified that Ct triggered Th17 cells to produce IL-22, which combined with IL-22RA1 expressed in the epithelial cells. Moreover, Ct was unable to enhance the levels of short-chain fatty acids (SCFAs) in the ileum, suggesting that the protective role of Ct in the ileum was independent of SCFAs. This study uncovered the role of Ct in alleviating diarrhea and inflammation with the mechanism of stimulating Th17 cells in the lamina propria to produce IL-22, highlighting its potential application as a probiotic for diarrhea and inflammation in the ileum.
Journal Article