The significance of proline on lignocellulose-derived inhibitors tolerance in Clostridium acetobutylicum ATCC 824

Synthetic biology approaches to improve tolerance of inhibitors in lignocellulosic hydrolysates

Increasing attention is being focused on using lignocellulose for valuable products. Microbial decomposition can convert lignocellulose into renewable biofuels and other high-value bioproducts, contributing to sustainable development. However, the presence of inhibitors in lignocellulosic hydrolysates can negatively affect microorganisms during fermentation. Improving microbial tolerance to these hydrolysates is a major focus in metabolic engineering. Traditional detoxification methods increase costs, so there is a need for cheap and efficient cell-based detoxification strategies. Synthetic biology approaches offer several strategies for improving microbial tolerance, including redox balancing, membrane engineering, omics-guided technologies, expression of protectants and transcription factors, irrational engineering, cell flocculation, and other novel technologies. Advances in molecular biology, high-throughput sequencing, and artificial intelligence (AI) allow for precise strain modification and efficient industrial production. Developing AI-based computational models to guide synthetic biology efforts and creating large-scale heterologous libraries with automation and high-throughput technologies will be important for future research.

Biosorption of Remazol Brilliant Blue R textile dye using Clostridium beijerinckii by biorefinery approach

The current study proposes RBBR biosorption by Clostridium beijerinckii DSMZ 6422 biomass remaining after biobutanol production from pumpkin peel (PP) by a zero-waste approach. Efficient biobutanol production was achieved by investigating initial PP concentrations (5-20% without or with enzymatic hydrolysis) and fermentation time. According to this, the highest concentrations of biobutanol and total ABE were obtained as 4.87 g/L and 8.13 g/L in the presence of 10% PP without enzymatic hydrolysis at 96 h. Furthermore, based on the zero-waste approach, C. beijerinckii DSMZ 6422 biomass obtained after biofuel production was used as a biosorbent for the removal of RBBR dye. Response surface methodology (RSM), commonly utilized for the experimental design, was used to specify the optimized biosorption conditions of RBBR, including initial dye concentration (50-200 mg/L), initial pH (2-6), biosorbent concentration (1-3 g/L), and contact time (0-240 min). The highest biosorption under optimized conditions with RSM was 98% in the presence of 194.36 mg/L RBBR and 2.65 g/L biosorbent at pH 2 and 15 min. This is the first report in the literature about the biosorption of RBBR dye by anaerobic C. beijerinckii biomass after the biobutanol production process. This study also shows the efficient usage of agricultural and microbial wastes in different areas based on zero-waste applications.

Application of fed-batch strategy to fully eliminate the negative effect of lignocellulose-derived inhibitors in ABE fermentation

BACKGROUND

Inhibitors that are released from lignocellulose biomass during its treatment represent one of the major bottlenecks hindering its massive utilization in the biotechnological production of chemicals. This study demonstrates that negative effect of inhibitors can be mitigated by proper feeding strategy. Both, crude undetoxified lignocellulose hydrolysate and complex medium supplemented with corresponding inhibitors were tested in acetone-butanol-ethanol (ABE) fermentation using Clostridium beijerinckii NRRL B-598 as the producer strain.

RESULTS

First, it was found that the sensitivity of C. beijerinckii to inhibitors varied with different growth stages, being the most significant during the early acidogenic phase and less pronounced during late acidogenesis and early solventogenesis. Thus, a fed-batch regime with three feeding schemes was tested for toxic hydrolysate (no growth in batch mode was observed). The best results were obtained when the feeding of an otherwise toxic hydrolysate was initiated close to the metabolic switch, resulting in stable and high ABE production. Complete utilization of glucose, and up to 88% of xylose, were obtained. The most abundant inhibitors present in the alkaline wheat straw hydrolysate were ferulic and coumaric acids; both phenolic acids were efficiently detoxified by the intrinsic metabolic activity of clostridia during the early stages of cultivation as well as during the feeding period, thus preventing their accumulation. Finally, the best feeding strategy was verified using a TYA culture medium supplemented with both inhibitors, resulting in 500% increase in butanol titer over control batch cultivation in which inhibitors were added prior to inoculation.

CONCLUSION

Properly timed sequential feeding effectively prevented acid-crash and enabled utilization of otherwise toxic substrate. This study unequivocally demonstrates that an appropriate biotechnological process control strategy can fully eliminate the negative effects of lignocellulose-derived inhibitors.

Engineering of Clostridium tyrobutyricum for butyric acid and butyl butyrate production from cassava starch

Clostridium tyrobutyricum has been successfully engineered to produce butyrate, butanol, butyl butyrate, and γ-aminobutyric acid. It would be interesting to produce bio-chemicals and bio-fuels directly using starch from non-food crop, e.g., cassava, by engineered C. tyrobutyricum. In this study, heterologous α-amylases were screened and expressed in C. tyrobutyricum, resulting in successfully starch hydrolyzation. Furthermore, α-glucosidase (AgluI) was co-expressed with α-amylases, resulting in enhancement in the capacity of starch hydrolyzation and butyrate production. When increasing the cassava starch concentration to 100 g/L, the engineered strain CTAA05 produced 27.0 g/L butyrate. In addition, when introducing butyl butyrate synthetic pathway, strain MU3-AAV produced 26.8 g/L butyl butyrate with 100 g/L cassava starch as substrate. This study showed a generalizable framework to engineered anaerobes for anaerobic production of bio-chemicals and bio-fuels from starchy biomass.

Clostridium as microbial cell factory to enable the sustainable utilization of three generations of feedstocks

The sustainable production of chemicals and biofuels from non-fossil carbon sources is considered key to reducing greenhouse gas (GHG) emissions. Clostridium sp. can convert various substrates, including the 1st-generation (biomass crops), the 2nd-generation (lignocellulosic biomass), and the 3rd-generation (C1 gases) feedstocks, into high-value products, which makes Clostridia attractive for biorefinery applications. However, the complexity of lignocellulosic catabolism and C1 gas utilization make it difficult to construct efficient production routes. Accordingly, this review highlights the advances in the development of three generations of feedstocks with Clostridia as cell factories. At the same time, more attention was given to using agro-industrial wastes (lignocelluloses and C1 gases) as the feedstocks, for which metabolic and process engineering efforts were comprehensively analyzed. In addition, the challenges of using agro-industrial wastes are also discussed. Lastly, several new synthetic biology tools and regulatory strategies are emphasized as promising technologies to be developed to address the aforementioned challenges in Clostridia and realize the efficient utilization of agro-industrial wastes.

Transcriptomic studies of solventogenic clostridia, Clostridium acetobutylicum and Clostridium beijerinckii

Solventogenic clostridia are not a strictly defined group within the genus Clostridium but its representatives share some common features, i.e. they are anaerobic, non-pathogenic, non-toxinogenic and endospore forming bacteria. Their main metabolite is typically 1-butanol but depending on species and culture conditions, they can form other metabolites such as acetone, isopropanol, ethanol, butyric, lactic and acetic acids, and hydrogen. Although these organisms were previously used for the industrial production of solvents, they later fell into disuse, being replaced by more efficient chemical production. A return to a more biological production of solvents therefore requires a thorough understanding of clostridial metabolism. Transcriptome analysis, which reflects the involvement of individual genes in all cellular processes within a population, at any given (sampling) moment, is a valuable tool for gaining a deeper insight into clostridial life. In this review, we describe techniques to study transcription, summarize the evolution of these techniques and compare methods for data processing and visualization of solventogenic clostridia, particularly the species Clostridium acetobutylicum and Clostridium beijerinckii. Individual approaches for evaluating transcriptomic data are compared and their contributions to advancements in the field are assessed. Moreover, utilization of transcriptomic data for reconstruction of computational clostridial metabolic models is considered and particular models are described. Transcriptional changes in glucose transport, central carbon metabolism, the sporulation cycle, butanol and butyrate stress responses, the influence of lignocellulose-derived inhibitors on growth and solvent production, and other respective topics, are addressed and common trends are highlighted.

Butanol production from Saccharina japonica hydrolysate by engineered Clostridium tyrobutyricum: The effects of pretreatment method and heat shock protein overexpression

Macroalgal biomass is currently considered as a potential candidate for biofuel production. In this study, the effects of pretreatment method and heat shock protein overexpression were investigated for efficient butanol production from Saccharina japonica using engineered Clostridium tyrobutyricum. First, various pretreatment methods including acid hydrolysis, acid hydrolysis and enzymatic saccharification, and ultrasonic-assisted acid hydrolysis were employed to obtain the fermentable sugars, and the resulted hydrolysates were evaluated for butanol fermentation. The results showed that ultrasonic-assisted acid hydrolysate obtained the highest butanol yield (0.26 g/g) and productivity (0.19 g/L⋅h). Then, the effects of homologous or heterologous heat shock protein overexpression on butanol production and tolerance were examined. Among all the engineered strains, Ct-pMA12G exhibited improved butanol tolerance and enhanced butanol production (12.15 g/L butanol with a yield of 0.34 g/g and productivity of 0.15 g/L⋅h) from 1.8-fold concentrated S. japonica hydrolysate, which was the highest level ever reported for macroalgal biomass.

Emerging technologies for genetic modification of solventogenic clostridia: From tool to strategy development

Solventogenic clostridia has been considered as one of the most potential microbial cell factories for biofuel production in the biorefinery industry. However, the inherent shortcomings of clostridia strains such as low productivity, by-products formation and toxic tolerance still strongly restrict the large-scale application. Therefore, concerns regarding the genetic modification of solventogenic clostridia have spurred interests into the development of modern gene-editing tools. In this review, we summarize the latest advances of genetic tools involved in modifying solventogenic clostridia. Following a systematic comparison on their respective characteristics, we then review the corresponding strategies for overcoming the obstacles to the enhanced production. Discussing the progress of other microbial cell factories for solventogenesis, we finally describe the key challenges and trends with valuable recommendations for future large-scale biosolvent industrial application.

Exogenous l-proline improved Rhodosporidium toruloides lipid production on crude glycerol

BACKGROUND

Crude glycerol as a promising feedstock for microbial lipid production contains several impurities that make it toxic stress inducer at high amount. Under stress conditions, microorganisms can accumulate l-proline as a safeguard. Herein, l-proline was assessed as an anti-stress agent in crude glycerol media.

RESULTS

Crude glycerol was converted to microbial lipids by the oleaginous yeast Rhodosporidium toruloides CGMCC 2.1389 in a two-staged culture mode. The media was supplied with exogenous l-proline to improve lipid production efficiency in high crude glycerol stress. An optimal amount of 0.5 g/L l-proline increased lipid titer and lipid yield by 34% and 28%, respectively. The lipid titer of 12.2 g/L and lipid content of 64.5% with a highest lipid yield of 0.26 g/g were achieved with l-proline addition, which were far higher than those of the control, i.e., lipid titer of 9.1 g/L, lipid content of 58% and lipid yield of 0.21 g/g. Similarly, l-proline also improved cell growth and glycerol consumption. Moreover, fatty acid compositional profiles of the lipid products was found suitable as a potential feedstock for biodiesel production.

CONCLUSION

Our study suggested that exogenous l-proline improved cell growth and lipid production on crude glycerol by R. toruloides. The fact that higher lipid yield as well as glycerol consumption indicated that l-proline might act as a potential anti-stress agent for the oleaginous yeast strain.

Engineering Thermoanaerobacterium aotearoense SCUT27 with argR knockout for enhanced ethanol production from lignocellulosic hydrolysates

Although Thermoanaerobacterium aotearoense SCUT27 (SCUT27) could co-utilize glucose and xylose, the presence of glucose still repressed xylose catabolism. Arginine repressors (ArgRs) were involved in several key metabolic pathways and might be the global regulator. In SCUT27, three genes (V518_0585; V518_1870; V518_1864) were annotated as argR and only the deficiency of argR₁₈₆₄ could greatly improve the co-utilization of glucose and xylose, due to the enhanced activity of xylose isomerase, xylulokinase and the higher energy level. The metabolic flux of SCUT27/ΔargR₁₈₆₄ indicated that new carbon distribution had been re-established and the ethanol yield had increased by 82.95%, strains growth and acetate yield improved by ~35.91% without detectable lactate for the poor activity of lactate dehydrogenase. The improved concentration of ATP and NAD(H) in SCUT27/ΔargR₁₈₆₄ provided more energy to respond the stress, which enabled the mutant the better cell viability to utilize lignocellulosic hydrolysates for enhanced ethanol formation.

Reactive oxygen species and their applications toward enhanced lipid accumulation in oleaginous microorganisms

Oleaginous microorganisms are among the most promising alternative sources of lipids for oleochemicals and biofuels. However, in the course of lipid production, reactive oxygen species (ROS) are generated inevitably as byproducts of aerobic metabolisms. Although excessive accumulation of ROS leads to lipid peroxidation, DNA damage, and protein denaturation, ROS accumulation has been suggested to enhance lipid synthesis in these microorganisms. There are many unresolved questions concerning this dichotomous view of ROS influence on lipid accumulation. These include what level of ROS triggers lipid overproduction, what mechanisms and targets are vital and whether ROS act as toxic byproducts or cellular messengers in these microorganisms? Here we review the current state of knowledge on ROS generation, antioxidative defense system, the dual effects of ROS on microbial lipid production, and ROS-induced lipid peroxidation and accumulation mechanisms. Toward the end, the review summarizes strategies that enhance lipid production based on ROS manipulation.

Butyric acid production from spent coffee grounds by engineered Clostridium tyrobutyricum overexpressing galactose catabolism genes

Clostridium tyrobutyricum cannot utilize galactose, which is abundant in lignocellulose and red algae, as a carbon source for butyric acid production. Hence, when using galactose-rich coffee ground hydrolysate as the substrate, the fermentation performance of C. tyrobutyricum is poor. In this work, a recombinant strain, C. tyrobutyricum ATCC 25755/ketp, overexpressing galactose catabolism genes (galK, galE, galT, and galP) from Clostridium acetobutylicum ATCC 824 was constructed for the co-utilization of glucose and galactose. Batch fermentation in the bioreactor showed that ATCC 25755/ketp could efficiently utilize galactose without glucose-induced carbon catabolite repression and consume nearly 100% of the galactose present in the spent coffee ground hydrolysate. Correspondingly, the butyric acid concentration and productivity of ATCC 25755/ketp reached 34.3 g/L and 0.36 g/L·h, respectively, an increase of 78.6% and 56.5% compared with the wild-type strain, indicating its potential for butyric acid production from hydrolysates of inexpensive and galactose-rich biomass.

Smart fermentation engineering for butanol production: designed biomass and consolidated bioprocessing systems

There is a renewed interest in acetone-butanol-ethanol (ABE) fermentation from renewable substrates for the sustainable and environment-friendly production of biofuel and platform chemicals. However, the ABE fermentation is associated with several challenges due to the presence of heterogeneous components in the renewable substrates and the intrinsic characteristics of ABE fermentation process. Hence, there is a need to select optimal substrates and modify their characteristics suitable for the ABE fermentation process or microbial strain. This "designed biomass" can be used to establish the consolidated bioprocessing systems. As there are very few reports on designed biomass, the main objectives of this review are to summarize the main challenges associated with ABE fermentation from renewable substrates and to introduce feasible strategies for designing the substrates through pretreatment and hydrolysis technologies as well as through the establishment of consolidated bioprocessing systems. This review offers new insights on improving the efficiency of ABE fermentation from designed renewable substrates.

Strategic intensification in butanol production by exogenous amino acid supplementation: Fermentation kinetics and thermodynamic studies

Amino acids are vital precursors in many biochemical production pathways in addition to efficient nitrogen source which could enhance microbial growth yields. Therefore, in present study, the effect of amino acids from aliphatic and aromatic family was comprehensively evaluated in batch and integrated fed batch fermentation system. Clostridium acetobutylicum NRRL B-527 was able to utilize 54.15 ± 1.0 g/L glucose to produce 12.43 ± 0.10 g/L butanol under batch cultivation. Interestingly, a significant step up in butanol titer (20.82 ± 0.33 g/L) was achieved by using fed-batch fermentation process integrated with liquid-liquid extraction module. Besides, mathematical modeling studies demonstrated the best fitting of experimental data with first order reaction kinetics. Overall, an enhancement in solvent titer by induction of essential cellular components coupled with advance bioprocess strategy was successfully utilized in this study for its further applications.