Engineering Clostridium acetobutylicum for alcohol production

Pathway dissection, regulation, engineering and application: lessons learned from biobutanol production by solventogenic clostridia

The global energy crisis and limited supply of petroleum fuels have rekindled the interest in utilizing a sustainable biomass to produce biofuel. Butanol, an advanced biofuel, is a superior renewable resource as it has a high energy content and is less hygroscopic than other candidates. At present, the biobutanol route, employing acetone-butanol-ethanol (ABE) fermentation in Clostridium species, is not economically competitive due to the high cost of feedstocks, low butanol titer, and product inhibition. Based on an analysis of the physiological characteristics of solventogenic clostridia, current advances that enhance ABE fermentation from strain improvement to product separation were systematically reviewed, focusing on: (1) elucidating the metabolic pathway and regulation mechanism of butanol synthesis; (2) enhancing cellular performance and robustness through metabolic engineering, and (3) optimizing the process of ABE fermentation. Finally, perspectives on engineering and exploiting clostridia as cell factories to efficiently produce various chemicals and materials are also discussed.

Control of solvent production by sigma-54 factor and the transcriptional activator AdhR in Clostridium beijerinckii

Clostridia are obligate anaerobic bacteria that can produce solvents such as acetone, butanol and ethanol. Alcohol dehydrogenases (ADHs) play a key role in solvent production; however, their regulatory mechanisms remain largely unknown. In this study, we characterized the regulatory mechanisms of two ADH-encoding genes in C. beijerinckii. SigL (sigma factor σ⁵⁴ ) was found to be required for transcription of adhA1 and adhA2 genes. Moreover, a novel transcriptional activator AdhR was identified, which binds to the σ⁵⁴ promoter and activates σ⁵⁴ -dependent transcription of adhA1 and adhA2. Clostridia beijerinckii mutants deficient in SigL or AdhR showed severely impaired butanol and ethanol production as well as altered acetone and butyrate synthesis. Overexpression of SigL resulted in significantly improved solvent production by C. beijerinckii when butyrate was added to cultures. Our results reveal SigL as a novel engineering target for improving solvent production by C. beijerinckii and other solvent-producing clostridia. Moreover, this study gains an insight into regulation of alcohol metabolism in diverse clostridia.

Enhancement of acid re-assimilation and biosolvent production in Clostridium saccharoperbutylacetonicum through metabolic engineering for efficient biofuel production from lignocellulosic biomass

In the clostridial acetone-butanol-ethanol (ABE) fermentation, the intermediate acetate and butyrate are re-assimilated for solvent production. Here, key genes in ABE pathways in Clostridium saccharoperbutylacetonicum N1-4 were overexpressed to enhance acid re-assimilation and solvent production. With the overexpression of sol operon, acid re-assimilation was enhanced, and ABE production was increased by 20%, with ethanol production increased by six times but almost no increase in butanol production. To further drive carbon flux for C4 metabolites and ultimate butanol production, key genes including hbd, thl, crt and bcd in butanol production pathway were further overexpressed. Compared to the control, butanol, acetone and total ABE production in the new strain was increased by 8%, 18%, and 12.4%, respectively. Finally, simultaneous saccharification and fermentation was carried out using acetate-pretreated switchgrass. 15.4 g/L total ABE (with a yield of 0.31 g/g) was produced in both engineered strains, which was significantly higher than the control.

Enhancement of solvent production by overexpressing key genes of the acetone-butanol-ethanol fermentation pathway in Clostridium saccharoperbutylacetonicum N1-4

Clostridium saccharoperbutylacetonicum N1-4 is well known as a hyper-butanol producing strain. However, little information is available concerning its butanol production mechanism and the development of more robust strains. In this study, key biosynthetic genes (either endogenous or exogenous) including the sol operon (bld-ctfA-ctfB-adc), adhE1, adhE1^D485G, thl, thlA1^V5A, thlA^V5A and the expression cassette EC (thl-hbd-crt-bcd) were overexpressed in C. saccharoperbutylacetonicum N1-4 to evaluate their potential in enhancement of butanol production. The overexpression of sol operon increased ethanol production by 400%. The overexpression of adhE1 and adhE^D485G resulted in a 5.6- and 4.9-fold higher ethanol production, respectively, producing final acetone-butanol-ethanol (ABE) titers (30.6 and 30.1gL^-1) of among the highest as ever reported for solventogenic clostridia. The most significant increase of butanol production (by 13.7%) and selectivity (73.7%) was achieved by the overexpression of EC. These results provides a solid foundation and essential references for the further development of more robust strains.

Engineering redox homeostasis to develop efficient alcohol-producing microbial cell factories

The biosynthetic pathways of most alcohols are linked to intracellular redox homeostasis, which is crucial for life. This crucial balance is primarily controlled by the generation of reducing equivalents, as well as the (reduction)-oxidation metabolic cycle and the thiol redox homeostasis system. As a main oxidation pathway of reducing equivalents, the biosynthesis of most alcohols includes redox reactions, which are dependent on cofactors such as NADH or NADPH. Thus, when engineering alcohol-producing strains, the availability of cofactors and redox homeostasis must be considered. In this review, recent advances on the engineering of cellular redox homeostasis systems to accelerate alcohol biosynthesis are summarized. Recent approaches include improving cofactor availability, manipulating the affinity of redox enzymes to specific cofactors, as well as globally controlling redox reactions, indicating the power of these approaches, and opening a path towards improving the production of a number of different industrially-relevant alcohols in the near future.

Highly Selective Upgrading of Biomass-Derived Alcohol Mixtures for Jet/Diesel-Fuel Components

In light of the increasing concern about the energy and environmental problems caused by the combustion of petroleum-based fuels (e.g., jet and diesel fuels), the development of new procedures for their sustainable production from renewable biomass-derived platform compounds has attracted tremendous attention recently. Long-chain ketones/alcohols are promising fuel components owing to the fuel properties that closely resemble those of traditional fuels. The focus of this report is the production of long-chain ketones/alcohols by direct upgrading of biomass-derived short-chain alcohol mixtures (e.g., isopropanol-butanol-ethanol mixtures) in pure water. An efficient Pd catalyst system was developed for these highly selective transformations. Long-chain ketones/alcohols (C₈ -C₁₉ ), which can be used as precursors for renewable jet/diesel fuel, were obtained in good-to-high selectivity (>90 %) by using the developed Pd catalyst.

Deciphering Clostridium tyrobutyricum Metabolism Based on the Whole-Genome Sequence and Proteome Analyses

Clostridium tyrobutyricum is a Gram-positive anaerobic bacterium that efficiently produces butyric acid and is considered a promising host for anaerobic production of bulk chemicals. Due to limited knowledge on the genetic and metabolic characteristics of this strain, however, little progress has been made in metabolic engineering of this strain. Here we report the complete genome sequence of C. tyrobutyricum KCTC 5387 (ATCC 25755), which consists of a 3.07-Mbp chromosome and a 63-kbp plasmid. The results of genomic analyses suggested that C. tyrobutyricum produces butyrate from butyryl-coenzyme A (butyryl-CoA) through acetate reassimilation by CoA transferase, differently from Clostridium acetobutylicum, which uses the phosphotransbutyrylase-butyrate kinase pathway; this was validated by reverse transcription-PCR (RT-PCR) of related genes, protein expression levels, in vitro CoA transferase assay, and fed-batch fermentation. In addition, the changes in protein expression levels during the course of batch fermentations on glucose were examined by shotgun proteomics. Unlike C. acetobutylicum, the expression levels of proteins involved in glycolytic and fermentative pathways in C. tyrobutyricum did not decrease even at the stationary phase. Proteins related to energy conservation mechanisms, including Rnf complex, NfnAB, and pyruvate-phosphate dikinase that are absent in C. acetobutylicum, were identified. Such features explain why this organism can produce butyric acid to a much higher titer and better tolerate toxic metabolites. This study presenting the complete genome sequence, global protein expression profiles, and genome-based metabolic characteristics during the batch fermentation of C. tyrobutyricum will be valuable in designing strategies for metabolic engineering of this strain.

IMPORTANCE

Bio-based production of chemicals from renewable biomass has become increasingly important due to our concerns on climate change and other environmental problems. C. tyrobutyricum has been used for efficient butyric acid production. In order to further increase the performance and expand the capabilities of this strain toward production of other chemicals, metabolic engineering needs to be performed. For this, better understanding on the metabolic and physiological characteristics of this bacterium at the genome level is needed. This work reporting the results of complete genomic and proteomic analyses together with new insights on butyric acid biosynthetic pathway and energy conservation will allow development of strategies for metabolic engineering of C. tyrobutyricum for the bio-based production of various chemicals in addition to butyric acid.

Insights from genome of Clostridium butyricum INCQS635 reveal mechanisms to convert complex sugars for biofuel production

Clostridium butyricum is widely used to produce organic solvents such as ethanol, butanol and acetone. We sequenced the entire genome of C. butyricum INCQS635 by using Ion Torrent technology. We found a high contribution of sequences assigned for carbohydrate subsystems (15-20 % of known sequences). Annotation based on protein-conserved domains revealed a higher diversity of glycoside hydrolases than previously found in C. acetobutylicum ATCC824 strain. More than 30 glycoside hydrolases (GH) families were found; families of GH involved in degradation of galactan, cellulose, starch and chitin were identified as most abundant (close to 50 % of all sequences assigned as GH) in C. butyricum INCQS635. KEGG metabolic pathways reconstruction allowed us to verify possible routes in the C. butyricum INCQS635 and C. acetobutylicum ATCC824 genomes. Metabolic pathways for ethanol synthesis are similar for both species, but alcohol dehydrogenase of C. butyricum INCQS635 and C. acetobutylicum ATCC824 was different. The genomic repertoire of C. butyricum is an important resource to underpin future studies towards improved solvents production.

Redox regulation by reversible protein S-thiolation in bacteria

Low molecular weight (LMW) thiols function as thiol-redox buffers to maintain the reduced state of the cytoplasm. The best studied LMW thiol is the tripeptide glutathione (GSH) present in all eukaryotes and Gram-negative bacteria. Firmicutes bacteria, including Bacillus and Staphylococcus species utilize the redox buffer bacillithiol (BSH) while Actinomycetes produce the related redox buffer mycothiol (MSH). In eukaryotes, proteins are post-translationally modified to S-glutathionylated proteins under conditions of oxidative stress. S-glutathionylation has emerged as major redox-regulatory mechanism in eukaryotes and protects active site cysteine residues against overoxidation to sulfonic acids. First studies identified S-glutathionylated proteins also in Gram-negative bacteria. Advances in mass spectrometry have further facilitated the identification of protein S-bacillithiolations and S-mycothiolation as BSH- and MSH-mixed protein disulfides formed under oxidative stress in Firmicutes and Actinomycetes, respectively. In Bacillus subtilis, protein S-bacillithiolation controls the activities of the redox-sensing OhrR repressor and the methionine synthase MetE in vivo. In Corynebacterium glutamicum, protein S-mycothiolation was more widespread and affected the functions of the maltodextrin phosphorylase MalP and thiol peroxidase (Tpx). In addition, novel bacilliredoxins (Brx) and mycoredoxins (Mrx1) were shown to function similar to glutaredoxins in the reduction of BSH- and MSH-mixed protein disulfides. Here we review the current knowledge about the functions of the bacterial thiol-redox buffers glutathione, bacillithiol, and mycothiol and the role of protein S-thiolation in redox regulation and thiol protection in model and pathogenic bacteria.

Biobutanol from cheese whey

At present, due to environmental and economic concerns, it is urgent to evolve efficient, clean and secure systems for the production of advanced biofuels from sustainable cheap sources. Biobutanol has proved better characteristics than the more widely used bioethanol, however the main disadvantage of biobutanol is that it is produced in low yield and titer by ABE (acetone-butanol-ethanol) fermentation, this process being not competitive from the economic point of view. In this review we summarize the natural metabolic pathways for biobutanol production by Clostridia and yeasts, together with the metabolic engineering efforts performed up to date with the aim of either enhancing the yield of the natural producer Clostridia or transferring the butanol production ability to other hosts with better attributes for industrial use and facilities for genetic manipulation. Molasses and starch-based feedstocks are main sources for biobutanol production at industrial scale hitherto. We also review herewith (and for the first time up to our knowledge) the research performed for the use of whey, the subproduct of cheese making, as another sustainable source for biobutanol production. This represents a promising alternative that still needs further research. The use of an abundant waste material like cheese whey, that would otherwise be considered an environmental pollutant, for biobutanol production, makes economy of the process more profitable.

Comparative transcriptome analysis between csrA-disruption Clostridium acetobutylicum and its parent strain

This study represented the first attempt to investigate the global regulation of CsrA through transcriptome analysis in Gram-positive bacteria.

Metabolic engineering of microorganisms for the production of higher alcohols

Due to the increasing concerns about limited fossil resources and environmental problems, there has been much interest in developing biofuels from renewable biomass. Ethanol is currently used as a major biofuel, as it can be easily produced by existing fermentation technology, but it is not the best biofuel due to its low energy density, high vapor pressure, hygroscopy, and incompatibility with current infrastructure. Higher alcohols, including 1-propanol, 1-butanol, isobutanol, 2-methyl-1-butanol, and 3-methyl-1-butanol, which possess fuel properties more similar to those of petroleum-based fuel, have attracted particular interest as alternatives to ethanol. Since microorganisms isolated from nature do not allow production of these alcohols at high enough efficiencies, metabolic engineering has been employed to enhance their production. Here, we review recent advances in metabolic engineering of microorganisms for the production of higher alcohols.

Xylanase and cellulase systems of Clostridium sp.: an insight on molecular approaches for strain improvement

Bioethanol and biobutanol hold great promise as alternative biofuels, especially for transport sector, because they can be produced from lignocellulosic agro-industrial residues. From techno-economic point of view, the bioprocess for biofuels production should involve minimal processing steps. Consolidated bioprocessing (CBP), which combines various processing steps such as pretreatment, hydrolysis and fermentation in a single bioreactor, could be of great relevance for the production of bioethanol and biobutanol or solvents (acetone, butanol, ethanol), employing clostridia. For CBP, Clostridium holds best promise because it possesses multi-enzyme system involving cellulosome and xylanosome, which comprise several enzymes such as cellulases and xylanases. The aim of this article was to review the recent developments on enzyme systems of clostridia, especially xylanase and cellulase with an effort to analyse the information available on molecular approaches for the improvement of strains with ultimate aim to improve the efficiencies of hydrolysis and fermentation.

Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model

BACKGROUND

Clostridia are anaerobic Gram-positive Firmicutes containing broad and flexible systems for substrate utilization, which have been used successfully to produce a range of industrial compounds. In particular, Clostridium acetobutylicum has been used to produce butanol on an industrial scale through acetone-butanol-ethanol (ABE) fermentation. A genome-scale metabolic (GSM) model is a powerful tool for understanding the metabolic capacities of an organism and developing metabolic engineering strategies for strain development. The integration of stress-related specific transcriptomics information with the GSM model provides opportunities for elucidating the focal points of regulation.

RESULTS

We describe here the construction and validation of a GSM model for C. acetobutylicum ATCC 824, iCac802. iCac802 spans 802 genes and includes 1,137 metabolites and 1,462 reactions, along with gene-protein-reaction associations. Both (13)C-MFA and gene deletion data in the ABE fermentation pathway were used to test the predicted flux ranges allowed by the model. We also describe the CoreReg method, introduced in this paper, to integrate transcriptomic data and identify core sets of reactions that, when their flux was selectively restricted, reproduced flux and biomass-formation ranges seen under all regulatory constraints. CoreReg was used in response to butanol and butyrate stress to tighten bounds for 50 reactions within the iCac802 model. These bounds affected the flux of tens of reactions in core metabolism. The model, incorporating the regulatory restrictions from CoreReg under chemical stress, exhibited an approximate 70% reduction in biomass yield for most stress conditions.

CONCLUSIONS

The regulation placed on the model for the two stresses using CoreReg identified differences in the respective responses, including distinct core sets and the restriction of biomass production similar to experimental observations. Given the core sets predicted by the CoreReg method, remedial actions can be taken to counteract the effect of stress on metabolism. For less well-known systems, plausible regulatory loops can be suggested around the affected metabolic reactions, and the hypotheses can be tested experimentally.