Physiology of carbohydrate to solvent conversion by clostridia

Dietary supplementation of rumen native microbes improves lactation performance and feed efficiency in dairy cows

Objectives were to determine the effects of 2 dietary microbial additives supplemented to diets of Holstein cows on productive performance and feed efficiency. One-hundred and 17 Holstein cows were enrolled at 61 d (31 to 87 d) postpartum in a randomized complete block design experiment. Cows were blocked by parity group, as nulliparous or multiparous cows and, within parity, by pre-treatment energy-corrected milk yield. Within block, cows were randomly assigned to one of 3 treatments administered as top-dress for 140 d. Treatments consisted of either 100 g of corn meal containing no microbial additive (CON; 15 primiparous and 25 multiparous), 100 g of corn meal containing 5 g of a mixture of Clostridium beijerinckii and Pichia kudriavzevii (G1; 4 × 107 cfu of C. beijerinckii and 1 × 109 cfu of P. kudriavzevii; 14 primiparous and 24 multiparous), or 100 g of corn meal containing 5 g of a mixture of C. beijerinckii, P. kudriavzevii, Butyrivibrio fibrisolvens, and Ruminococcus bovis (G2; 4 × 107 cfu of C. beijerinckii, 1 × 109 cfu of P. kudriavzevii, 1 × 108 cfu of B. fibrisolvens, and 1 × 108 cfu of R. bovis; 15 primiparous and 24 multiparous). Intake of DM, milk yield, and BW were measured daily, whereas milk composition was analyzed at each milking 2 d a week, and body condition was scored twice weekly. Milk samples were collected on d 60 and 62 in the experiment and analyzed for individual fatty acids. The data were analyzed with mixed-effects models with orthogonal contrast to determine the impact of microbial additive (MA; CON vs. 1/2 G1 + 1/2 G2) and type of microbial additive (TMA; G1 vs. G2). Results are described in sequence as CON, G1, and G2. Intake of DM (22.2 vs. 22.4 vs. 22.4 kg/d), BW (685 vs. 685 vs. 685 kg) and the daily BW change (0.40 vs. 0.39 vs. 0.39 kg/d) did not differ among treatments; however, feeding MA tended to increase BCS (3.28 vs. 3.33 vs. 3.36). Supplementing MA increased yields of milk (39.9 vs. 41.3 vs. 41.5 kg/d), ECM (37.9 vs. 39.3 vs. 39.9 kg/d), fat (1.31 vs. 1.37 vs. 1.40 kg/d), total solids (4.59 vs. 4.75 vs. 4.79 kg/d), and ECM per kg of DMI (1.72 vs. 1.76 vs. 1.80 kg/kg). Furthermore, cows fed MA increased yields of pre-formed fatty acids in milk fat (>16C; 435 vs. 463 vs. 488 g/d), particularly unsaturated fatty acids (367 vs. 387 vs. 410 g/d), such as linoleic (C18:2 cis-9, cis-12; 30.9 vs. 33.5 vs. 35.4 g/d) and α-linolenic acids (C18:3 cis-9, cis-12, cis-15; 2.46 vs. 2.68 vs. 2.82 g/d) on d 60 and 62 in the experiment. Collectively, supplementing G1 and G2 improved productive performance of cows with no differences between the 2 MA.

Lipid membrane remodeling and metabolic response during isobutanol and ethanol exposure in Zymomonas mobilis

BACKGROUND

Recent engineering efforts have targeted the ethanologenic bacterium Zymomonas mobilis for isobutanol production. However, significant hurdles remain due this organism's vulnerability to isobutanol toxicity, adversely affecting its growth and productivity. The limited understanding of the physiological impacts of isobutanol on Z. mobilis constrains our ability to overcome these production barriers.

RESULTS

We utilized a systems-level approach comprising LC-MS/MS-based lipidomics, metabolomics, and shotgun proteomics, to investigate how exposure to ethanol and isobutanol impact the lipid membrane composition and overall physiology of Z. mobilis. Our analysis revealed significant and distinct alterations in membrane phospholipid and fatty acid composition resulting from ethanol and isobutanol exposure. Notably, ethanol exposure increased membrane cyclopropane fatty acid content and expression of cyclopropane fatty acid (CFA) synthase. Surprisingly, isobutanol decreased cyclopropane fatty acid content despite robust upregulation of CFA synthase. Overexpression of the native Z. mobilis' CFA synthase increased cyclopropane fatty acid content in all phospholipid classes and was associated with a significant improvement in growth rates in the presence of added ethanol and isobutanol. Heterologous expression of CFA synthase from Clostridium acetobutylicum resulted in a near complete replacement of unsaturated fatty acids with cyclopropane fatty acids, affecting all lipid classes. However, this did not translate to improved growth rates under isobutanol exposure. Correlating with its greater susceptibility to isobutanol, Z. mobilis exhibited more pronounced alterations in its proteome, metabolome, and overall cell morphology-including cell swelling and formation of intracellular protein aggregates -when exposed to isobutanol compared to ethanol. Isobutanol triggered a broad stress response marked by the upregulation of heat shock proteins, efflux transporters, DNA repair systems, and the downregulation of cell motility proteins. Isobutanol also elicited widespread dysregulation of Z. mobilis' primary metabolism evidenced by increased levels of nucleotide degradation intermediates and the depletion of biosynthetic and glycolytic intermediates.

CONCLUSIONS

This study provides a comprehensive, systems-level evaluation of the impact of ethanol and isobutanol exposure on the lipid membrane composition and overall physiology of Z. mobilis. These findings will guide engineering of Z. mobilis towards the creation of isobutanol-tolerant strains that can serve as robust platforms for the industrial production of isobutanol from lignocellulosic sugars.

Deciphering of the Mannitol Metabolism Pathway in Clostridium tyrobutyricum ATCC 25755 by Comparative Transcriptome Analysis

Clostridium tyrobutyricum has great potential for bio-based chemicals and biofuel production from mannitol; however, the mannitol metabolic pathway and its metabolic regulatory mechanism have not been elucidated. To this end, the RNA-seq analysis on the mid-log growth phase of C. tyrobutyricum grown on mannitol or xylose was performed. Comparative transcriptome analysis and co-transcription experiment indicated that mtlARFD, which encodes the mannitol-specific IIA component, transcription activator, mannitol-specific IIBC components, and mannitol-1-phosphate 5-dehydrogenase, respectively, formed a polycistronic operon and could be responsible for mannitol uptake and metabolism. In addition, comparative genomic analysis of the mtlARFD organization and the MtlR protein structural domain among various Firmicutes strains identified the putative cre (catabolite-responsive element) sites and conserved phosphorylation sites, but whether the expression of mannitol operon was affected by CcpA- and MtlR-mediated metabolic regulation during mixed substrate fermentation needs to be further verified experimentally. Based on the gene knockout and complementation results, the predicted mannitol operon mtlARFD was confirmed to be responsible for mannitol utilization in C. tyrobutyricum. The results of this study could be used to enhance the mannitol metabolic pathway and explore the potential metabolic regulation mechanism of mannitol during mixed substrate fermentation.

Live yeast supplementation altered the bacterial community's composition and function in rumen and hindgut and alleviated the detrimental effects of heat stress on dairy cows

The objective of this study was to investigate the effects of live yeast (LY, Saccharomyces cerevisiae) on the lactation performance, bacterial community, and functions in the rumen and hindgut of dairy cows under heat stress. Thirty-three multiparous (parity 3.9 ± 0.8) Holstein dairy cows (189.1 ± 6.6 d in milk at the beginning of the experiment) were randomly assigned to three groups (11 cows per treatment). Cows in the three groups were fed a diet without yeast (CON), with 10 g yeast/d/head (LY-10), and with 20 g yeast/d/head (LY-20). The yeast product contained 2.0 × 1010 CFU/g. Supplementing LY decreased the rectal temperature and respiratory rate of cows, and increased dry matter intake, milk yield, milk fat yield, milk protein yield, and milk lactose yield (P < 0.001), yet decreased milk urea nitrogen concentration (P = 0.035). Interaction effects of treatment × week were observed for rectal temperature (P < 0.05), respiratory rate (P < 0.05), milk yield (P = 0.015), milk urea nitrogen (P = 0.001), milk protein yield (P = 0.008), and milk lactose yield (P = 0.030). In rumen, LY increased the concentrations of acetate, isobutyrate, isovaterate, valerate, total volatile fatty acids (VFAs), and NH3-N (P < 0.05). Miseq sequencing of the 16S rRNA genes showed that LY increased the relative abundance of Prevotella and Prevotellaceae UCG-003 at the genus level with a series of enriched pathways in the metabolism of carbohydrates and protein. In fecal samples, LY did not affect the profile of VFAs (P > 0.05). Clostridium sensu stricto 1 (P = 0.013) and Actinobacillus (P = 0.011) increased in the relative abundance by LY, whereas Bacteroides (P = 0.016) and Oscillospirales UCG-010 (P = 0.005) decreased with a series of enriched pathways in carbohydrate metabolism, secondary bile acid biosynthesis. In summary, LY supplementation altered the bacterial community's composition and function in rumen and hindgut, and simultaneously alleviated the detrimental effects of heat stress on dairy cows. These findings provide extended insight into the effects of LY in the rumen and hindgut of dairy cows exposed to heat stress.

Probiotics Bacillus cereus and B. subtilis reshape the intestinal microbiota of Pengze crucian carp (Carassius auratus var. Pengze) fed with high plant protein diets

The intestinal dysfunction induced by high plant protein diets is frequently observed in farmed fish, and probiotics of Bacillus genus were documented to benefit the intestinal health through the modulation of intestinal microbiota without clearness in its underlying mechanism yet. Fusobacteria, Proteobacteria, and Firmicutes were observed to be the dominate phyla, but their proportion differentiated in the intestinal bacterial community of Pengze crucian carp (Carassius auratus var. Pengze) fed different diets in this study. Dietary supplementation of B. cereus and B. subtilis could reshape the intestinal bacterial community altered by high plant protein diets through a notable reduction in opportunistic pathogen Aeromonas together with an increase in Romboutsia and/or Clostridium_sensu_stricto from Firmicutes. Due to the alteration in the composition of bacterial community, Pengze crucian carp exhibited characteristic ecological networks dominated by cooperative interactions. Nevertheless, the increase in Aeromonas intensified the competition within bacterial communities and reduced the number of specialists within ecological network, contributing to the microbial dysbiosis induced by high plant protein diets. Two probiotics diets promoted the cooperation within the intestinal bacterial community and increased the number of specialists preferred to module hubs, and then further improved the homeostasis of the intestinal microbiota. Microbial dysbiosis lead to microbial dysfunction, and microbial lipopolysaccharide biosynthesis was observed to be elevated in high plant protein diets due to the increase in Aeromonas, gram-negative microbe. Probiotics B. cereus and B. subtilis restored the microbial function by elevating their amino acid and carbohydrate metabolism together with the promotion in the synthesis of primary and secondary bile acids. These results suggested that dietary supplementation of probiotics B. cereus and B. subtilis could restore the homeostasis and functions of intestinal microbiota in Pengze crucian carp fed high plant protein diets.

An updated review on advancement in fermentative production strategies for biobutanol using Clostridium spp

A significant concern of our fuel-dependent era is the unceasing exhaustion of petroleum fuel supplies. In parallel to this, environmental issues such as the greenhouse effect, change in global climate, and increasing global temperature must be addressed on a priority basis. Biobutanol, which has fuel characteristics comparable to gasoline, has attracted global attention as a viable green fuel alternative among the many biofuel alternatives. Renewable biomass could be used for the sustainable production of biobutanol by the acetone-butanol-ethanol (ABE) pathway. Non-extinguishable resources, such as algal and lignocellulosic biomass, and starch are some of the most commonly used feedstock for fermentative production of biobutanol, and each has its particular set of advantages. Clostridium, a gram-positive endospore-forming bacterium that can produce a range of compounds, along with n-butanol is traditionally known for its biobutanol production capabilities. Clostridium fermentation produces biobased n-butanol through ABE fermentation. However, low butanol titer, a lack of suitable feedstock, and product inhibition are the primary difficulties in biobutanol synthesis. Critical issues that are essential for sustainable production of biobutanol include (i) developing high butanol titer producing strains utilizing genetic and metabolic engineering approaches, (ii) renewable biomass that could be used for biobutanol production at a larger scale, and (iii) addressing the limits of traditional batch fermentation by integrated bioprocessing technologies with effective product recovery procedures that have increased the efficiency of biobutanol synthesis. Our paper reviews the current progress in all three aspects of butanol production and presents recent data on current practices in fermentative biobutanol production technology.

Butanol-isopropanol fermentation with oxygen-tolerant Clostridium beijerinckii XH29

Acetone–butanol–ethanol (ABE) fermentation is a traditional way for solvents production through bioconversion by Clostridium species. It is still a challenge to obtain metabolic engineering strains with high ABE yield. Screening strains with remarkable characteristics from nature and improving ABE yield by mutation are viable approaches. Clostridium beijerinckii XH 0906, a newly isolated strain, produces butanol and isopropanol (BI) as the main end-products (9.1 g/L BI) during fermentation with glucose as the sole carbon source. The screening process for this strain was performed under aerobic conditions rather than anaerobic environment. Thus, it is a robust stain capable of oxygen-tolerant BI fermentation. Furthermore, C. beijerinckii XH 0906 fermented xylose and glucose simultaneously to produce BI. A mutant strain obtained by ultraviolet (UV) mutagenesis, C. beijerinckii XH 29, had improved BI production capacity and could produce 17.0 g/L BI and 18.4 g/L BI using glucose or corn stover hydrolysate, respectively as the carbon source. Interestingly, C. beijerinckii XH 29 also produced up to 19.3 g/L isopropanol through fermentation of a glucose–acetone mix. These results indicate that C. beijerinckii XH 29 is an excellent BI producer with great potential for industrial applications.

A newly isolated strain produces butanol and isopropanol (BI) rather than acetone butanol and ethanol (ABE).

The strain is oxygen-tolerant and robust in the fermentation.

A mutant obtained by ultraviolet mutagenesis produces higher levels of BI than the wild type strain using corn stover as a carbon source.

Ribozyme-Mediated Downregulation Uncovers DNA Integrity Scanning Protein A (DisA) as a Solventogenesis Determinant in Clostridium beijerinckii

Carbon catabolite repression (CCR) limits microbial utilization of lignocellulose-derived pentoses. To relieve CCR in Clostridium beijerinckii NCIMB 8052, we sought to downregulate catabolite control protein A (CcpA) using the M1GS ribozyme technology. A CcpA-specific ribozyme was constructed by tethering the catalytic subunit of Escherichia coli RNase P (M1 RNA) to a guide sequence (GS) targeting CcpA mRNA (M1GS^CcpA). As negative controls, the ribozyme M1GS^CcpA–Sc (constructed with a scrambled GS^CcpA) or the empty plasmid pMTL500E were used. With a ∼3-fold knockdown of CcpA mRNA in C. beijerinckii expressing M1GS^CcpA (C. beijerinckii_M1GS^CcpA) relative to both controls, a modest enhancement in mixed-sugar utilization and solvent production was achieved. Unexpectedly, C. beijerinckii_M1GS^CcpA–Sc produced 50% more solvent than C. beijerinckii_pMTL500E grown on glucose + arabinose. Sequence complementarity (albeit suboptimal) suggested that M1GS^CcpA–Sc could target the mRNA encoding DNA integrity scanning protein A (DisA), an expectation that was confirmed by a 53-fold knockdown in DisA mRNA levels. Therefore, M1GS^CcpA–Sc was renamed M1GS^DisA. Compared to C. beijerinckii_M1GS^CcpA and _pMTL500E, C. beijerinckii_M1GS^DisA exhibited a 7-fold decrease in the intracellular c-di-AMP level after 24 h of growth and a near-complete loss of viability upon exposure to DNA-damaging antibiotics. Alterations in c-di-AMP-mediated signaling and cell cycling likely culminate in a sporulation delay and the solvent production gains observed in C. beijerinckii_M1GS^DisA. Successful knockdown of the CcpA and DisA mRNAs demonstrate the feasibility of using M1GS technology as a metabolic engineering tool for increasing butanol production in C. beijerinckii.

Shifts in short-chain fatty acid profile, Fe(III) reduction and bacterial community with biochar amendment in rice paddy soil

Biochar, a valuable product from the pyrolysis of agricultural and forestry residues, has been widely applied as soil amendment. However, the effect of different types of biochar on soil microorganisms and associated biochemical processes in paddy soil remains ambiguous. In this study, we investigated the impact of biochars derived from different feedstocks (rice straw, orange peel and bamboo powder) on the dynamics of short-chain fatty acids (SCFAs), iron concentration and bacterial community in paddy soil within 90 days of anaerobic incubation. Results showed that biochar amendment overall inhibited the accumulation of SCFAs while accelerating the Fe(III) reduction process in paddy soil. In addition, 16S rRNA gene sequencing results demonstrated that the α-diversity of the bacterial community significantly decreased in response to biochar amendments at day 1 but was relatively unaffected at the end of incubation, and incubation time was the major driver for the succession of the bacterial community. Furthermore, significant correlations between parameters (e.g. SCFAs and iron concentration) and bacterial taxa (e.g. Clostridia, Syntrophus, Syntrophobacter and Desulfatiglans) were observed. Overall, our findings demonstrated amendment with different types of biochar altered SCFA profile, Fe(III) reduction and bacterial biodiversity in rice paddy soil.

Compositional variability of food wastes and its effects on acetone-butanol-ethanol fermentation

Converting food waste into butanol via acetone, butanol, and ethanol (ABE) fermentation provides the potential to recover energy and value-added chemicals from food waste. However, the high variability of food waste compositions has hindered the consistency and predictability of butanol production, impeding the development of a robust industrial fermentation process. This study characterized the compositional variation of collected food wastes and determined correlations between food waste compositional attributes and butanol yields for a better prediction of food waste fermentation with Clostridium. The total sugar, starch, fiber, crude protein, fat and ash contents (on dry basis) in the food waste samples were in a range of 0.5-53.5%, 0-25.2%, 0.6-26.9%, 5.5-21.5%, 0.1-37.9%, and 1.4-13.7%, respectively. The high variability of food waste composition resulted in a wide range (3.5-11.5 g/L) of butanol concentrations with an average of 8.2 g/L. Pearson's correlation analysis revealed that the butanol concentrations were strongly and positively correlated with equivalent glucose and starch contents in food waste, strongly and negatively correlated with fiber content, and weakly correlated with total sugar, protein, fat, and ash contents. The regression models constructed based on equivalent glucose and fiber contents reasonably predicted the butanol concentration, with the R² of 0.80. Our study investigated the variability of food waste composition and, for the first time, unveiled relationships between food waste compositional attributes and fermentation yields, contributing to a greater understanding of food waste fermentation, which, in turn, assists in developing new strategies for increased consistency and predictability of food waste fermentation.

Chinese Medicinal Herbs Targeting the Gut-Liver Axis and Adipose Tissue-Liver Axis for Non-Alcoholic Fatty Liver Disease Treatments: The Ancient Wisdom and Modern Science

Non-alcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases worldwide. The pathogenesis of NAFLD is complex. Frontline western medicines only ameliorate the symptoms of NAFLD. On the contrary, the uniqueness of Chinese medicine in its interpretation of NAFLD and the holistic therapeutic approach lead to a promising therapeutic efficacy. Recent studies reveal that the gut-liver axis and adipose tissue-liver axis play important roles in the development of NAFLD. Interestingly, with advanced technology, many herbal formulae are found to target the gut-liver axis and adipose tissue-liver axis and resolve the inflammation in NAFLD. This is the first review summarizes the current findings on the Chinese herbal formulae that target the two axes in NAFLD treatment. This review not only demonstrates how the ancient wisdom of Chinese medicine is being interpreted by modern pharmacological studies, but also provides valuable information for the further development of the herbal-based treatment for NAFLD.

Transcriptional analysis of amino acid, metal ion, vitamin and carbohydrate uptake in butanol-producing Clostridium beijerinckii NRRL B-598

In-depth knowledge of cell metabolism and nutrient uptake mechanisms can lead to the development of a tool for improving acetone-butanol-ethanol (ABE) fermentation performance and help to overcome bottlenecks in the process, such as the high cost of substrates and low production rates. Over 300 genes potentially encoding transport of amino acids, metal ions, vitamins and carbohydrates were identified in the genome of the butanol-producing strain Clostridium beijerinckii NRRL B-598, based on similarity searches in protein function databases. Transcriptomic data of the genes were obtained during ABE fermentation by RNA-Seq experiments and covered acidogenesis, solventogenesis and sporulation. The physiological roles of the selected 81 actively expressed transport genes were established on the basis of their expression profiles at particular stages of ABE fermentation. This article describes how genes encoding the uptake of glucose, iron, riboflavin, glutamine, methionine and other nutrients take part in growth, production and stress responses of C. beijerinckii NRRL B-598. These data increase our knowledge of transport mechanisms in solventogenic Clostridium and may be used in the selection of individual genes for further research.

EMUlator: An Elementary Metabolite Unit (EMU) Based Isotope Simulator Enabled by Adjacency Matrix

Stable isotope based metabolic flux analysis is currently the unique methodology that allows the experimental study of the integrated responses of metabolic networks. This method primarily relies on isotope labeling and modeling, which could be a challenge in both experimental and computational biology. In particular, the algorithm implementation for isotope simulation is a critical step, limiting extensive usage of this powerful approach. Here, we introduce EMUlator a Python-based isotope simulator which is developed on Elementary Metabolite Unit (EMU) algorithm, an efficient and powerful algorithm for isotope modeling. We propose a novel adjacency matrix method to implement EMU modeling and exemplify it stepwise. This method is intuitively straightforward and can be conveniently mastered for various customized purposes. We apply this arithmetic pipeline to understand the phosphoketolase flux in the metabolic network of an industrial microbe Clostridium acetobutylicum. The resulting design enables a high-throughput and non-invasive approach for estimating phosphoketolase flux in vivo. Our computational insights allow the systematic design and prediction of isotope-based metabolic models and yield a comprehensive understanding of their limitations and potentials.

Butanol Synthesis Routes for Biofuel Production: Trends and Perspectives

Butanol has similar characteristics to gasoline, and could provide an alternative oxygenate to ethanol in blended fuels. Butanol can be produced either via the biotechnological route, using microorganisms such as clostridia, or by the chemical route, using petroleum. Recently, interest has grown in the possibility of catalytic coupling of bioethanol into butanol over various heterogenic systems. This reaction has great potential, and could be a step towards overcoming the disadvantages of bioethanol as a sustainable transportation fuel. This paper summarizes the latest research on butanol synthesis for the production of biofuels in different biotechnological and chemical ways; it also compares potentialities and limitations of these strategies.

A new process to improve short-chain fatty acids and bio-methane generation from waste activated sludge

As an important intermediate product, short-chain fatty acids (SCFAs) can be generated after hydrolysis and acidification from waste activated sludge, and then can be transformed to methane during anaerobic digestion process. In order to obtain more SCFA and methane, most studies in literatures were centered on enhancing the hydrolysis of sludge anaerobic digestion which was proved as un-efficient. Though the alkaline pretreatment in our previous study increased both the hydrolysis and acidification processes, it had a vast chemical cost which was considered uneconomical. In this paper, a low energy consumption pretreatment method, i.e. enhanced the whole three stages of the anaerobic fermentation processes at the same time, was reported, by which hydrolysis and acidification were both enhanced, and the SCFA and methane generation can be significantly improved with a small quantity of chemical input. Firstly, the effect of different pretreated temperatures and pretreatment time on sludge hydrolyzation was compared. It was found that sludge pretreated at 100°C for 60min can achieve the maximal hydrolyzation. Further, effects of different initial pHs on acidification of the thermal pretreated sludge were investigated and the highest SCFA was observed at initial pH9.0 with fermentation time of 6d, the production of which was 348.63mg COD/gVSS (6.8 times higher than the blank test) and the acetic acid was dominant acid. Then, the mechanisms for this new pretreatment significantly improving SCFA production were discussed. Finally, the effect of this low energy consumption pretreatment on methane generation was investigated.

Sugar uptake by the solventogenic clostridia

The acetone–butanol–ethanol fermentation of solventogenic clostridia was operated as a successful, worldwide industrial process during the first half of the twentieth century, but went into decline for economic reasons. The recent resurgence in interest in the fermentation has been due principally to the recognised potential of butanol as a biofuel, and development of reliable molecular tools has encouraged realistic prospects of bacterial strains being engineered to optimise fermentation performance. In order to minimise costs, emphasis is being placed on waste feedstock streams containing a range of fermentable carbohydrates. It is therefore important to develop a detailed understanding of the mechanisms of carbohydrate uptake so that effective engineering strategies can be identified. This review surveys present knowledge of sugar uptake and its control in solventogenic clostridia. The major mechanism of sugar uptake is the PEP-dependent phosphotransferase system (PTS), which both transports and phosphorylates its sugar substrates and plays a central role in metabolic regulation. Clostridial genome sequences have indicated the presence of numerous phosphotransferase systems for uptake of hexose sugars, hexose derivatives and disaccharides. On the other hand, uptake of sugars such as pentoses occurs via non-PTS mechanisms. Progress in characterization of clostridial sugar transporters and manipulation of control mechanisms to optimise sugar fermentation is described.

Excess sludge and herbaceous plant co-digestion for volatile fatty acids generation improved by protein and cellulose conversion enhancement

Volatile fatty acids (VFA), the substrate for the bio-methane yield, can be generated from excess sludge or herbaceous plant waste during the anaerobic fermentation process. However, due to the high protein content and the low carbon-to-nitrogen (C/N) ratio of excess sludge, the nutrient utilization of excess sludge to generate VFA and bio-methane usually becomes inefficient and uneconomical. In this study, the laboratory findings showed that both the organic conversion and VFA generation from the mixture of excess sludge and herbaceous plant waste (e.g., the tall fescue was used as model), could be significantly enhanced, especially when the C/N ratio was adjusted to 20/1. In order to get more VFA and bio-methane generation, the effects of different thermal pretreatment strategies on the excess sludge and tall fescue co-fermentation were investigated. The study of thermal pretreatment revealed that the maximal VFA generation (585.2 g COD/kg of total solids (TS)) from the mixture of sludge and tall fescue by thermal pretreatment at 100 °C was almost 9.9 and 4.1 times higher than un-pretreated sole sludge and tall fescue, respectively. Then the mechanism of enhanced VFA generation from the mixture by thermal pretreatment was investigated. It was observed that pretreating the mixture of excess sludge and tall fescue at 100 °C caused the greatest hydrolysis and acidification. The produced VFA was applied to generate the bio-methane, and it was showed that the bio-methane produced from the thermal-pretreated (100 °C) mixture was almost 9.6 and 4.9 times as high as un-pretreated sole sludge and tall fescue, respectively. In addition, the detection of enzyme activities showed that the main enzymes related to cellulose, hemicelluloses, lignin degradation, and acid forming were more active when VFA was produced from the thermal-pretreated (100 °C) mixture than other cases. Class Bacteroidia, class β-Proteobateria, α-Proteobateria, and phylum Firmicutes of the reactor with 100 °C pretreated mixture were more active than that of the reactor with un-pretreated sludge.

Combination of RNA sequencing and metabolite data to elucidate improved toxic compound tolerance and butanol fermentation of Clostridium acetobutylicum from wheat straw hydrolysate by supplying sodium sulfide

Sodium sulfide (SS) was added to the non-detoxified wheat straw hydrolysate for ABE fermentation by Clostridium acetobutylicum CICC8012. Biochemical measurements demonstrated that supplementation with SS promoted earlier and enhanced conversion of acid to ABE and led to a 27.48% improvement in sugar consumption, a 20.48% improvement in the sugar-based ABE yield, a 47.63% improvement in the butanol titer, and a 53.50% improvement in the ABE concentration. The response of C. acetobutylicum CICC8012 at the mRNA level was examined by a transcriptional analysis performed with RNA sequencing. The expression of genes involved in the membrane transport of carbohydrates, glycolysis, and ABE formation increased following SS-supplemented fermentation, whereas the expression of genes encoding enzymes involved in acid formation decreased, which indicates that supplemental SS affected the central fermentative pathway, down-regulated the metabolic flux toward the acid formation branches, and up-regulated the metabolic flux toward the ABE formation branches.

Redox-switch regulatory mechanism of thiolase from Clostridium acetobutylicum

Thiolase is the first enzyme catalysing the condensation of two acetyl-coenzyme A (CoA) molecules to form acetoacetyl-CoA in a dedicated pathway towards the biosynthesis of n-butanol, an important solvent and biofuel. Here we elucidate the crystal structure of Clostridium acetobutylicum thiolase (CaTHL) in its reduced/oxidized states. CaTHL, unlike those from other aerobic bacteria such as Escherichia coli and Zoogloea ramegera, is regulated by the redox-switch modulation through reversible disulfide bond formation between two catalytic cysteine residues, Cys88 and Cys378. When CaTHL is overexpressed in wild-type C. acetobutylicum, butanol production is reduced due to the disturbance of acidogenic to solventogenic shift. The CaTHL(V77Q/N153Y/A286K) mutant, which is not able to form disulfide bonds, exhibits higher activity than wild-type CaTHL, and enhances butanol production upon overexpression. On the basis of these results, we suggest that CaTHL functions as a key enzyme in the regulation of the main metabolism of C. acetobutylicum through a redox-switch regulatory mechanism.

The Phosphotransferase System in Solventogenic Clostridia

The acetone-butanol-ethanol fermentation employing solventogenic clostridia was a major industrial process during the 20th century, but declined for economic reasons. In recent times, interest in the process has been revived due to the perceived potential of butanol as a superior biofuel. Redevelopment of an efficient fermentation process will require a detailed understanding of the physiology of carbohydrate utilization by the bacteria. Genome sequences have revealed that, as in other anaerobes, the phosphotransferase system (PTS) and associated regulatory functions are likely to play an important role in sugar uptake and its regulation. The genomes of <i>Clostridium acetobutylicum</i> and <i>C. beijerinckii</i> encode 13 and 43 phosphotransferases, respectively. Characterization of clostridial phosphotransferases has demonstrated that they are involved in the uptake and phosphorylation of hexoses, hexose derivatives and disaccharides, although the functions of many systems remain to be determined. Glucose is a dominant sugar which represses the utilization of other carbon sources, including the non-PTS pentose sugars xylose and arabinose, by the clostridia. Targeting of the CcpA-dependent mechanism of carbon catabolite repression has been shown to be an effective strategy for reducing the repressive effects of glucose, indicating potential for developing strains with improved fermentation performance.

Structural insights into substrate specificity of crotonase from the n-butanol producing bacterium Clostridium acetobutylicum

Crotonase from Clostridium acetobutylicum (CaCRT) is an enzyme that catalyzes the dehydration of 3-hydroxybutyryl-CoA to crotonyl-CoA in the n-butanol biosynthetic pathway. To investigate the molecular mechanism underlying n-butanol biosynthesis, we determined the crystal structures of the CaCRT protein in apo- and acetoacetyl-CoA bound forms. Similar to other canonical crotonase enzymes, CaCRT forms a hexamer by the dimerization of two trimers. A crystal structure of CaCRT in complex with acetoacetyl-CoA revealed that Ser69 and Ala24 to be signature residues of CaCRT, which results in a distinct ADP binding mode wherein the ADP moiety is bound at a different position compared with other crotonases. We also revealed that the substrate specificity of crotonase enzymes is determined by both the structural feature of the α3 helix region and the residues contributing the enoyl-CoA binding pocket. A tight formed α3 helix and two phenylalanine residues, Phe143 and Phe233, aid CaCRT to accommodate crotonyl-CoA as the substrate. The key residues involved in substrate binding, enzyme catalysis and substrate specificity were confirmed by site-directed mutagenesis.

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of the (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 from Ralstonia eutropha H16

The (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 from Ralstonia eutropha (RePaaH1) is an enzyme used in the biosynthesis of n-butanol from acetyl-CoA by the reduction of acetoacetyl-CoA to (S)-3-hydroxybutyryl-CoA. The RePaaH1 protein was crystallized using the hanging-drop vapour-diffusion method in the presence of 1.4 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.0, 0.2 M sodium chloride at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.6 Å on a synchrotron beamline. The crystal belonged to space group P3221, with unit-cell parameters a=b=135.4, c=97.2 Å. With three molecules per asymmetric unit, the crystal volume per unit protein weight (VM) is 2.68 Å3 Da(-1), which corresponds to a solvent content of approximately 54.1%. The structure was solved by the single-wavelength anomalous dispersion method and refinement of the structure is in progress.

Simultaneous fermentation of glucose and xylose to butanol by Clostridium sp. strain BOH3

Cellulose and hemicellulose constitute the major components in sustainable feedstocks which could be used as substrates for biofuel generation. However, following hydrolysis to monomer sugars, the solventogenic Clostridium will preferentially consume glucose due to transcriptional repression of xylose utilization genes. This is one of the major barriers in optimizing lignocellulosic hydrolysates that produce butanol. Unlike studies on existing bacteria, this study demonstrates that newly reported Clostridium sp. strain BOH3 is capable of fermenting 60 g/liter of xylose to 14.9 g/liter butanol, which is similar to the 14.5 g/liter butanol produced from 60 g/liter of glucose. More importantly, strain BOH3 consumes glucose and xylose simultaneously, which is shown by its capability for generating 11.7 g/liter butanol from a horticultural waste cellulosic hydrolysate containing 39.8 g/liter glucose and 20.5 g/liter xylose, as well as producing 11.9 g/liter butanol from another horticultural waste hemicellulosic hydrolysate containing 58.3 g/liter xylose and 5.9 g/liter glucose. The high-xylose-utilization capability of strain BOH3 is attributed to its high xylose-isomerase (0.97 U/mg protein) and xylulokinase (1.16 U/mg protein) activities compared to the low-xylose-utilizing solventogenic strains, such as Clostridium sp. strain G117. Interestingly, strain BOH3 was also found to produce riboflavin at 110.5 mg/liter from xylose and 76.8 mg/liter from glucose during the fermentation process. In summary, Clostridium sp. strain BOH3 is an attractive candidate for application in efficiently converting lignocellulosic hydrolysates to biofuels and other value-added products, such as riboflavin.

Biobutanol

China initiated its acetone-butanol-ethanol (ABE) industry in the 1950s; it peaked in the 1980s, and ended at the end of the last century owing to the development of more competitive petrochemical pathways. However, driven by the high price of crude oil and environmental concerns raised by the over-consumption of petrochemical products, biofuels and bio-based chemicals including butanol have garnered global attention again. Currently, butanol produced from ABE fermentation is mainly used as an industrial solvent or a platform chemical for several bulk derivatives, and is also believed to be a potential biofuel. A number of plants have been built or rebuilt in recent years in China for butanol production with the ABE process. Chinese researchers also show great interest in the improvement of the production strains and corresponding processes. They have applied conventional mutagenesis methods to improve butanol-producing strains such as the Clostridium acetobutylicum mutant strains EA2018 (butanol ratio of 70%) and Rh8 (butanol tolerance of 19 g/L). The omics technologies, such as genome sequencing, proteomic and transcriptomic analysis, have been adapted to elucidate the characteristics of different butanol-producing bacteria. Based on the group II intron method, the genetic manipulation system of C. acetobutylicum was greatly improved, and some successful engineering strains were developed. In addition, research in China also covers the downstream processes. This article reviews up-to-date progress on biobutanol production in China.

Crystal structure and biochemical properties of the (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 from Ralstonia eutropha

3-Hydroxybutyryl-CoA dehydrogenase is an enzyme involved in the synthesis of the biofuel n-butanol by converting acetoacetyl-CoA to 3-hydroxybutyryl-CoA. To investigate the molecular mechanism of n-butanol biosynthesis, we determined crystal structures of the Ralstonia eutropha-derived 3-hydroxybutyryl-CoA dehydrogenase (RePaaH1) in complex with either its cofactor NAD(+) or its substrate acetoacetyl-CoA. While the biologically active structure is dimeric, the monomer of RePaaH1 comprises two separated domains with an N-terminal Rossmann fold and a C-terminal helical bundle for dimerization. In this study, we show that the cofactor-binding site is located on the Rossmann fold and is surrounded by five loops and one helix. The binding mode of the acetoacetyl-CoA substrate was found to be that the adenosine diphosphate moiety is not highly stabilized compared with the remainder of the molecule. Residues involved in catalysis and substrate binding were further confirmed by site-directed mutagenesis experiments, and kinetic properties of RePaaH1were examined as well. Our findings contribute to the understanding of 3-hydroxybutyryl-CoA dehydrogenase catalysis, and will be useful in enhancing the efficiency of n-butanol biosynthesis by structure based protein engineering.

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of (S)-3-hydroxybutyryl-CoA dehydrogenase from Clostridium butyricum

(S)-3-Hydroxybutyryl-CoA dehydrogenase from Clostridium butyricum (CbHBD) is an enzyme that catalyzes the second step in the biosynthesis of n-butanol from acetyl-CoA by the reduction of acetoacetyl-CoA to 3-hydroxybutyryl-CoA. The CbHBD protein was crystallized using the hanging-drop vapour-diffusion method in the presence of 2 M ammonium sulfate, 0.1 M CAPS pH 10.5, 0.2 M lithium sulfate at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.3 Å on a synchrotron beamline. The crystal belonged to space group R3, with unit-cell parameters a = b = 148.5, c = 201.6 Å. With four molecules per asymmetric unit, the crystal volume per unit protein weight (VM) is 3.52 Å(3) Da(-1), which corresponds to a solvent content of approximately 65.04%. The structure was solved by the molecular-replacement method and refinement of the structure is in progress.

Comparative phenotypic analysis and genome sequence of Clostridium beijerinckii SA-1, an offspring of NCIMB 8052

Production of butanol by solventogenic clostridia is controlled through metabolic regulation of the carbon flow and limited by its toxic effects. To overcome cell sensitivity to solvents, stress-directed evolution methodology was used three decades ago on Clostridium beijerinckii NCIMB 8052 that spawned the SA-1 strain. Here, we evaluated SA-1 solventogenic capabilities when growing on a previously validated medium containing, as carbon- and energy-limiting substrates, sucrose and the products of its hydrolysis d-glucose and d-fructose and only d-fructose. Comparative small-scale batch fermentations with controlled pH (pH 6.5) showed that SA-1 is a solvent hyper-producing strain capable of generating up to 16.1 g l(-1) of butanol and 26.3 g l(-1) of total solvents, 62.3 % and 63 % more than NCIMB 8052, respectively. This corresponds to butanol and solvent yields of 0.3 and 0.49 g g(-1), respectively (63 % and 65 % increase compared with NCIMB 8052). SA-1 showed a deficiency in d-fructose transport as suggested by its 7 h generation time compared with 1 h for NCIMB 8052. To potentially correlate physiological behaviour with genetic mutations, the whole genome of SA-1 was sequenced using the Illumina GA IIx platform. PCR and Sanger sequencing were performed to analyse the putative variations. As a result, four errors were confirmed and validated in the reference genome of NCIMB 8052 and a total of 10 genetic polymorphisms in SA-1. The genetic polymorphisms included eight single nucleotide variants, one small deletion and one large insertion that it is an additional copy of the insertion sequence ISCb1. Two of the genetic polymorphisms, the serine threonine phosphatase cbs_4400 and the solute binding protein cbs_0769, may possibly explain some of the observed physiological behaviour, such as rerouting of the metabolic carbon flow, deregulation of the d-fructose phosphotransferase transport system and delayed sporulation.

A novel process for direct production of acetone-butanol-ethanol from native starches using granular starch hydrolyzing enzyme by Clostridium saccharoperbutylacetonicum N1-4

In this work, a new approach for acetone-butanol-ethanol (ABE) production has been proposed. Direct fermentation of native starches (uncooked process) was investigated by using granular starch hydrolyzing enzyme (GSHE) and Clostridium saccharoperbutylacetonicum N1-4. Even the process was carried out under suboptimal condition for activity of GSHE, the production of ABE was similar with that observed in conventional process or cooked process in terms of final solvent concentration (21.3 ± 0.4 to 22.4 ± 0.4 g/L), butanol concentration (17.5 ± 0.4 to 17.8 ± 0.3 g/L) and butanol yield (0.33 to 0.37 g/g). The production of solvents was significantly dependent on the source of starches. Among investigated starches, corn starch was more susceptible to GSHE while cassava starch was the most resistant to this enzyme. Fermentation using native corn starch resulted in the solvent productivity of 0.47 g/L h, which was about 15 % higher than that achieved in cooked process. On the contrary, uncooked process using cassava and wheat starch resulted in the solvent productivity of 0.30 and 0.37 g/L h, which were respectively about 30 % lower than those obtained in cooked process. No contamination was observed during all trials even fermentation media were prepared without sterilization. During the fermentation using native starches, no formation of foam is observed. This uncooked process does not require cooking starchy material; therefore, the thermal energy consumption for solvent production would remarkably be reduced in comparison with cooked process.

Improved bioproduction of short-chain fatty acids from waste activated sludge by perennial ryegrass addition

To improve short-chain fatty acids (SCFAs) production from waste activated sludge (WAS), studies that focus on pre-treatment methods, pH control or adding extra carbon like rice were reported. In this study, a kind of green waste (perennial ryegrass) was used as carbon source to adjust carbon to nitrogen ratio (C/N) in WAS to enhance SCFAs production. The effects of different C/N ratio ranging from 26/1 to 7/1 on SCFAs production and cellulose, hemicellulose, and lignin consumption were investigated in detail. It was observed that the maximal SCFAs yield was 368.71 g COD per kilogram of total solids (TS) at C/N 20/1 with fermentation time of 12 d, which was, respectively, over 4 and 12 times than that at C/N 26/1 (sole perennial ryegrass) and C/N 7/1 (sole WAS). Meanwhile, cellulose, hemicellulose and lignin consumptions were 109.12, 148.74, 20.90 g COD/kg TS, respectively, at C/N 20/1 with fermentation time of 12 d. The analysis of the composition of SCFAs showed that acetic acid ranked the first among other acids from C/N ratio of 26/1 to 18/1, whereas propionic acid was the dominant product from C/N ratio of 16/1 to 7/1. Because the results of this study were different from previous studies of SCFAs generation, the mechanism of improved SCFAs at C/N ratio of 20/1 by perennial ryegrass addition was investigated. Results showed that as soluble COD, soluble protein and soluble carbohydrate increased, more substrates were available for SCFAs production at C/N ratio of 20/1. In addition, with the drop of pH to 4.82, methane generating was inhabitant and the SCFAs production was therefore significantly enhanced. Additionally, the mechanism of improved SCFAs generation was analyzed from the view of enzyme activities and microbial community. The experiments revealed that at C/N ratio of 20/1 the activities of enzymes were the highest comparing with other C/N ratios and lignin was the rate-limiting steps in WAS anaerobic digestion by perennial ryegrass addition. The 16S rRNA gene clone library demonstrated that Clostridia, Spirochaetes, and Bacteroidetes were the dominant microbial community at C/N ratio of 20/1.

Dual substrate specificity of an N-acetylglucosamine phosphotransferase system in Clostridium beijerinckii

The solventogenic clostridia have a considerable capacity to ferment carbohydrate substrates with the production of acetone and butanol, making them attractive organisms for the conversion of waste materials to valuable products. In common with other anaerobes, the clostridia show a marked dependence on the phosphoenolpyruvate (PEP)-dependent phosphotransferase system (PTS) to accumulate sugars and sugar derivatives. In this study, we demonstrate that extracts of Clostridium beijerinckii grown on N-acetylglucosamine (GlcNAc) exhibit PTS activity for the amino sugar. The PTS encoded by the divergent genes cbe4532 (encoding the IIC and IIB domains) and cbe4533 (encoding a IIA domain) was shown to transport and phosphorylate GlcNAc and also glucose. When the genes were recombined in series under the control of the lac promoter in pUC18 and transformed into a phosphotransferase mutant (nagE) of Escherichia coli lacking GlcNAc PTS activity, the ability to take up and ferment GlcNAc was restored, and extracts of the transformant showed PEP-dependent phosphorylation of GlcNAc. The gene products also complemented an E. coli mutant lacking glucose PTS activity but were unable to complement the same strain for PTS-dependent mannose utilization. Both GlcNAc and glucose induced the expression of cbe4532 and cbe4533 in C. beijerinckii, and consistent with this observation, extracts of cells grown on glucose exhibited PTS activity for GlcNAc, and glucose did not strongly repress utilization of GlcNAc by growing cells. On the basis of the phylogeny and function of the encoded PTS, we propose that the genes cbe4532 and cbe4533 should be designated nagE and nagF, respectively.

De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes

BACKGROUND

Understanding the biological mechanisms used by microorganisms for plant biomass degradation is of considerable biotechnological interest. Despite of the growing number of sequenced (meta)genomes of plant biomass-degrading microbes, there is currently no technique for the systematic determination of the genomic components of this process from these data.

RESULTS

We describe a computational method for the discovery of the protein domains and CAZy families involved in microbial plant biomass degradation. Our method furthermore accurately predicts the capability to degrade plant biomass for microbial species from their genome sequences. Application to a large, manually curated data set of microbial degraders and non-degraders identified gene families of enzymes known by physiological and biochemical tests to be implicated in cellulose degradation, such as GH5 and GH6. Additionally, genes of enzymes that degrade other plant polysaccharides, such as hemicellulose, pectins and oligosaccharides, were found, as well as gene families which have not previously been related to the process. For draft genomes reconstructed from a cow rumen metagenome our method predicted Bacteroidetes-affiliated species and a relative to a known plant biomass degrader to be plant biomass degraders. This was supported by the presence of genes encoding enzymatically active glycoside hydrolases in these genomes.

CONCLUSIONS

Our results show the potential of the method for generating novel insights into microbial plant biomass degradation from (meta-)genome data, where there is an increasing production of genome assemblages for uncultured microbes.

Phosphoketolase pathway for xylose catabolism in Clostridium acetobutylicum revealed by 13C metabolic flux analysis

Solvent-producing clostridia are capable of utilizing pentose sugars, including xylose and arabinose; however, little is known about how pentose sugars are catabolized through the metabolic pathways in clostridia. In this study, we identified the xylose catabolic pathways and quantified their fluxes in Clostridium acetobutylicum based on [1-(13)C]xylose labeling experiments. The phosphoketolase pathway was found to be active, which contributed up to 40% of the xylose catabolic flux in C. acetobutylicum. The split ratio of the phosphoketolase pathway to the pentose phosphate pathway was markedly increased when the xylose concentration in the culture medium was increased from 10 to 20 g liter(-1). To our knowledge, this is the first time that the in vivo activity of the phosphoketolase pathway in clostridia has been revealed. A phosphoketolase from C. acetobutylicum was purified and characterized, and its activity with xylulose-5-P was verified. The phosphoketolase was overexpressed in C. acetobutylicum, which resulted in slightly increased xylose consumption rates during the exponential growth phase and a high level of acetate accumulation.

Elucidating and reprogramming Escherichia coli metabolisms for obligate anaerobic n-butanol and isobutanol production

Elementary mode (EM) analysis based on the constraint-based metabolic network modeling was applied to elucidate and compare complex fermentative metabolisms of Escherichia coli for obligate anaerobic production of n-butanol and isobutanol. The result shows that the n-butanol fermentative metabolism was NADH-deficient, while the isobutanol fermentative metabolism was NADH redundant. E. coli could grow and produce n-butanol anaerobically as the sole fermentative product but not achieve the maximum theoretical n-butanol yield. In contrast, for the isobutanol fermentative metabolism, E. coli was required to couple with either ethanol- or succinate-producing pathway to recycle NADH. To overcome these "defective" metabolisms, EM analysis was implemented to reprogram the native fermentative metabolism of E. coli for optimized anaerobic production of n-butanol and isobutanol through multiple gene deletion (~8-9 genes), addition (~6-7 genes), up- and downexpression (~6-7 genes), and cofactor engineering (e.g., NADH, NADPH). The designed strains were forced to couple both growth and anaerobic production of n-butanol and isobutanol, which is a useful characteristic to enhance biofuel production and tolerance through metabolic pathway evolution. Even though the n-butanol and isobutanol fermentative metabolisms were quite different, the designed strains could be engineered to have identical metabolic flux distribution in "core" metabolic pathways mainly supporting cell growth and maintenance. Finally, the model prediction in elucidating and reprogramming the native fermentative metabolism of E. coli for obligate anaerobic production of n-butanol and isobutanol was validated with published experimental data.

Ribulokinase and transcriptional regulation of arabinose metabolism in Clostridium acetobutylicum

The transcription factor AraR controls utilization of L-arabinose in Bacillus subtilis. In this study, we combined a comparative genomic reconstruction of AraR regulons in nine Clostridium species with detailed experimental characterization of AraR-mediated regulation in Clostridium acetobutylicum. Based on the reconstructed AraR regulons, a novel ribulokinase, AraK, present in all analyzed Clostridium species was identified, which was a nonorthologous replacement of previously characterized ribulokinases. The predicted function of the araK gene was confirmed by inactivation of the araK gene in C. acetobutylicum and biochemical assays using purified recombinant AraK. In addition to the genes involved in arabinose utilization and arabinoside degradation, extension of the AraR regulon to the pentose phosphate pathway genes in several Clostridium species was revealed. The predicted AraR-binding sites in the C. acetobutylicum genome and the negative effect of L-arabinose on DNA-regulator complex formation were verified by in vitro binding assays. The predicted AraR-controlled genes in C. acetobutylicum were experimentally validated by testing gene expression patterns in both wild-type and araR-inactivated mutant strains during growth in the absence or presence of L-arabinose.

Adaptive evolution for fast growth on glucose and the effects on the regulation of glucose transport system in Clostridium tyrobutyricum

Laboratory adaptive evolution of microorganisms offers the possibility of relating acquired mutations to increased fitness of the organism under the conditions used. By combining a fibrous-bed bioreactor, we successfully developed a simple and valuable adaptive evolution strategy in repeated-batch fermentation mode with high initial substrate concentration and evolved Clostridium tyrobutyricum mutant with significantly improved butyric acid volumetric productivity up to 2.25 g/(L h), which is the highest value in batch fermentation reported so far. Further experiments were conducted to pay attention to glucose transport system in consideration of the high glucose consumption rate resulted from evolution. Complete characterization and comparison of the glucose phosphoenolpyruvate (PEP)-dependent phosphotransferase system (PTS) were carried out in the form of toluene-treated cells and cell-free extracts derived from both C. tyrobutyricum wide-type and mutant, while an alternative glucose transport route that requires glucokinase was confirmed by the phenomena of resistance to the glucose analogue 2-deoxyglucose and ATP-dependent glucose phosphorylation. Our results suggest that C. tyrobutyricum mutant is defective in PTS activity and compensates for this defect with enhanced glucokinase activity, resulting in the efficient uptake and consumption of glucose during the whole metabolism.

Structure of cellobiose phosphorylase from Clostridium thermocellum in complex with phosphate

Clostridium thermocellum is a cellulosome-producing bacterium that is able to efficiently degrade and utilize cellulose as a sole carbon source. Cellobiose phosphorylase (CBP) plays a critical role in cellulose degradation by catalyzing the reversible phosphate-dependent hydrolysis of cellobiose, the major product of cellulose degradation, into α-D-glucose 1-phosphate and D-glucose. CBP from C. thermocellum is a modular enzyme composed of four domains [N-terminal domain, helical linker, (α/α)(6)-barrel domain and C-terminal domain] and is a member of glycoside hydrolase family 94. The 2.4 Å resolution X-ray crystal structure of C. thermocellum CBP reveals the residues involved in coordinating the catalytic phosphate as well as the residues that are likely to be involved in substrate binding and discrimination.

Confirmation and elimination of xylose metabolism bottlenecks in glucose phosphoenolpyruvate-dependent phosphotransferase system-deficient Clostridium acetobutylicum for simultaneous utilization of glucose, xylose, and arabinose

Efficient cofermentation of D-glucose, D-xylose, and L-arabinose, three major sugars present in lignocellulose, is a fundamental requirement for cost-effective utilization of lignocellulosic biomass. The Gram-positive anaerobic bacterium Clostridium acetobutylicum, known for its excellent capability of producing ABE (acetone, butanol, and ethanol) solvent, is limited in using lignocellulose because of inefficient pentose consumption when fermenting sugar mixtures. To overcome this substrate utilization defect, a predicted glcG gene, encoding enzyme II of the D-glucose phosphoenolpyruvate-dependent phosphotransferase system (PTS), was first disrupted in the ABE-producing model strain Clostridium acetobutylicum ATCC 824, resulting in greatly improved D-xylose and L-arabinose consumption in the presence of D-glucose. Interestingly, despite the loss of GlcG, the resulting mutant strain 824glcG fermented D-glucose as efficiently as did the parent strain. This could be attributed to residual glucose PTS activity, although an increased activity of glucose kinase suggested that non-PTS glucose uptake might also be elevated as a result of glcG disruption. Furthermore, the inherent rate-limiting steps of the D-xylose metabolic pathway were observed prior to the pentose phosphate pathway (PPP) in strain ATCC 824 and then overcome by co-overexpression of the D-xylose proton-symporter (cac1345), D-xylose isomerase (cac2610), and xylulokinase (cac2612). As a result, an engineered strain (824glcG-TBA), obtained by integrating glcG disruption and genetic overexpression of the xylose pathway, was able to efficiently coferment mixtures of D-glucose, D-xylose, and L-arabinose, reaching a 24% higher ABE solvent titer (16.06 g/liter) and a 5% higher yield (0.28 g/g) compared to those of the wild-type strain. This strain will be a promising platform host toward commercial exploitation of lignocellulose to produce solvents and biofuels.

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

BACKGROUND

Solventogenic clostridia offer a sustainable alternative to petroleum-based production of butanol--an important chemical feedstock and potential fuel additive or replacement. C. beijerinckii is an attractive microorganism for strain design to improve butanol production because it (i) naturally produces the highest recorded butanol concentrations as a byproduct of fermentation; and (ii) can co-ferment pentose and hexose sugars (the primary products from lignocellulosic hydrolysis). Interrogating C. beijerinckii metabolism from a systems viewpoint using constraint-based modeling allows for simulation of the global effect of genetic modifications.

RESULTS

We present the first genome-scale metabolic model (iCM925) for C. beijerinckii, containing 925 genes, 938 reactions, and 881 metabolites. To build the model we employed a semi-automated procedure that integrated genome annotation information from KEGG, BioCyc, and The SEED, and utilized computational algorithms with manual curation to improve model completeness. Interestingly, we found only a 34% overlap in reactions collected from the three databases--highlighting the importance of evaluating the predictive accuracy of the resulting genome-scale model. To validate iCM925, we conducted fermentation experiments using the NCIMB 8052 strain, and evaluated the ability of the model to simulate measured substrate uptake and product production rates. Experimentally observed fermentation profiles were found to lie within the solution space of the model; however, under an optimal growth objective, additional constraints were needed to reproduce the observed profiles--suggesting the existence of selective pressures other than optimal growth. Notably, a significantly enriched fraction of actively utilized reactions in simulations--constrained to reflect experimental rates--originated from the set of reactions that overlapped between all three databases (P = 3.52 × 10-9, Fisher's exact test). Inhibition of the hydrogenase reaction was found to have a strong effect on butanol formation--as experimentally observed.

CONCLUSIONS

Microbial production of butanol by C. beijerinckii offers a promising, sustainable, method for generation of this important chemical and potential biofuel. iCM925 is a predictive model that can accurately reproduce physiological behavior and provide insight into the underlying mechanisms of microbial butanol production. As such, the model will be instrumental in efforts to better understand, and metabolically engineer, this microorganism for improved butanol production.