Engineering Escherichia coli cells for cellobiose assimilation through a phosphorolytic mechanism

Development and preclinical validation of 2-deoxy 2-[18F]fluorocellobiose as an Aspergillus-specific PET tracer

The global incidence of invasive fungal infections (IFIs) has increased over the past few decades, mainly in immunocompromised patients, and is associated with high mortality and morbidity. Aspergillus fumigatus is one of the most common and deadliest IFI pathogens. Major hurdles to treating fungal infections remain the lack of rapid and definitive diagnosis, including the frequent need for invasive procedures to provide microbiological confirmation, and the lack of specificity of structural imaging methods. To develop an Aspergillus-specific positron emission tomography (PET) imaging agent, we focused on fungal-specific sugar metabolism. We radiolabeled cellobiose, a disaccharide known to be metabolized by Aspergillus species, and synthesized 2-deoxy-2-[18F]fluorocellobiose ([18F]FCB) by enzymatic conversion of 2-deoxy-2-[18F]fluoroglucose ([18F]FDG) with a radiochemical yield of 60 to 70%, a radiochemical purity of >98%, and 1.5 hours of synthesis time. Two hours after [18F]FCB injection in A. fumigatus pneumonia as well as A. fumigatus, bacterial, and sterile inflammation myositis mouse models, retained radioactivity was only seen in foci with live A. fumigatus infection. In vitro testing confirmed production of β-glucosidase enzyme by A. fumigatus and not by bacteria, resulting in hydrolysis of [18F]FCB into glucose and [18F]FDG, the latter being retained by the live fungus. The parent molecule was otherwise promptly excreted through the kidneys, resulting in low background radioactivity and high target-to-nontarget ratios at A. fumigatus infectious sites. We conclude that [18F]FCB is a promising and clinically translatable Aspergillus-specific PET tracer.

Metabolomics and in-vitro bioactivities studies of fermented Musa paradisiaca pulp: A potential alpha-amylase inhibitor

The in-vitro synthesis of bio-compounds via fermentation is a promising route for bioactive molecules intended for disease control and management. Therefore, this study evaluated the effect of fermentation on the antioxidants, antihyperglycemic and anti-inflammatory properties and the resultant chemometric phytochemical profiles of unripe plantain fruits. The results revealed that Escherichia coli and Propionibacterium spp. are suspected as the key fermenters. The E coli showed negative results to the pathogenicity test; Propionibacterium appeared to be opportunistic. A significant increase in the total polyphenols and protein and decreased flavonoids was recorded in the phytochemical profile of the methanolic extract of the fermented unripe plantain pulp; however, the ascorbic acid content was not significantly altered. The 1H NMR fingerprint showed that there is a closely related chemical shift among the shorter fermentation time (days 2-6) and the unfermented, while the more extended fermentation periods (days 7-12) with enhanced bioactivities were closely related based on the chemometrics analyses. Furthermore, the UPLC-QTOF-MS analysis annotated the presence of bioactive compounds in the day-9 fermented sample: polyhydroxy glucose conjugates (3-Methoxy-4-hydroxyphenyl 6-O-(3,4,5-trihydroxybenzoyl)-beta-D-glucopyranoside), short chain peptide (leucyl-glycyl-glycine), amino acid derivatives (4-Aminophenylalanine, and N-Acetylhistidine), linear and cyclic fatty acid derivatives (palmitoyl putrescine, ricinoleic acid, phytosphingosine, gabalid, rubrenoic acid, 2-aminocyclopentanecarboxylic and cystodienioc acid). The synergistic effect of these newly formed compounds and the increase in the phenolic content of the day-9 fermented unripe plantain may account for its more potent antioxidant, anti-inflammatory and antihyperglycemic activity. Therefore, the products obtained from the day 9 fermentation of unripe plantain pulp may serve as potential nutraceutical agents against gastro-enteric sugar digestion and absorption and sugar-induced oxidative stress, inflammation and metabolic disease.

Efficient and Economic Utilization of Cellobiose for Glycosylation Modification by Regulating Carbon Source Supply and Metabolic Pathway In Vivo

Glycosylation, one of the most common and significant modifications in nature, has prompted the development of a cellobiose phosphorolysis route for glycosylation in vivo. However, the process of glycosylation is hampered by the notably low conversion rate of cellobiose. In this work, regulation of the carbon source supply by changing the ratio of glucose to cellobiose improved the conversion rate of cellobiose, resulting in enhancing the efficiency of glycosylation and the production of vitexin. Moreover, three genes (pgm, agp, and ushA) involved in the degradation of UDP-glucose were knocked out to relieve the degradation and diversion of the cellobiose phosphorolysis route. Finally, through the optimization of conversion conditions, we observed a continuous enhancement in cellobiose conversion rate and vitexin production in BL21ΔushAΔagp-TcCGT-CepA, corresponding to an increased concentration of added glucose. The maximum production of vitexin reached 2228 mg/L with the addition of 2 g/L cellobiose and 6 g/L glucose, which was 312% of that in BL21-TcCGT-CepA with the addition of 2 g/L cellobiose. The conversion rate of cellobiose in BL21ΔushAΔagp-TcCGT-CepA reached 88%, which was the highest conversion rate of cellobiose to date. Therefore, this study presents a cost-effective and efficient method to enhance the conversion rate of cellobiose during the glycosylation process.

Engineering of Pseudomonas putida for accelerated co-utilization of glucose and cellobiose yields aerobic overproduction of pyruvate explained by an upgraded metabolic model

Pseudomonas putida KT2440 is an attractive bacterial host for biotechnological production of valuable chemicals from renewable lignocellulosic feedstocks as it can valorize lignin-derived aromatics or glucose obtainable from cellulose. P. putida EM42, a genome-reduced variant of strain KT2440 endowed with advantageous physiological properties, was recently engineered for growth on cellobiose, a major cellooligosaccharide product of enzymatic cellulose hydrolysis. Co-utilization of cellobiose and glucose was achieved in a mutant lacking periplasmic glucose dehydrogenase Gcd (PP_1444). However, the cause of the co-utilization phenotype remained to be understood and the Δgcd strain had a significant growth defect. In this study, we investigated the basis of the simultaneous uptake of the two sugars and accelerated the growth of P. putida EM42 Δgcd mutant for the bioproduction of valuable compounds from glucose and cellobiose. We show that the gcd deletion lifted the inhibition of the exogenous β-glucosidase BglC from Thermobifida fusca exerted by the intermediates of the periplasmic glucose oxidation pathway. The additional deletion of hexR gene, which encodes a repressor of the upper glycolysis genes, failed to restore rapid growth on glucose. The reduced growth rate of the Δgcd mutant was partially compensated by the implantation of heterologous glucose and cellobiose transporters (Glf from Zymomonas mobilis and LacY from Escherichia coli, respectively). Remarkably, this intervention resulted in the accumulation of pyruvate in aerobic P. putida cultures. We demonstrated that the excess of this key metabolic intermediate can be redirected to the enhanced biosynthesis of ethanol and lactate. The pyruvate overproduction phenotype was then unveiled by an upgraded genome-scale metabolic model constrained with proteomic and kinetic data. The model pointed to the saturation of glucose catabolism enzymes due to unregulated substrate uptake and it predicted improved bioproduction of pyruvate-derived chemicals by the engineered strain. This work sheds light on the co-metabolism of cellulosic sugars in an attractive biotechnological host and introduces a novel strategy for pyruvate overproduction in bacterial cultures under aerobic conditions.

Engineering of a new Escherichia coli strain efficiently metabolizing cellobiose with promising perspectives for plant biomass-based application design

The necessity to decrease our fossil energy dependence requests bioprocesses based on biomass degradation. Cellobiose is the main product released by cellulases when acting on the major plant cell wall polysaccharide constituent, the cellulose. Escherichia coli, one of the most common model organisms for the academy and the industry, is unable to metabolize this disaccharide. In this context, the remodeling of E. coli to catabolize cellobiose should thus constitute an important progress for the design of such applications. Here, we developed a robust E. coli strain able to metabolize cellobiose by integration of a small set of modifications in its genome. Contrary to previous studies that use adaptative evolution to achieve some growth on this sugar by reactivating E. coli cryptic operons coding for cellobiose metabolism, we identified easily insertable modifications impacting the cellobiose import (expression of a gene coding a truncated variant of the maltoporin LamB, modification of the expression of lacY encoding the lactose permease) and its intracellular degradation (genomic insertion of a gene encoding either a cytosolic β-glucosidase or a cellobiose phosphorylase). Taken together, our results provide an easily transferable set of mutations that confers to E. coli an efficient growth phenotype on cellobiose (doubling time of 2.2 ​h in aerobiosis) without any prior adaptation.

Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments

A major open question in microbial community ecology is whether we can predict how the components of a diet collectively determine the taxonomic composition of microbial communities. Motivated by this challenge, we investigate whether communities assembled in pairs of nutrients can be predicted from those assembled in every single nutrient alone. We find that although the null, naturally additive model generally predicts well the family-level community composition, there exist systematic deviations from the additive predictions that reflect generic patterns of nutrient dominance at the family level. Pairs of more-similar nutrients (e.g. two sugars) are on average more additive than pairs of more dissimilar nutrients (one sugar-one organic acid). Furthermore, sugar-acid communities are generally more similar to the sugar than the acid community, which may be explained by family-level asymmetries in nutrient benefits. Overall, our results suggest that regularities in how nutrients interact may help predict community responses to dietary changes.

Enhanced glycolic acid yield through xylose and cellobiose utilization by metabolically engineered Escherichia coli

Microbial biorefinery is a promising route toward sustainable production of glycolic acid (GA), a valuable raw material for various industries. However, inherent microbial GA production has limited substrate consumption using either D-xylose or D-glucose as carbon catabolite repression (CCR) averts their co-utilization. To bypass CCR, a GA-producing strain using D-xylose via Dahms pathway was engineered to allow cellobiose uptake. Unlike glucose, cellobiose was assimilated and intracellularly degraded without repressing D-xylose uptake. The final GA-producing E. coli strain (CLGA8) has an overexpressed cellobiose phosphorylase (cep94A) from Saccharophagus degradans 2-40 and an activated glyoxylate shunt pathway. Expression of cep94A improved GA production reaching the maximum theoretical yield (0.51 g GA g^-1 xylose), whereas activation of glyoxylate shunt pathway enabled GA production from cellobiose, which further increased the GA titer (2.25 g GA L^-1). To date, this is the highest reported GA yield from D-xylose through Dahms pathway in an engineered E. coli with cellobiose as co-substrate.

Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity

BACKGROUND

The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis.

RESULTS

One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with aminoglycoside, beta-lactam, bacitracin, cationic antimicrobial peptide, fluoroquinolone, and rifampin. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei.

CONCLUSIONS

Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.

Genome analyses of uncultured TG2/ZB3 bacteria in 'Margulisbacteria' specifically attached to ectosymbiotic spirochetes of protists in the termite gut

We investigated the phylogenetic diversity, localisation and metabolism of an uncultured bacterial clade, Termite Group 2 (TG2), or ZB3, in the termite gut, which belongs to the candidate phylum 'Margulisbacteria'. We performed 16S rRNA amplicon sequencing analysis and detected TG2/ZB3 sequences in 40 out of 72 termite and cockroach species, which exclusively constituted a monophyletic cluster in the TG2/ZB3 clade. Fluorescence in situ hybridisation analysis in lower termites revealed that these bacteria are specifically attached to ectosymbiotic spirochetes of oxymonad gut protists. Draft genomes of four TG2/ZB3 phylotypes from a small number of bacterial cells were reconstructed, and functional genome analysis suggested that these bacteria hydrolyse and ferment cellulose/cellobiose to H2, CO2, acetate and ethanol. We also assembled a draft genome for a partner Treponema spirochete and found that it encoded genes for reductive acetogenesis from H2 and CO2. We hypothesise that the TG2/ZB3 bacteria we report here are commensal or mutualistic symbionts of the spirochetes, exploiting the spirochetes as H2 sinks. For these bacteria, we propose a novel genus, 'Candidatus Termititenax', which represents a hitherto uncharacterised class-level clade in 'Margulisbacteria'. Our findings add another layer, i.e., cellular association between bacteria, to the multi-layered symbiotic system in the termite gut.

Efficient Biotransformation of Luteolin to Isoorientin through Adjusting Induction Strategy, Controlling Acetic Acid, and Increasing UDP-Glucose Supply in Escherichia coli

Isoorientin is a C-glycosylated derivative of luteolin and exhibits a number of biological properties. In this study, multiple strategies were adopted to improve isoorientin production from luteolin in Escherichia coli. Isoorientin production was improved substantially by adjusting induction strategies and controlling acetic acid accumulation, with maximum isoorientin production reaching 826 mg/L. Additionally, a novel UDP-glucose synthesis pathway was reconstructed in E. coli through cellobiose phosphorylase-catalyzed phosphorolysis of cellobiose for the production of glucose 1-phosphate, which serves as a precursor in UDP-glucose formation. The results from two mechanisms of UDP-glucose formation in E. coli, cellobiose phosphorolysis and sucrose phosphorolysis, were compared. Increasing the UDP-glucose supply resulted in maximal isoorientin production reaching 1371 mg/L. Finally, isoorientin (1059 mg) was obtained from 1 L of fermentation broth by simple purification steps with a yield of 81.5%. Therefore, this study provides an efficient method for isoorientin production and a novel UDP-glucose synthesis pathway.

Simultaneous consumption of cellobiose and xylose by Bacillus coagulans to circumvent glucose repression and identification of its cellobiose-assimilating operons

BACKGROUND

The use of inedible lignocellulosic biomasses for biomanufacturing provides important environmental and economic benefits for society. Efficient co-utilization of lignocellulosic biomass-derived sugars, primarily glucose and xylose, is critical for the viability of lignocellulosic biorefineries. However, the phenomenon of glucose repression prevents co-utilization of both glucose and xylose in cellulosic hydrolysates.

RESULTS

To circumvent glucose repression, co-utilization of cellobiose and xylose by Bacillus coagulans NL01 was investigated. During co-fermentation of cellobiose and xylose, B. coagulans NL01 simultaneously consumed the sugar mixtures and exhibited an improved lactic acid yield compared with co-fermentation of glucose and xylose. Moreover, the cellobiose metabolism of B. coagulans NL01 was investigated for the first time. Based on comparative genomic analysis, two gene clusters that encode two different operons of the cellobiose-specific phosphoenolpyruvate-dependent phosphotransferase system (assigned as CELO1 and CELO2) were identified. For CELO1, five genes were arranged as celA (encoding EIIA^cel), celB (encoding EIIB^cel), celC (encoding EIIC^cel), pbgl (encoding 6-phospho-β-glucosidase), and celR (encoding a transcriptional regulator), and these genes were found to be ubiquitous in different B. coagulans strains. Based on gene knockout results, CELO1 was confirmed to be responsible for the transport and assimilation of cellobiose. For CELO2, the five genes were arranged as celR, celB, celA, celX (encoding DUF871 domain-containing protein), and celC, and these genes were only found in some B. coagulans strains. However, through a comparison of cellobiose fermentation by NL01 and DSM1 that only possess CELO1, it was observed that CELO2 might also play an important role in the utilization of cellobiose in vivo despite the fact that no pbgl gene was found. When CELO1 or CELO2 was expressed in Escherichia coli, the recombinant strain exhibited distinct cellobiose uptake and consumption.

CONCLUSIONS

This study demonstrated the cellobiose-assimilating pathway of B. coagulans and provided a new co-utilization strategy of cellobiose and xylose to overcome the obstacles that result from glucose repression in a biorefinery system.

Development of a novel cellulase biosensor that detects crystalline cellulose hydrolysis using a transcriptional regulator

Successful utilization of cellulose as renewable biomass depends on the development of economically feasible technologies, which can aid in enzymatic hydrolysis. In this study, we developed a whole-cell biosensor for detecting cellulolytic activity that relies on the recognition of cellobiose using the transcriptional factor CelR from Thermobifida fusca and transcriptional activation of its downstream gfp reporter gene. The fluorescence intensity of whole-cell biosensor, which was named as cellobiose-detectible genetic enzyme screening system (CBGESS), was directly proportional to the concentration of cellobiose. The strong fluorescence intensity of CBGESS demonstrated the ability to detect cellulolytic activity with two cellulosic substrates, carboxymethyl cellulose and p-nitrophenyl β-D-cellobioside in cellulase-expressing Escherichia coli. In addition, CBGESS easily sensed crystalline cellulolytic activity when commercial Celluclast 1.5L was dropped on an Avicel plate. Therefore, CBGESS is a powerful tool for detecting cellulolytic activity with high sensitivity in the presence of soluble or insoluble cellulosic substrates. CBGESS may be further applied to excavate novel cellulases or microbes from both genetic libraries and various environments.

Intracellular cellobiose metabolism and its applications in lignocellulose-based biorefineries

Complete hydrolysis of cellulose has been a key characteristic of biomass technology because of the limitation of industrial production hosts to use cellodextrin, the partial hydrolysis product of cellulose. Cellobiose, a β-1,4-linked glucose dimer, is a major cellodextrin of the enzymatic hydrolysis (via endoglucanase and exoglucanase) of cellulose. Conversion of cellobiose to glucose is executed by β-glucosidase. The complete extracellular hydrolysis of celluloses has several critical barriers in biomass technology. An alternative bioengineering strategy to make the bioprocessing less challenging is to engineer microbes with the abilities to hydrolyze and assimilate the cellulosic-hydrolysate cellodextrin. Microorganisms engineered to metabolize cellobiose rather than the monomeric glucose can provide several advantages for lignocellulose-based biorefineries. This review describes the recent advances and challenges in engineering efficient intracellular cellobiose metabolism in industrial hosts. This review also describes the limitations of and future prospectives in engineering intracellular cellobiose metabolism.

Biochemical properties of GH94 cellodextrin phosphorylase THA_1941 from a thermophilic eubacterium Thermosipho africanus TCF52B with cellobiose phosphorylase activity

A hypothetic gene (THA_1941) encoding a putative cellobiose phosphorylase (CBP) from Thermosipho africanus TCF52B has very low amino acid identities (less than 12%) to all known GH94 enzymes. This gene was cloned and over-expressed in Escherichia coli BL21(DE3). The recombinant protein was hypothesized to be a CBP enzyme and it showed an optimum temperature of 75 °C and an optimum pH of 7.5. Beyond its CBP activity, this enzyme can use cellobiose and long-chain cellodextrins with a degree of polymerization of greater than two as a glucose acceptor, releasing phosphate from glucose 1-phosphate. The catalytic efficiencies (k_cat/K_m) indicated that cellotetraose and cellopentaose were the best substrates for the phosphorolytic and reverse synthetic reactions, respectively. These results suggested that this enzyme was the first enzyme having both cellodextrin and cellobiose phosphorylases activities. Because it preferred cellobiose and cellodextrins to glucose in the synthetic direction, it was categorized as a cellodextrin phosphorylase (CDP). Due to its unique ability of the reverse synthetic reaction, this enzyme could be a potential catalyst for the synthesis of various oligosaccharides. The speculative function of this CDP in the carbohydrate metabolism of T. africanus TCF52B was also discussed.

A seven-gene cluster in Ruminiclostridium cellulolyticum is essential for signalization, uptake and catabolism of the degradation products of cellulose hydrolysis

BACKGROUND

Like a number of anaerobic and cellulolytic Gram-positive bacteria, the model microorganism Ruminiclostridium cellulolyticum produces extracellular multi-enzymatic complexes called cellulosomes, which efficiently degrade the crystalline cellulose. Action of the complexes on cellulose releases cellobiose and longer cellodextrins but to date, little is known about the transport and utilization of the produced cellodextrins in the bacterium. A better understanding of the uptake systems and fermentation of sugars derived from cellulose could have a major impact in the field of biofuels production.

RESULTS

We characterized a putative ABC transporter devoted to cellodextrins uptake, and a cellobiose phosphorylase (CbpA) in R. cellulolyticum. The genes encoding the components of the ABC transporter (a binding protein CuaA and two integral membrane proteins) and CbpA are expressed as a polycistronic transcriptional unit induced in the presence of cellobiose. Upstream, another polycistronic transcriptional unit encodes a two-component system (sensor and regulator), and a second binding protein CuaD, and is constitutively expressed. The products might form a three-component system inducing the expression of cuaABC and cbpA since we showed that CuaR is able to recognize the region upstream of cuaA. Biochemical analysis showed that CbpA is a strict cellobiose phosphorylase inactive on longer cellodextrins; CuaA binds to all cellodextrins (G2-G5) tested, whereas CuaD is specific to cellobiose and presents a higher affinity to this sugar. This results are in agreement with their function in transport and signalization, respectively. Characterization of a cuaD mutant, and its derivatives, indicated that the ABC transporter and CbpA are essential for growth on cellobiose and cellulose.

CONCLUSIONS

For the first time in a Gram-positive strain, we identified a three-component system and a conjugated ABC transporter/cellobiose phosphorylase system which was shown to be essential for the growth of the model cellulolytic bacterium R. cellulolyticum on cellobiose and cellulose. This efficient and energy-saving system of transport and phosphorolysis appears to be the major cellobiose utilization pathway in R. cellulolyticum, and seems well adapted to cellulolytic life-style strain. It represents a new way to enable engineered strains to utilize cellodextrins for the production of biofuels or chemicals of interest from cellulose.

Metabolic engineering of Agrobacterium sp. ATCC31749 for curdlan production from cellobiose

Curdlan is a commercial polysaccharide made by fermentation of Agrobacterium sp. Its anticipated expansion to larger volume markets demands improvement in its production efficiency. Metabolic engineering for strain improvement has so far been limited due to the lack of genetic tools. This research aimed to identify strong promoters and to engineer a strain that converts cellobiose efficiently to curdlan. Three strong promoters were identified and were used to install an energy-efficient cellobiose phosphorolysis mechanism in a curdlan-producing strain. The engineered strains were shown with enhanced ability to utilize cellobiose, resulting in a 2.5-fold increase in titer. The availability of metabolically engineered strain capable of producing β-glucan from cellobiose paves the way for its production from cellulose. The identified native promoters from Agrobacterium open up opportunities for further metabolic engineering for improved production of curdlan and other products. The success shown here marks the first such metabolic engineering effort in this microbe.

Fungal Enzymes for Bio-Products from Sustainable and Waste Biomass

Lignocellulose, the most abundant renewable carbon source on earth, is the logical candidate to replace fossil carbon as the major biofuel raw material. Nevertheless, the technologies needed to convert lignocellulose into soluble products that can then be utilized by the chemical or fuel industries face several challenges. Enzymatic hydrolysis is of major importance, and we review the progress made in fungal enzyme technology over the past few years with major emphasis on (i) the enzymes needed for the conversion of polysaccharides (cellulose and hemicellulose) into soluble products, (ii) the potential uses of lignin degradation products, and (iii) current progress and bottlenecks for the use of the soluble lignocellulose derivatives in emerging biorefineries.

Biofuels and bio-based chemicals from lignocellulose: metabolic engineering strategies in strain development

Interest in developing a sustainable technology for fuels and chemicals has unleashed tremendous creativity in metabolic engineering for strain development over the last few years. This is driven by the exceptionally recalcitrant substrate, lignocellulose, and the necessity to keep the costs down for commodity products. Traditional methods of gene expression and evolutionary engineering are more effectively used with the help of synthetic biology and -omics techniques. Compared to the last biomass research peak during the 1980s oil crisis, a more diverse range of microorganisms are being engineered for a greater variety of products, reflecting the broad applicability and effectiveness of today's gene technology. We review here several prominent and successful metabolic engineering strategies with emphasis on the following four areas: xylose catabolism, inhibitor tolerance, synthetic microbial consortium, and cellulosic oligomer assimilation.

Isobutanol production from cellobionic acid in Escherichia coli

Background

Liquid fuels needed for the global transportation industry can be produced from sugars derived from plant-based lignocellulosics. Lignocellulosics contain a range of sugars, only some of which (such as cellulose) have been shown to be utilizable by microorganisms capable of producing biofuels. Cellobionic acid makes up a small but significant portion of lignocellulosic degradation products, and had not previously been investigated as an utilizable substrate. However, aldonic acids such as cellobionic acid are the primary products of a promising new group of lignocellulosic-degrading enzymes, which makes this compound group worthy of study. Cellobionic acid doesn’t inhibit cellulose degradation enzymes and so its inclusion would increase lignocellulosic degradation efficiency. Also, its use would increase overall product yield from lignocellulose substrate. For these reasons, cellobionic acid has gained increased attention for cellulosic biofuel production.

Results

This study describes the discovery that Escherichia coli are naturally able to utilize cellobionic acid as a sole carbon source with efficiency comparable to that of glucose and the construction of an E. coli strain able to produce the drop-in biofuel candidate isobutanol from cellobionic acid. The gene primarily responsible for growth of E. coli on cellobionic acid is ascB, a gene previously thought to be cryptic (expressed only after incurring specific mutations in nearby regulatory genes). In addition to AscB, the ascB knockout strain can be complemented by the cellobionic acid phosphorylase from the fungus Neurospora crassa. An E. coli strain engineered to express the isobutanol production pathway was successfully able to convert cellobionic acid into isobutanol. Furthermore, to demonstrate potential application of this strain in a sequential two-step bioprocessing system, E. coli was grown on hydrolysate (that was degraded by a fungus) and was successfully able to produce isobutanol.

Conclusions

These results demonstrate that cellobionic acid is a viable carbon source for biofuel production. This work suggests that with further optimization, a bacteria-fungus co-culture could be used in decreased-cost biomass-based biofuel production systems.

A paradigm shift in biomass technology from complete to partial cellulose hydrolysis: lessons learned from nature

A key characteristic of current biomass technology is the requirement for complete hydrolysis of cellulose and hemicellulose, which stems from the inability of microbial strains to use partially hydrolyzed cellulose, or cellodextrin. The complete hydrolysis paradigm has been practiced over the past 4 decades with major enzyme companies perfecting their cellulase mix for maximal yield of monosaccharides, with corresponding efforts in strain development focus almost solely on the conversion of monosaccharides, not cellodextrin, to products. While still in its nascent infancy, a new paradigm requiring only partial hydrolysis has begun to take hold, promising a shift in the biomass technology at its fundamental core. The new paradigm has the potential to reduce the requirement for cellulase enzymes in the hydrolysis step and provides new strategies for metabolic engineers, synthetic biologists and alike in engineering fermenting organisms. Several recent publications reveal that microorganisms engineered to metabolize cellodextrins, rather than monomer glucose, can reap significant energy gains in both uptake and subsequent phosphorylation. These energetic benefits can in turn be directed for enhanced robustness and increased productivity of a bioprocess. Furthermore, the new cellodextrin metabolism endows the biocatalyst the ability to evade catabolite repression, a cellular regulatory mechanism that is hampering rapid conversion of biomass sugars to products. Together, the new paradigm offers significant advantages over the old and promises to overcome several critical barriers in biomass technology. More research, however, is needed to realize these promises, especially in discovery and engineering of cellodextrin transporters, in developing a cost-effective method for cellodextrin generation, and in better integration of cellodextrin metabolism to endogenous glycolysis.

Isobutanol production from cellobiose in Escherichia coli

Converting lignocellulosics into biofuels remains a promising route for biofuel production. To facilitate strain development for specificity and productivity of cellulosic biofuel production, a user friendly Escherichia coli host was engineered to produce isobutanol, a drop-in biofuel candidate, from cellobiose. A beta-glucosidase was expressed extracellularly by either excretion into the media, or anchoring to the cell membrane. The excretion system allowed for E. coli to grow with cellobiose as a sole carbon source at rates comparable to those with glucose. The system was then combined with isobutanol production genes in three different configurations to determine whether gene arrangement affected isobutanol production. The most productive strain converted cellobiose to isobutanol in titers of 7.64 ± 0.19 g/L with a productivity of 0.16 g/L/h. These results demonstrate that efficient cellobiose degradation and isobutanol production can be achieved by a single organism, and provide insight for optimization of strains for future use in a consolidated bioprocessing system for renewable production of isobutanol.

Biotechnological applications of bacterial protein secretion: from therapeutics to biofuel production

Recent years have witnessed significant progresses in engineering of recombinant protein secretion. The relatively simple secretion mechanisms, Type I and Type V (autotransporters), are increasingly used for secretion of recombinant proteins. The secretion level of target proteins varied from milligrams to grams per liter. The range of proteins was significantly expanded beyond medical application. Notable additions include biofuel productions from renewable feedstock. Despite the progress, almost all successes in the engineering efforts come with significant trials and errors, highlighting the need for a better understanding of secretion systems and rational based methods.