Bioethanol production involving recombinant C. thermocellum hydrolytic hemicellulase and fermentative microbes

Sustainable bioconversion of food waste into high-value products by immobilized enzymes to meet bio-economy challenges and opportunities - A review

Over the past few years, food waste has intensified much attention from the local public, national and international organizations as well as a wider household territory due to increasing environmental, social and economic concerns, climate change and scarcity of fossil fuel resources. On one aspect, food-processing waste represents a substantial ecological burden. On the other hand, these waste streams are rich in carbohydrates, proteins, and lipids, thus hold significant potential for biotransformation into an array of high-value compounds. Indeed, the high sugar, protein, and fat content render food waste streams as attractive feedstocks for enzymatic valorization given the plentiful volumes generated annually. Enzymes as industrial biocatalysts offer unique advantages over traditional chemical processes with regard to eco-sustainability, and process efficiency. Herein, an effort has been made to delineate immobilized enzyme-driven valorization of food waste streams into marketable products such as biofuels, bioactive compounds, biodegradable plastics, prebiotics, sweeteners, rare sugars, surfactants, etc. Current challenges and prospects are also highlighted with respect to the development of industrially adaptable biocatalytic systems to achieve the ultimate objectives of sustainable manufacturing combined with minimum waste generation. Applications-based strategies to enzyme immobilization are imperative to design cost-efficient and sustainable industrially applicable biocatalysts. With a deeper apprehension of support material influences, and analyzing the extreme environment, enzymes might have significant potential in improving the overall sustainability of food processing.

A Review on Bioconversion of Agro-Industrial Wastes to Industrially Important Enzymes

Agro-industrial waste is highly nutritious in nature and facilitates microbial growth. Most agricultural wastes are lignocellulosic in nature; a large fraction of it is composed of carbohydrates. Agricultural residues can thus be used for the production of various value-added products, such as industrially important enzymes. Agro-industrial wastes, such as sugar cane bagasse, corn cob and rice bran, have been widely investigated via different fermentation strategies for the production of enzymes. Solid-state fermentation holds much potential compared with submerged fermentation methods for the utilization of agro-based wastes for enzyme production. This is because the physical⁻chemical nature of many lignocellulosic substrates naturally lends itself to solid phase culture, and thereby represents a means to reap the acknowledged potential of this fermentation method. Recent studies have shown that pretreatment technologies can greatly enhance enzyme yields by several fold. This article gives an overview of how agricultural waste can be productively harnessed as a raw material for fermentation. Furthermore, a detailed analysis of studies conducted in the production of different commercially important enzymes using lignocellulosic food waste has been provided.

Exploitation of Food Industry Waste for High-Value Products

A growing global population leads to an increasing demand for food production and the processing industry associated with it and consequently the generation of large amounts of food waste. This problem is intensified due to slow progress in the development of effective waste management strategies and measures for the proper treatment and disposal of waste. Food waste is a reservoir of complex carbohydrates, proteins, lipids, and nutraceuticals and can form the raw materials for commercially important metabolites. The current legislation on food waste treatment prioritises the prevention of waste generation and least emphasises disposal. Recent valorisation studies for food supply chain waste opens avenues to the production of biofuels, enzymes, bioactive compounds, biodegradable plastics, and nanoparticles among many other molecules.

Bioethanol production from hemicellulose rich Populus nigra involving recombinant hemicellulases from Clostridium thermocellum

Bioethanol was produced from poplar leafy biomass rich in hemicelluloses content involving recombinant Clostridium thermocellum hemicellulases and pentose sugar utilizing Candida shehatae. FT-IR analysis revealed effective AFEX pretreatment of poplar leaves. Repetitive batch strategy yielded ∼1.5-fold rise in cell biomass and specific activity of both, acetylxylanesterase (Axe) and GH43 hemicellulase. TLC and HPAEC exhibited xylose and arabinose release from hydrolyzed biomass. SSF trial with 1% (wv(-1)) pretreated poplar and mixed enzymes showed ∼1.5-fold higher ethanol titre as compared with SHF. The shake flask SSF with 5% (wv(-1)) pretreated poplar furnished 4.56 and 5.43gL(-1) ethanol with Axe and mixed enzymes, respectively. Whereas, bioreactor scale-up exhibited ∼1.25-fold increase in ethanol titres (5.68, 6.75gL(-1)) as compared with shake flask with an yield of 0.295 (gg(-1)) and 0.351 (gg(-1)), respectively with Axe and mixed enzymes.

Construction of GH16 β-glucanase mini-cellulosomes to improve the nutritive value of barley-based diets for broilers

Anaerobic cellulolytic bacteria organize a comprehensive range of cellulases and hemicellulases in high molecular weight multienzyme complexes termed cellulosomes. Integration of cellulosomal components occurs via highly ordered protein-protein interactions between cohesins and dockerins. This paper reports the production of mini-cellulosomes containing one (GH16-1C) or three (GH16-3C) copies of Clostridium thermocellum glucanase 16A (CtGlc16A). Barley β-1,3-1,4-glucans are known to be antinutritive for monogastric animals, particularly for poultry. GH16-1C and GH16-3C were used to supplement barley-based diets for broilers. The data revealed that the two mini-cellulosomes effectively improved the nutritive value of barley-based diets for broilers. Analysis of mini-cellulosome molecular integrity revealed that linker sequences separating protein domains in scaffoldins and cellulosomal catalytic units are highly susceptible to proteolytic attack in vivo. The data suggest that linker protection could result in further improvements in enzyme efficacy to improve the nutritive value of barley-based diets for monogastric animals.

Crystallization and preliminary X-ray crystallographic analysis of a novel α-L-arabinofuranosidase (CtGH43) from Clostridium thermocellum ATCC 27405

The truncated carbohydrate-active enzyme belonging to family 43 glycoside hydrolase from Clostridium thermocellum (CtGH43) is an α-L-arabinofuranosidase that in combination with endoxylanase leads to complete breakdown of L-arabinosyl-substituted xylans. The recombinant enzyme CtGH43 from C. thermocellum was overexpressed in Escherichia coli and purified by immobilized metal-ion affinity chromatography. The recombinant CtGH43 has a molecular mass of 35.86 kDa. Preliminary structural characterization was carried out on CtGH43 crystallized from different conditions, which gave either cube-shaped or brick-shaped crystals. These diffracted to a resolution of 1.65 Å for the cubic form and 1.1 Å for the monoclinic form. Molecular replacement was used to solve the CtGH43 structure.

Bioethanol production from leafy biomass of mango (Mangifera indica) involving naturally isolated and recombinant enzymes

The present study describes the usage of dried leafy biomass of mango (Mangifera indica) containing 26.3% (w/w) cellulose, 54.4% (w/w) hemicellulose, and 16.9% (w/w) lignin, as a substrate for bioethanol production from Zymomonas mobilis and Candida shehatae. The substrate was subjected to two different pretreatment strategies, namely, wet oxidation and an organosolv process. An ethanol concentration (1.21 g/L) was obtained with Z. mobilis in a shake-flask simultaneous saccharification and fermentation (SSF) trial using 1% (w/v) wet oxidation pretreated mango leaves along with mixed enzymatic consortium of Bacillus subtilis cellulase and recombinant hemicellulase (GH43), whereas C. shehatae gave a slightly higher (8%) ethanol titer of 1.31 g/L. Employing 1% (w/v) organosolv pretreated mango leaves and using Z. mobilis and C. shehatae separately in the SSF, the ethanol titers of 1.33 g/L and 1.52 g/L, respectively, were obtained. The SSF experiments performed with 5% (w/v) organosolv-pretreated substrate along with C. shehatae as fermentative organism gave a significantly enhanced ethanol titer value of 8.11 g/L using the shake flask and 12.33 g/L at the bioreactor level. From the bioreactor, 94.4% (v/v) ethanol was recovered by rotary evaporator with 21% purification efficiency.

Statistical Optimization of Fermentation Process Parameters by Taguchi Orthogonal Array Design for Improved Bioethanol Production

The statistical optimization of different fermentation process parameters in SSF of mixed MAA and organosolv pretreated 1% (w v−1) wild grass, namely, recombinant Clostridium thermocellum hydrolytic enzymes’ volume (GH5 cellulase, GH43 hemicellulase), fermentative microbes’ inoculum volume (Saccharomyces cerevisiae, Candida shehatae), pH, and temperature, was accomplished by Taguchi orthogonal array design. The optimized parameters in 100 mL of fermentation medium were (%, v v−1) as follows: 1.0, recombinant GH5 cellulase (5.7 mg−1, 0.45 mg mL−1); 2.0, recombinant GH43 hemicellulase (3.7 U mg−1, 0.32 mg mL−1); 1.5, S. cerevisiae (3.9 × 108 cells mL−1); 0.25, C. shehatae (2.7 × 107 cells mL−1); pH, 4.3; and temperature, 35∘C. pH with p-value 0.001 was found to be the most significant factor affecting SSF. The ethanol titre obtained in Taguchi optimized shake flask SSF was 2.0 g L−1 implying a 1.3-fold increase as compared to ethanol titre of 1.5 g L−1 in unoptimized shake flask SSF. A 1.5-fold gain in ethanol titre (3.1 g L−1) was obtained with the same substrate concentration in lab scale bioreactor on scaling up the shake flask SSF with Taguchi optimized process parameters.

Thermostable recombinant β-(1→4)-mannanase from C. thermocellum: biochemical characterization and manno-oligosaccharides production

Functional attributes of a thermostable β-(1→4)-mannanase were investigated from Clostridium thermocellum ATCC 27405. Its sequence comparison the exhibited highest similarity with Man26B of C. thermocellum F1. The full length CtManf and truncated CtManT were cloned in the pET28a(+) vector and expressed in E. coli BL21(DE3) cells, exhibiting 53 kDa and 38 kDa proteins, respectively. On the basis of the substrate specificity and hydrolyzed product profile, CtManf and CtManT were classified as β-(1→4)-mannanase. A 1.5 fold higher activity of both enzymes was observed by Ca(2+) and Mg(2+) salts. Plausible mannanase activity of CtManf was revealed by the classical hydrolysis pattern of carob galactomannan and the release of manno-oligosaccharides. Notably highest protein concentrations of CtManf and CtManT were achieved in tryptone yeast extract (TY) medium, as compared with other defined media. Both CtManf and CtManT displayed stability at 60 and 50 °C, respectively, and Ca(2+) ions imparted higher thermostability, resisting their melting up to 100 °C.

Highlights from the Indo-US workshop "Cyanobacteria: molecular networks to biofuels" held at Lonavala, India during December 16-20, 2012

An Indo-US workshop on "Cyanobacteria: molecular networks to biofuels" was held December 16-20, 2012 at Lagoona Resort, Lonavala, India. The workshop was jointly organized by two of the authors, PPW, a chemical engineer and LAS, a biologist, thereby ensuring a broad and cross-disciplinary participation. The main objective of the workshop was to bring researchers from academia and industry of the two countries together with common interests in cyanobacteria or microalgae and derived biofuels. An exchange of ideas resulted from a series of oral and poster presentations and, importantly, through one-on-one discussions during tea breaks and meals. Another key objective was to introduce young researchers of India to the exciting field of cyanobacterial physiology, modeling, and biofuels. PhD students and early stage researchers were especially encouraged to participate and about half of the 75 participants belonged to this category. The rest were comprised of senior researchers, including 13-15 invited speakers from each country. Overall, twenty-four institutes from 12 states of India were represented. The deliberations, which are being compiled in the present special issue, revolved mainly around molecular aspects of cyanobacterial biofuels including metabolic engineering, networks, genetic regulation, circadian rhythms, and stress responses. Representatives of some key funding agencies and industry provided a perspective and opportunities in the field and for bilateral collaboration. This article summarizes deliberations that took place at the meeting and provides a bird's eye view of the ongoing research in the field in the two countries.

Scale up and efficient bioethanol production involving recombinant cellulase (Glycoside hydrolase family 5) from Clostridium thermocellum

Background

Lignocellulose degrading fungal enzymes have been in use at industrial level for more than three decades. However, the main drawback is the high cost of the commercially available Trichoderma reesei cellulolytic enzymes.

Results

The hydrolytic performance of a novel Clostridium thermocellum cellulolytic recombinant cellulase expressed in Escherichia coli cells was compared with the naturally isolated cellulases in different modes of fermentation trials using steam explosion pretreated thatch grass and Zymomonas mobilis. Fourier transform infrared (FT-IR) spectroscopic analysis confirmed the efficiency of steam explosion pretreatment in significant release of free glucose moiety from complex lignocellulosic thatch grass. The recombinant GH5 cellulase with 1% (w v-1) substrate and Z. mobilis in shake flask separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF) trials demonstrated highest ethanol titre (0.99 g L-1, 1.2 g L-1) as compared to Bacillus subtilis (0.51 g L-1, 0.72 g L-1) and Trichoderma reesei (0.67 g L-1, 0.94 g L-1). A 5% (w v-1) substrate with recombinant enzyme in shake flask SSF resulted in a 7 fold increment of ethanol titre (8.8 g L-1). The subsequent scale up in a 2 L bioreactor with 1 L working volume yielded 16.13 g L-1 ethanol titre implying a 2 fold upturn. The rotary evaporator based product recovery from bioreactor contributed 94.4 (%, v v-1) pure ethanol with purification process efficiency of 22.2%.

Conclusions

The saccharification of steam exploded thatch grass (Hyparrhenia rufa) by recombinant cellulase (GH5) along with Z. mobilis in bioethanol production was studied for the first time. The effective pretreatment released substantial hexose sugars from cellulose as confirmed by FT-IR studies. In contrast to two modes of fermentation, SSF processes utilizing recombinant C. thermocellum enzymes have the capability of yielding a value-added product, bioethanol with the curtailment of the production costs in industry.

Novel perspectives for evolving enzyme cocktails for lignocellulose hydrolysis in biorefineries

The unstable and uncertain availability of petroleum sources as well as rising cost of fuels have shifted global efforts to utilize renewable resources for the production of greener energy and a replacement which can also meet the high energy demand of the world. Bioenergy routes suggest that atmospheric carbon can be cycled through biofuels in carefully designed systems for sustainability. Significant potential exists for bioconversion of biomass, the most abundant and also the most renewable biomaterial on our planet. However, the requirements of enzyme complexes which act synergistically to unlock and saccharify polysaccharides from the lignocellulose complex to fermentable sugars incur major costs in the overall process and present a great challenge. Currently available cellulase preparations are subject to tight induction and regulation systems and also suffer inhibition from various end products. Therefore, more potent and efficient enzyme preparations need to be developed for the enzymatic saccharification process to be more economical. Approaches like enzyme engineering, reconstitution of enzyme mixtures and bioprospecting for superior enzymes are gaining importance. The current scenario, however, also warrants the need for research and development of integrated biomass production and conversion systems.

Lignocellulosic fermentation of wild grass employing recombinant hydrolytic enzymes and fermentative microbes with effective bioethanol recovery

Simultaneous saccharification and fermentation (SSF) studies of steam exploded and alkali pretreated different leafy biomass were accomplished by recombinant Clostridium thermocellum hydrolytic enzymes and fermentative microbes for bioethanol production. The recombinant C. thermocellum GH5 cellulase and GH43 hemicellulase genes expressed in Escherichia coli cells were grown in repetitive batch mode, with the aim of enhancing the cell biomass production and enzyme activity. In batch mode, the cell biomass (A_600 nm) of E. coli cells and enzyme activities of GH5 cellulase and GH43 hemicellulase were 1.4 and 1.6 with 2.8 and 2.2 U·mg⁻¹, which were augmented to 2.8 and 2.9 with 5.6 and 3.8 U·mg⁻¹ in repetitive batch mode, respectively. Steam exploded wild grass (Achnatherum hymenoides) provided the best ethanol titres as compared to other biomasses. Mixed enzyme (GH5 cellulase, GH43 hemicellulase) mixed culture (Saccharomyces cerevisiae, Candida shehatae) system gave 2-fold higher ethanol titre than single enzyme (GH5 cellulase) single culture (Saccharomyces cerevisiae) system employing 1% (w/v) pretreated substrate. 5% (w/v) substrate gave 11.2 g·L⁻¹ of ethanol at shake flask level which on scaling up to 2 L bioreactor resulted in 23 g·L⁻¹ ethanol. 91.6% (v/v) ethanol was recovered by rotary evaporator with 21.2% purification efficiency.

A novel α-L-arabinofuranosidase of family 43 glycoside hydrolase (Ct43Araf) from Clostridium thermocellum

The study describes a comparative analysis of biochemical, structural and functional properties of two recombinant derivatives from Clostridium thermocellum ATCC 27405 belonging to family 43 glycoside hydrolase. The family 43 glycoside hydrolase encoding α-L-arabinofuranosidase (Ct43Araf) displayed an N-terminal catalytic module CtGH43 (903 bp) followed by two carbohydrate binding modules CtCBM6A (405 bp) and CtCBM6B (402 bp) towards the C-terminal. Ct43Araf and its truncated derivative CtGH43 were cloned in pET-vectors, expressed in Escherichia coli and functionally characterized. The recombinant proteins displayed molecular sizes of 63 kDa (Ct43Araf) and 34 kDa (CtGH43) on SDS-PAGE analysis. Ct43Araf and CtGH43 showed optimal enzyme activities at pH 5.7 and 5.4 and the optimal temperature for both was 50°C. Ct43Araf and CtGH43 showed maximum activity with rye arabinoxylan 4.7 Umg(-1) and 5.0 Umg(-1), respectively, which increased by more than 2-fold in presence of Ca(2+) and Mg(2+) salts. This indicated that the presence of CBMs (CtCBM6A and CtCBM6B) did not have any effect on the enzyme activity. The thin layer chromatography and high pressure anion exchange chromatography analysis of Ct43Araf hydrolysed arabinoxylans (rye and wheat) and oat spelt xylan confirmed the release of L-arabinose. This is the first report of α-L-arabinofuranosidase from C. thermocellum having the capacity to degrade both p-nitrophenol-α-L-arabinofuranoside and p-nitrophenol-α-L-arabinopyranoside. The protein melting curves of Ct43Araf and CtGH43 demonstrated that CtGH43 and CBMs melt independently. The presence of Ca(2+) ions imparted thermal stability to both the enzymes. The circular dichroism analysis of CtGH43 showed 48% β-sheets, 49% random coils but only 3% α-helices.

Genomic evaluation of Thermoanaerobacter spp. for the construction of designer co-cultures to improve lignocellulosic biofuel production

The microbial production of ethanol from lignocellulosic biomass is a multi-component process that involves biomass hydrolysis, carbohydrate transport and utilization, and finally, the production of ethanol. Strains of the genus Thermoanaerobacter have been studied for decades due to their innate abilities to produce comparatively high ethanol yields from hemicellulose constituent sugars. However, their inability to hydrolyze cellulose, limits their usefulness in lignocellulosic biofuel production. As such, co-culturing Thermoanaerobacter spp. with cellulolytic organisms is a plausible approach to improving lignocellulose conversion efficiencies and yields of biofuels. To evaluate native lignocellulosic ethanol production capacities relative to competing fermentative end-products, comparative genomic analysis of 11 sequenced Thermoanaerobacter strains, including a de novo genome, Thermoanaerobacter thermohydrosulfuricus WC1, was conducted. Analysis was specifically focused on the genomic potential for each strain to address all aspects of ethanol production mentioned through a consolidated bioprocessing approach. Whole genome functional annotation analysis identified three distinct clades within the genus. The genomes of Clade 1 strains encode the fewest extracellular carbohydrate active enzymes and also show the least diversity in terms of lignocellulose relevant carbohydrate utilization pathways. However, these same strains reportedly are capable of directing a higher proportion of their total carbon flux towards ethanol, rather than non-biofuel end-products, than other Thermoanaerobacter strains. Strains in Clade 2 show the greatest diversity in terms of lignocellulose hydrolysis and utilization, but proportionately produce more non-ethanol end-products than Clade 1 strains. Strains in Clade 3, in which T. thermohydrosulfuricus WC1 is included, show mid-range potential for lignocellulose hydrolysis and utilization, but also exhibit extensive divergence from both Clade 1 and Clade 2 strains in terms of cellular energetics. The potential implications regarding strain selection and suitability for industrial ethanol production through a consolidated bioprocessing co-culturing approach are examined throughout the manuscript.