Secretory pathway of cellulase: a mini-review

Impact of a random TN5 mutation on endoglucanase secretion in ruminal cellulolytic Escherichia coli

OBJECTIVE

Most protein secretion systems are found in gram-negative bacteria, but the mechanism of endoglucanase (BcsZ) secretion in Escherichia coli (E. coli) remains unclear.

METHODS

In this study, we used JBZ-DH5α (which overexpresses BcsZ on the E. coli DH5α genome) as the initial strain. A mutant library was created by randomly inserting the TN5 transposon into the genome, and mutants with reduced transparent circles were identified on Congo red plates. The insertion sites of transposons in the genome were determined through whole-genome sequencing.

RESULTS

The results revealed that the genes rnc, lon, and suhB, which encode RNC-ribonuclease III (RNC), LON-protease (LON), and SuhB-inositol phosphatase (SuhB), respectively, were disrupted. BcsZ secretion decreased in E. coli DH5α when the lon, rnc, or suhB genes were deleted, but the overexpression of these genes restored their secretion levels.

CONCLUSION

These findings suggest that the lon, rnc, and suhB genes play a role in BcsZ secretion in E. coli, potentially enhancing our knowledge of BcsZ secretion and offering a strategy to increase protein secretion in E. coli as a cell factory.

Membrane Vesicles Can Contribute to Cellulose Degradation by Teredinibacter turnerae, a Cultivable Intracellular Endosymbiont of Shipworms

Teredinibacter turnerae is a cultivable cellulolytic Gammaproteobacterium (Cellvibrionaceae) that commonly occurs as an intracellular endosymbiont in the gills of wood-eating bivalves of the family Teredinidae (shipworms). The genome of T. turnerae encodes a broad range of enzymes that deconstruct cellulose, hemicellulose and pectin and contribute to wood (lignocellulose) digestion in the shipworm gut. However, the mechanisms by which T. turnerae secretes lignocellulolytic enzymes are incompletely understood. Here, we show that T. turnerae cultures grown on carboxymethyl cellulose (CMC) produce membrane vesicles (MVs) that include a variety of proteins identified by liquid chromatography-mass spectrometry (LC-MS/MS) as carbohydrate-active enzymes (CAZymes) with predicted activities against cellulose, hemicellulose and pectin. Reducing sugar assays and zymography confirm that these MVs exhibit cellulolytic activity, as evidenced by the hydrolysis of CMC. Additionally, these MVs were enriched with TonB-dependent receptors, which are essential to carbohydrate and iron acquisition by free-living bacteria. These observations indicate a potential role for MVs in lignocellulose utilisation by T. turnerae in the free-living state, suggest possible mechanisms for host-symbiont interaction and may be informative for commercial applications such as enzyme production and lignocellulosic biomass conversion.

Membrane vesicles can contribute to cellulose degradation by Teredinibacter turnerae, a cultivable intracellular endosymbiont of shipworms

Teredinibacter turnerae is a cultivable cellulolytic Gammaproteobacterium (Cellvibrionaceae) that commonly occurs as an intracellular endosymbiont in the gills of wood-eating bivalves of the family Teredinidae (shipworms). The genome of T. turnerae encodes a broad range of enzymes that deconstruct cellulose, hemicellulose, and pectin and contribute to wood (lignocellulose) digestion in the shipworm gut. However, the mechanisms by which T. turnerae secretes lignocellulolytic enzymes are incompletely understood. Here, we show that T. turnerae cultures grown on carboxymethyl cellulose (CMC) produce membrane vesicles (MVs) that include a variety of proteins identified by LC-MS/MS as carbohydrate-active enzymes (CAZymes) with predicted activities against cellulose, hemicellulose, and pectin. Reducing sugar assays and zymography confirm that these MVs exhibit cellulolytic activity, as evidenced by the hydrolysis of CMC. Additionally, these MVs were enriched with TonB-dependent receptors, which are essential to carbohydrate and iron acquisition by free-living bacteria. These observations indicate a potential role for MVs in lignocellulose utilization by T. turnerae in the free-living state, suggest possible mechanisms for host-symbiont interaction, and may be informative for commercial applications such as enzyme production and lignocellulosic biomass conversion.

Genome-wide analysis of the mulberry (Morus abla L.) GH9 gene family and the functional characterization of MaGH9B6 during the development of the abscission zone

Plant glycoside hydrolase family 9 genes (GH9s) are widely distributed in plants and involved in a variety of cellular and physiological processes. In the current study, nine GH9 genes were identified in the mulberry and were divided into two subfamilies based on the phylogenetic analysis. Conserved motifs and gene structure analysis suggested that the evolution of the two subfamilies is relatively conserved and the glycoside hydrolase domain almost occupy the entire coding region of the GH9s gene. Only segmental duplication has played a role in the expansion of gene family. Collinearity analysis showed that mulberry GH9s had the closest relationship with poplar GH9s. MaGH9B1, MaGH9B6, MaGH9B5, and MaGH9B3 were detected to have transcript accumulation in the stalk of easy-to drop mature fruit drop, suggesting that these could play a role in mulberry fruit drop. Multiple cis-acting elements related to plant hormones and abiotic stress responses were found in the mulberry GH9 promoter regions and showed different activities under exogenous abscisic acid (ABA) and 2,4- dichlorophenoxyacetic acid (2,4-D) stresses. We found that the lignin content in the fruit stalk decreased with the formation of the abscission zone (AZ), which could indirectly reflect the formation process of the AZ. These results provide a theoretical basis for further research on the role of GH9s in mulberry abscission.

Enzymatic degradation of cellulose in soil: A review

Cellulose degradation is a critical process in soil ecosystems, playing a vital role in nutrient cycling and organic matter decomposition. Enzymatic degradation of cellulosic biomass is the most sustainable and green method of producing liquid biofuel. It has gained intensive research interest with future perspective as the majority of terrestrial lignocellulose biomass has a great potential to be used as a source of bioenergy. However, the recalcitrant nature of lignocellulose limits its use as a source of energy. Noteworthy enough, enzymatic conversion of cellulose biomass could be a leading future technology. Fungal enzymes play a central role in cellulose degradation. Our understanding of fungal cellulases has substantially redirected in the past few years with the discovery of a new class of enzymes and Cellulosome. Efforts have been made from time to time to develop an economically viable method of cellulose degradation. This review provides insights into the current state of knowledge regarding cellulose degradation in soil and identifies areas where further research is needed.

Disruption of vacuolar protein sorting receptor gene Poxvps10 improves cellulolytic enzyme production by Penicillium oxalicum

Penicillium oxalicum can secrete numerous of plant biomass-degrading enzymes, but limited information is available regarding the mechanisms associated with their secretion. In the Golgi-to-vacuole pathway, the type I transmembrane receptor Vps10p is involved in the sorting of the soluble vacuolar proteins and can also target recombinant and aberrant proteins from the Golgi to the vacuole for degradation. Here, we used the combination of phenotypic characterization and comparative secretome analysis to explore the effect of disruption of the vps10 gene in P. oxalicum (Poxvps10) on endogenous cellulolytic enzyme secretion. The study found that PoxVps10p is required for the targeting and delivery of vacuolar PoxCpyA to the vacuole in P. oxalicum. Poxvps10p deletion enhances extracellular protein and cellulase production by P. oxalicum when the cells are grown on a cellulosic substrate (wheat bran and Avicel). Furthermore, secretome analysis revealed higher relative amount of cellulases, lytic polysaccharide monooxygenase and post-translational modification-related proteins in the ΔPoxvps10 mutant than in the wild-type (WT) strain, which may explain the higher cellulase production by the ΔPoxvps10 than the WT strain. This study thus provides a new target for manipulating the secretory pathway to enhance the cellulolytic enzyme production.

Valorization of Agro-industrial Discards in Fermentation for the Production of Cellulase Enzyme

Cellulases are commercially important enzymes with application in various industries such as biofuel, detergent, food processing, brewery, pulp and paper. To make its production cost-effective, a preferred method is to use solid-state fermentation and with use of inexpensive substrates. Solid-state fermentation is an alternative culturing method and yields higher enzymes compared to submerged fermentation. In the current study, Aspergillus niger was isolated and further developed as inoculum for solid-state fermentation. Agroindustrial discards like banana pseudostem, jackfruit waste were used as the substrates. The substrates were pretreated by acid and were characterized by FTIR analysis to confirm the presence of cellulosic content. Different concentrations of the substrates were attempted for fermentation and the yield of the enzyme was compared. The solid-state fermentation was stable for enzyme production as well as microbial growth. The cellulase activity per gram of the substrate (U/g) was obtained maximum for jackfruit waste-based media (17±1.1 U/g). Both the lignocellulosic substrates were potential substrates for the production of cellulase enzyme. With further optimization and scale-up, this could be a cheap and sustainable process. This study has validated agro-industrial waste’s bioconversion into value-added products that have a remarkable environmental and economic advantage.

Improving the Biocontrol Potential of Endophytic Bacteria Bacillus subtilis with Salicylic Acid against Phytophthora infestans-Caused Postharvest Potato Tuber Late Blight and Impact on Stored Tubers Quality

Potato (Solanum tuberosum L.) tubers are a highly important food crop in many countries due to their nutritional value and health-promoting properties. Postharvest disease caused by Phytophthora infestans leads to the significant decay of stored potatoes. The main objective of this study was to evaluate the effects of the endophytic bacteria, Bacillus subtilis (strain 10–4), or its combination with salicylic acid (SA), on some resistance and quality traits of stored Ph. infestans-infected potato tubers. The experiments were conducted using hydroponically grown potato mini-tubers, infected prior to storage with Ph. infestans, and then coated with B. subtilis, alone and in combination with SA, which were then stored for six months. The results revealed that infection with Ph. infestans significantly increased tuber late blight incidence (up to 90–100%) and oxidative and osmotic damage (i.e., malondialdehyde and proline) in tubers. These phenomena were accompanied by a decrease in starch, reducing sugars (RS), and total dry matter (TDM) contents and an increase in amylase (AMY) activity. Moreover, total glycoalkaloids (GA) (α-solanine, α-chaconine) notably increased in infected tubers, exceeding (by 1.6 times) permissible safe levels (200 mg/kg FW). Treatments with B. subtilis or its combination with SA decreased Ph. infestans-activated tuber late blight incidence (by 30–40%) and reduced oxidative and osmotic damages (i.e., malondialdehyde and proline) and AMY activity in stored, infected tubers. Additionally, these treatments decreased pathogen-activated GA accumulation and increased ascorbic acid in stored tubers. Thus, the results indicated that endophytic bacteria B. subtilis, individually, and especially in combination with SA, have the potential to increase potato postharvest resistance to late blight and improve tuber quality in long-term storage.

Heterologous production of cellulose- and starch-degrading hydrolases to expand Saccharomyces cerevisiae substrate utilization: Lessons learnt

Selected strains of Saccharomyces cerevisiae are used for commercial bioethanol production from cellulose and starch, but the high cost of exogenous enzymes for substrate hydrolysis remains a challenge. This can be addressed through consolidated bioprocessing (CBP) where S. cerevisiae strains are engineered to express recombinant glycoside hydrolases during fermentation. Looking back at numerous strategies undertaken over the past four decades to improve recombinant protein production in S. cerevisiae, it is evident that various steps in the protein production "pipeline" can be manipulated depending on the protein of interest and its anticipated application. In this review, we briefly introduce some of the strategies and highlight lessons learned with regards to improved transcription, translation, post-translational modification and protein secretion of heterologous hydrolases. We examine how host strain selection and modification, as well as enzyme compatibility, are crucial determinants for overall success. Finally, we discuss how lessons from heterologous hydrolase expression can inform modern synthetic biology and genome editing tools to provide process-ready yeast strains in future. However, it is clear that the successful expression of any particular enzyme is still unpredictable and requires a trial-and-error approach.

Synthesis of digestive enzymes, food processing, and nutrient absorption in decapod crustaceans: a comparison to the mammalian model of digestion

The ∼15.000 decapod crustaceans that are mostly omnivorous have evolved a structurally and functionally complex digestive system. They have highly effective cuticular chewing and filtering structures in the stomach, which are regularly renewed by moulting. Decapods produce a broad range of digestive enzymes including chitinases, cellulases, and collagenases with unique properties. These enzymes are synthesized in the F-cells of the hepatopancreas and are encoded in the genome as pre-pro-proteins. In contrast to mammals, they are stored in a mature form in the lumen of the stomach to await the next meal, and therefore, the enzymes are particularly stable. The fat emulsifiers are fatty acyl-dipeptides rather than bile salts. After mechanical and chemical processing of the food in the cardiac stomach, the chyme is filtered by two unique filter systems of different mesh-size. The filtrate is then transferred to the hepatopancreas where the nutrients are absorbed by the R-cells, mostly via carriers, resembling nutrient absorption in the small intestine of mammals. The absorbed nutrients are used to fuel the metabolism of the hepatopancreas, are supplied to other organs, and are stored in the R-cells as glycogen and lipid reserves. Export lipids are secreted from the R-cells into the haemolymph as high density lipoproteins that mainly consist of phospholipids. In contrast to mammals, the midgut tube and hindgut contribute only little to food processing and nutrient absorption. The oesophagus, stomach and hindgut are well innervated but the hepatopancreas lacks nerves. Hormone cells are abundant in the midgut and hepatopancreas epithelia. Microorganisms are often present in the intestine of decapods, but they are apparently not essential for digestion and nutrition.

Exploiting strain diversity and rational engineering strategies to enhance recombinant cellulase secretion by Saccharomyces cerevisiae

Consolidated bioprocessing (CBP) of lignocellulosic material into bioethanol has progressed in the past decades; however, several challenges still exist which impede the industrial application of this technology. Identifying the challenges that exist in all unit operations is crucial and needs to be optimised, but only the barriers related to the secretion of recombinant cellulolytic enzymes in Saccharomyces cerevisiae will be addressed in this review. Fundamental principles surrounding CBP as a biomass conversion platform have been established through the successful expression of core cellulolytic enzymes, namely β-glucosidases, endoglucanases, and exoglucanases (cellobiohydrolases) in S. cerevisiae. This review will briefly address the challenges involved in the construction of an efficient cellulolytic yeast, with particular focus on the secretion efficiency of cellulases from this host. Additionally, strategies for studying enhanced cellulolytic enzyme secretion, which include both rational and reverse engineering approaches, will be discussed. One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development. Furthermore, with the advancement in next-generation sequencing, studies that utilise this method of exploiting intra-strain diversity for industrially relevant traits will be reviewed. Finally, future prospects are discussed for the creation of ideal CBP strains with high enzyme production levels.Key Points• Several challenges are involved in the construction of efficient cellulolytic yeast, in particular, the secretion efficiency of cellulases from the hosts.• Strategies for enhancing cellulolytic enzyme secretion, a core requirement for CBP host microorganism development, include both rational and reverse engineering approaches.• One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development.

Endoglucanase activity of cellulolytic bacteria from lake sediments and its application in hydrophyte degradation

Hydrophytes are plants that grow in or on water. Their overgrowth adversely affects the ecosystem because of crowding out other aquatic organisms and polluting the environment with plant residue. In principle, cellulolytic bacteria can be used to degrade hydrophyte biomass. We here isolated and characterized four cellulolytic bacterial strains from Lake Donghu sediments (Wuhan, China) that are rich in organic matter and plant residues. The isolates (WDHS-01 to 04) represent Bacillus, Micromonospora and Streptomyces genera. The bacteria exhibited pronounced endoglucanase activities (from 0.022 to 0.064 U mL-1). They did not extensively degrade the emerged plant Canna indica L. However, in an Hydrilla verticillata (submerged plant) degradation medium, strain WDHS-02 exhibited a high degradation rate (54.91%), endoglucanase activity of 0.35 U mL-1 and the conversion rate of cellulose to reducing sugars of 7.15%. Correlation analysis revealed that bacterial endoglucanase activity was significantly correlated with the degradation rate, and acid detergent lignin, ash and cellulose content of the residual H. verticillata powder. In conclusion, the identified bacteria efficiently decomposed submerged plants without the need for acid-base pretreatment. They expand the set of known cellulolytic bacteria and can be used for natural degradation of submerged plants.

De novo genome assembly and comparative annotation reveals metabolic versatility in cellulolytic bacteria from cropland and forest soils

Cellulose, the most abundant polysaccharide in nature, is a rich source of renewable energy and sustains soil nutrients. Among the microorganisms known to degrade cellulose, bacteria are less studied compared to fungi. In the present work, we have investigated the culturable bacteria actively involved in cellulose degradation in forest and crop field soils. Based on clear zone formation and enzyme activity assay, we identified 7 bacterial strains positive for cellulose degradation. Of these, two most efficient strains (Bacillus cereus strains BHU1 and BHU2) were selected for whole genome sequencing, annotation, and information regarding GC content, number of genes, total subsystems, starch, and cellulose degradation pathways. Average nucleotide identity (ANI) showed more than 90% similarity between both the strains (BHU1 and BHU2) and with B. cereus ATCC 14579. Both the strains have genes and enzyme families like endoglucanase and β-glucosidase as evident from whole genome sequence. Cellulase containing gene families (GH5, GH8, GH1), and many other carbohydrate-degrading enzymes, were present in both the bacterial strains. Taken together, the results suggest that the strains were efficient in cellulose degradation, and can be used for energy generation and production of value-added product.

Extracellular vesicles carry cellulases in the industrial fungus Trichoderma reesei

BACKGROUND

Trichoderma reesei is the most important industrial producer of lignocellulolytic enzymes. These enzymes play an important role in biomass degradation leading to novel applications of this fungus in the biotechnology industry, specifically biofuel production. The secretory pathway of fungi is responsible for transporting proteins addressed to different cellular locations involving some cellular endomembrane systems. Although protein secretion is an extremely efficient process in T. reesei, the mechanisms underlying protein secretion have remained largely uncharacterized in this organism.

RESULTS

Here, we report for the first time the isolation and characterization of T. reesei extracellular vesicles (EVs). Using proteomic analysis under cellulose culture condition, we have confidently identified 188 vesicular proteins belonging to different functional categories. Also, we characterized EVs production using transmission electron microscopy in combination with light scattering analysis. Biochemical assays revealed that T. reesei extracellular vesicles have an enrichment of filter paper (FPase) and β-glucosidase activities in purified vesicles from 24, 72 and 96, and 72 and 96 h, respectively. Furthermore, our results showed that there is a slight enrichment of small RNAs inside the vesicles after 96 h and 120 h, and presence of hsp proteins inside the vesicles purified from T. reesei grown in the presence of cellulose.

CONCLUSIONS

This work points to important insights into a better understanding of the cellular mechanisms underlying the regulation of cellulolytic enzyme secretion in this fungus.

Advances and challenges in the production of extracellular thermoduric pullulanases by wild-type and recombinant microorganisms: a review

Thermoduric pullulanases, acting as starch-debranching enzymes, are required in many industrial applications, mainly in the production of concentrated glucose, maltose, and fructose syrups. To date, however, a single pullulanase, from Bacillus acidopullulyticus, is available on the market for industrial purposes. This review is an investigation of the major advances as well as the major challenges being faced with regard to optimization of the production of extracellular thermoduric pullulanases either by their original hosts or by recombinant organisms. The critical aspects linked to industrial pullulanase production, which should always be considered, are emphasized, including those parameters influencing solubility, thermostability, and catalytic efficiency of the enzyme. This review provides new insights for improving the production of extracellular thermoduric pullulanases in the hope that such information may facilitate their commercial utilization and potentially be applied to the development of other industrially relevant enzymes.

Tolerance against butanol stress by disrupting succinylglutamate desuccinylase inEscherichia coli

The four-carbon alcohol, butanol, is emerging as a promising biofuel and efforts have been undertaken to improve several microbial hosts for its production.

Degradation of bamboo lignocellulose by bamboo snout beetle Cyrtotrachelus buqueti in vivo and vitro: efficiency and mechanism

BACKGROUND

As an important biomass raw material, the lignocellulose in bamboo is of significant value in energy conversion. The conversion of bamboo lignocellulose into fermentable reducing sugar, i.e. the degradation of bamboo lignocellulose, is an important step in lignocellulose conversion. However, little research has focussed on excavating the enzymes and microbes that are related to the degradation of bamboo lignocellulose, which is important for its utilisation. This study used Cyrtotrachelus buqueti (bamboo snout beetle) to evaluate the efficiency of bamboo lignocellulose degradation.

RESULTS

RNA sequencing was conducted to sequence the transcriptome of the insect before and after feeding on bamboo shoots. The expression levels of genes encoding several carbohydrate-active enzymes, such as endoglucanase (evgtrinloc27093t1 and evgtrinloc16407t0) and laccase (evgtrinloc15173t0 and evgtrinloc11252t0), were found to be upregulated after feeding. Faecal component analysis showed that the degradation efficiencies of cellulose, hemicellulose and lignin were 61.82%, 87.65% and 69.05%, respectively. After 6 days of co-culture with crude enzymes in vitro, the degradation efficiencies of cellulose, hemicellulose and lignin in bamboo shoot particles (BSPs) were 24.98%, 37.52% and 26.67%, respectively. These results indicated that lignocellulosic enzymes and related enzymes within the insect itself co-degraded bamboo lignocellulose. These finding can potentially be used for the pre-treatment and enzymatic hydrolysis of bamboo lignocellulose.

CONCLUSION

Our results showed that intestinal digestive enzymes from C. buqueti degraded bamboo shoot lignocellulose both in vivo and in vitro. In addition, the expression levels of many carbohydrate-active enzyme (CAZyme) genes were upregulated in the transcriptome, including those for cellulase, xylanase and ligninase genes. Therefore, we proposed a scheme for applying the lignocellulolytic enzymes from C. buqueti to degrade bamboo lignocellulose using genetic, enzymatic and fermentation engineering techniques to overexpress the lignocellulolytic enzymes genes in vitro and obtain large quantities of enzymes that could efficiently degrade bamboo lignocellulose and be used for lignocellulose bioconversion.

Quantitative proteomic analysis reveals the ethanologenic metabolism regulation of Ethanoligenens harbinense by exogenous ethanol addition

BACKGROUND

H₂-ethanol-coproducing bacteria, as primary fermenters, play important roles in the microbiome of bioreactors for bioenergy production from organic wastewater or solid wastes. Ethanoligenens harbinense YUAN-3 is an anaerobic ethanol-H₂-fermenting bacterium. Ethanol is one of the main end-products of strain YUAN-3 that influence its fermentative process. Until recently, the molecular mechanism of metabolic regulation in strain YUAN-3 during ethanol accumulation has still been unclear. This study aims to elucidate the metabolic regulation mechanisms in strain YUAN-3, which contributes to effectively shape the microbiome for biofuel and bioenergy production from waste stream.

RESULTS

This study reports that ethanol stress altered the distribution of end-product yields in the H₂-ethanol-coproducing Ethanoligenens harbinense strain YUAN-3. Decreasing trends of hydrogen yield from 1888.6 ± 45.8 to 837 ± 64.7 mL L^-1 and acetic acid yield from 1767.7 ± 45 to 160.6 ± 44.7 mg L^-1 were observed in strain YUAN-3 with increasing exogenous ethanol (0 mM-200 mM). However, the ethanol yield of strain YUAN-3 increased by 15.1%, 30.1%, and 27.4% in 50 mM, 100 mM, and 200 mM ethanol stress, respectively. The endogenous ethanol accounted for 96.1% (w/w) in liquid end-products when exogenous ethanol of 200 mM was added. The molar ratio of ethanol to acetic acid increased 14 times (exogenous ethanol of 200 mM) compared to the control. iTRAQ-based quantitative proteomic analysis indicated that 263 proteins of strain YUAN-3 were differentially expressed in 50 mM, 100 mM, and 200 mM of exogenous ethanol. These proteins are mainly involved in amino acid transport and metabolism, central carbon metabolism, and oxidative stress response.

CONCLUSION

These differentially expressed proteins play important roles in metabolic changes necessary for growth and survival of strain YUAN-3 during ethanol stress. The up-regulation of bifunctional acetaldehyde-CoA/alcohol dehydrogenase (ADHE) was the main reason why ethanol production was enhanced, while hydrogen gas and acetic acid yields declined in strain YUAN-3 during ethanol stress. This study also provides a new approach for the enhancement of ethanologenesis by H₂-ethanol-coproducing bacteria through exogenous ethanol addition.

De novo transcriptome assembly of the bamboo snout beetle Cyrtotrachelus buqueti reveals ability to degrade lignocellulose of bamboo feedstock

BACKGROUND

The bamboo weevil Cyrtotrachelus buqueti, which is considered a pest species, damages bamboo shoots via its piercing-sucking mode of feeding. C. buqueti is well known for its ability to transform bamboo shoot biomass into nutrients and energy for growth, development and reproduction with high specificity and efficacy of bioconversion. Woody bamboo is a perennial grass that is a potential feedstock for lignocellulosic biomass because of its high growth rate and lignocellulose content. To verify our hypothesis that C. buqueti efficiently degrades bamboo lignocellulose, we assessed the bamboo lignocellulose-degrading ability of this insect through RNA sequencing for identifying a potential route for utilisation of bamboo biomass.

RESULTS

Analysis of carbohydrate-active enzyme (CAZyme) family genes in the developmental transcriptome of C. buqueti revealed 1082 unigenes, including 55 glycoside hydrolases (GH) families containing 309 GHs, 51 glycosyltransferases (GT) families containing 329 GTs, 8 carbohydrate esterases (CE) families containing 174 CEs, 6 polysaccharide lyases (PL) families containing 11 PLs, 8 auxiliary activities (AA) families containing 131 enzymes with AAs and 17 carbohydrate-binding modules (CBM) families containing 128 CBMs. We used weighted gene co-expression network analysis to analyse developmental RNA sequencing data, and 19 unique modules were identified in the analysis. Of these modules, the expression of MEyellow module genes was unique and the module included numerous CAZyme family genes. CAZyme genes in this module were divided into two groups depending on whether gene expression was higher in the adult/larval stages or in the egg/pupal stages. Enzyme assays revealed that cellulase activity was highest in the midgut whereas lignin-degrading enzyme activity was highest in the hindgut, consistent with findings from intestinal gene expression studies. We also analysed the expression of CAZyme genes in the transcriptome of C. buqueti from two cities and found that several genes were also assigned to CAZyme families. The insect had genes and enzymes associated with lignocellulose degradation, the expression of which differed with developmental stage and intestinal region.

CONCLUSION

Cyrtotrachelus buqueti exhibits lignocellulose degradation-related enzymes and genes, most notably CAZyme family genes. CAZyme family genes showed differences in expression at different developmental stages, with adults being more effective at cellulose degradation and larvae at lignin degradation, as well as at different regions of the intestine, with the midgut being more cellulolytic than the hindgut. This degradative system could be utilised for the bioconversion of bamboo lignocellulosic biomass.

Engineering Bacillus megaterium Strains To Secrete Cellulases for Synergistic Cellulose Degradation in a Microbial Community

Recent environmental concerns have intensified the need to develop systems to degrade waste biomass for use as an inexpensive carbon source for microbial chemical production. Current approaches to biomass utilization rely on pretreatment processes that include expensive enzymatic purification steps for the requisite cellulases. We aimed to engineer a synthetic microbial community to synergistically degrade cellulose by compartmentalizing the system with multiple specialized Bacillus megaterium strains. EGI1, an endoglucanase, and Cel9AT, a multimodular cellulase, were targeted for secretion from B. megaterium. A small library of signal peptides (SPs) with five amino acid linkers was selected to tag each cellulase for secretion from B. megaterium. Cellulase activity against amorphous cellulose was confirmed through a series of bioassays, and the most active SP constructs were identified as EGI1 with the LipA SP and Cel9AT with the YngK SP. The activity of the optimized cellulase secretion strains was characterized individually and in tandem to assess synergistic cellulolytic activity. The combination of EGI1 and Cel9AT yielded higher activity than either single cellulase. A coculture of EGI1 and Cel9AT secreting B. megaterium strains demonstrated synergistic behavior with higher activity than either monoculture. This cellulose degradation module can be further integrated with bioproduct synthesis modules to build complex systems for the production of high value molecules.

Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems

Evidence shows that bacteria contribute actively to the decomposition of cellulose and hemicellulose in forest soil; however, their role in this process is still unclear. Here we performed the screening and identification of bacteria showing potential cellulolytic activity from litter and organic soil of a temperate oak forest. The genomes of three cellulolytic isolates previously described as abundant in this ecosystem were sequenced and their proteomes were characterized during the growth on plant biomass and on microcrystalline cellulose. Pedobacter and Mucilaginibacter showed complex enzymatic systems containing highly diverse carbohydrate-active enzymes for the degradation of cellulose and hemicellulose, which were functionally redundant for endoglucanases, β-glucosidases, endoxylanases, β-xylosidases, mannosidases and carbohydrate-binding modules. Luteibacter did not express any glycosyl hydrolases traditionally recognized as cellulases. Instead, cellulose decomposition was likely performed by an expressed GH23 family protein containing a cellulose-binding domain. Interestingly, the presence of plant lignocellulose as well as crystalline cellulose both trigger the production of a wide set of hydrolytic proteins including cellulases, hemicellulases and other glycosyl hydrolases. Our findings highlight the extensive and unexplored structural diversity of enzymatic systems in cellulolytic soil bacteria and indicate the roles of multiple abundant bacterial taxa in the decomposition of cellulose and other plant polysaccharides.

Two New Native β-Glucosidases from Clavispora NRRL Y-50464 Confer Its Dual Function as Cellobiose Fermenting Ethanologenic Yeast

Yeast strain Clavispora NRRL Y-50464 is able to produce cellulosic ethanol from lignocellulosic materials without addition of external β-glucosidase by simultaneous saccharification and fermentation. A β-glucosidase BGL1 protein from this strain was recently reported supporting its cellobiose utilization capability. Here, we report two additional new β-glucosidase genes encoding enzymes designated as BGL2 and BGL3 from strain NRRL Y-50464. Quantitative gene expression was analyzed and the gene function of BGL2 and BGL3 was confirmed by heterologous expression using cellobiose as a sole carbon source. Each gene was cloned and partially purified protein obtained separately for direct enzyme assay using varied substrates. Both proteins showed the highest specific activity at pH 5 and relatively strong affinity with a K_m of 0.08 and 0.18 mM for BGL2 and BGL3, respectively. The optimum temperature was found to be 50°C for BGL2 and 55°C for BGL3. Both proteins were able to hydrolyze 1,4 oligosaccharides evaluated in this study. They also showed a strong resistance to glucose product inhibition with a K_i of 61.97 and 38.33 mM for BGL2 and BGL3, respectively. While BGL3 was sensitive showing a significantly reduced activity to 4% ethanol, BGL2 demonstrated tolerance to ethanol. Its activity was enhanced in the presence of ethanol but reduced at concentrations greater than 16%. The presence of the fermentation inhibitors furfural and HMF did not affect the enzyme activity. Our results suggest that a β-glucosidase gene family exists in Clavispora NRRL Y-50464 with at least three members in this group that validate its cellobiose hydrolysis functions for lower-cost cellulosic ethanol production. Results of this study confirmed the cellobiose hydrolysis function of strain NRRL Y-50464, and further supported this dual functional yeast as a candidate for lower-cost cellulosic ethanol production and next-generation biocatalyst development in potential industrial applications.

Familiar Stranger: Ecological Genomics of the Model Saprotroph and Industrial Enzyme Producer Trichoderma reesei Breaks the Stereotypes

The filamentous fungus Trichoderma reesei (Hypocreales, Ascomycota) has properties of an efficient cell factory for protein production that is exploited by the enzyme industry, particularly with respect to cellulase and hemicellulase formation. Under conditions of industrial fermentations it yields more than 100g secreted protein L(-1). Consequently, T. reesei has been intensively studied in the 20th century. Most of these investigations focused on the biochemical characteristics of its cellulases and hemicellulases, on the improvement of their properties by protein engineering, and on enhanced enzyme production by recombinant strategies. However, as the fungus is rare in nature, its ecology remained unknown. The breakthrough in the understanding of the fundamental biology of T. reesei only happened during 2000s-2010s. In this review, we compile the current knowledge on T. reesei ecology, physiology, and genomics to present a holistic view on the natural behavior of the organism. This is not only critical for science-driven further improvement of the biotechnological applications of this fungus, but also renders T. reesei as an attractive model of filamentous fungi with superior saprotrophic abilities.

Involvement of the adaptor protein 3 complex in lignocellulase secretion in Neurospora crassa revealed by comparative genomic screening

BACKGROUND

Lignocellulase hypersecretion has been achieved in industrial fungal workhorses such as Trichoderma reesei, but the underlying mechanism associated with this process is not well understood. Although previous comparative genomic studies have revealed that the mutagenic T. reesei strain RUT-C30 harbors hundreds of mutations compared with its parental strain QM6a, how these mutations actually contribute to the hypersecretion phenotype remains to be elucidated.

RESULTS

In this study, we systematically screened gene knockout (KO) mutants in the cellulolytic fungus Neurospora crassa, which contains orthologs of potentially defective T. reesei RUT-C30 mutated genes. Of the 86 deletion mutants screened in N. crassa, 12 exhibited lignocellulase production more than 25% higher than in the wild-type (WT) strain and 4 showed nearly 25% lower secretion. We observed that the deletion of Ncap3m (NCU03998), which encodes the μ subunit of the adaptor protein 3 (AP-3) complex in N. crassa, led to the most significant increase in lignocellulase secretion under both Avicel and xylan culture conditions. Moreover, strains lacking the β subunit of the AP-3 complex, encoded by Ncap3b (NCU06569), had a similar phenotype to ΔNcap3m, suggesting that the AP-3 complex is involved in lignocellulase secretion in N. crassa. We also found that the transcriptional abundance of major lignocellulase genes in ΔNcap3m was maintained at a relatively higher level during the late stage of fermentation compared with the WT, which might add to the hypersecretion phenotype. Finally, we found that importation of the T. reesei ap3m ortholog Trap3m into ΔNcap3m can genetically restore secretion of lignocellulases to normal levels, which suggests that the effect of the AP-3 complex on lignocellulase secretion is conserved in cellulolytic ascomycetes.

CONCLUSIONS

Using the model cellulolytic fungus N. crassa, we explored potential hypersecretion-related mutations in T. reesei strain RUT-C30. Through systematic genetic screening of 86 corresponding orthologous KO mutants in N. crassa, we identified several genes, particularly those encoding the AP-3 complex that contribute to lignocellulase secretion. These findings will be useful for strain improvement in future lignocellulase and biomass-based chemical production.

Genome-wide analysis of the endoplasmic reticulum stress response during lignocellulase production in Neurospora crassa

BACKGROUND

Lignocellulolytic fungal cells suffer endoplasmic reticulum (ER) stress during lignocellulase synthesis; however, an understanding of this integrated process on a genome-wide scale remains poor. Here, we undertook a systematic investigation of this process in Neurospora crassa (N. crassa) using transcriptomic analysis coupled with genetic screens.

RESULTS

A set of 766 genes was identified as the ER stress response targets (ESRTs) in N. crassa under cellulose utilization conditions. Among these, the expression of 223 and 186 genes showed dependence on IRE-1 and HAC-1, respectively. A total of 527 available mutants for ESRT genes were screened, 249 of which exhibited ER stress susceptibility, including 100 genes with unknown function. Disruption of ire-1 or hac-1 in N. crassa did not affect transcriptional induction of lignocellulase genes by cellulose but severely affected secretion of the corresponding enzymes. A global investigation of transcription factors (TFs) discovered three novel regulators (RES-1, RES-2, RRG-2) involved in lignocellulase secretion. Production of lignocellulases in Δres-1 increased by more than 30% in comparison to wild type (WT), while secretion decreased by nearly 30% in strains Δres-2 and Δrrg-2. Transcriptional profiling of the three TF mutants suggests they are deeply involved in lignocellulase secretion and ER stress response.

CONCLUSIONS

Here, we determined the transcriptional scope of the ER stress response during lignocellulase synthesis in the model cellulolytic fungus N. crassa. Through genome-wide mutant screening and analysis, dozens of novel genes were discovered to be involved in the process. The findings of this work will be useful for strain improvement to facilitate lignocellulase and biomass-based chemical production.

Large-scale evolutionary analyses on SecB subunits of bacterial sec system

Protein secretion systems are extremely important in bacteria because they are involved in many fundamental cellular processes. Of the various secretion systems, the Sec system is composed of seven different subunits in bacteria, and subunit SecB brings secreted preproteins to subunit SecA, which with SecYEG and SecDF forms a complex for the translocation of secreted preproteins through the inner membrane. Because of the wide existence of Sec system across bacteria, eukaryota, and archaea, each subunit of the Sec system has a complicated evolutionary relationship. Until very recently, 5,162 SecB sequences have been documented in UniProtKB, however no phylogenetic study has been conducted on a large sampling of SecBs from bacterial Sec secretion system, and no statistical study has been conducted on such size of SecBs in order to exhaustively investigate their variances of pairwise p-distance along taxonomic lineage from kingdom to phylum, to class, to order, to family, to genus and to organism. To fill in these knowledge gaps, 3,813 bacterial SecB sequences with full taxonomic lineage from kingdom to organism covering 4 phyla, 11 classes, 41 orders, 82 families, 269 genera, and 3,744 organisms were studied. Phylogenetic analysis revealed how the SecBs evolved without compromising their function with examples of 3-D structure comparison of two SecBs from Proteobacteria, and possible factors that affected the SecB evolution were considered. The average pairwise p-distances showed that the variance varied greatly in each taxonomic group. Finally, the variance was further partitioned into inter- and intra-clan variances, which could correspond to vertical and horizontal gene transfers, with relevance for Achromobacter, Brevundimonas, Ochrobactrum, and Pseudoxanthomonas.

Extracellular secretion of β-glucosidase in ethanologenic E. coli enhances ethanol fermentation of cellobiose

Consolidated bioprocessing of lignocellulose for ethanol production is realized by expressing cellulase enzymes on ethanologenic strain. In this study, an ethanologenic Escherichia coli ZY81 was constructed by integrating pyruvate decarboxylase gene pdc and alcohol dehydrogenase gene adhB from Zymomonas mobilis into the genome of E. coli JM109 to obtain the capability of ethanol production. Then, the β-glucosidase gene bglB from Bacillus polymyxa was cloned and secretively expressed in E. coli ZY81. The recombinant strain E. coli ZY81/bglB showed an obvious activity of β-glucosidase in extracellular location with more than half in periplasmic space. EDTA was found to promote the release of the periplasmic proteins by approximately tenfold. E. coli ZY81/bglB utilized cellobiose as sole carbon source for ethanol production with 33.99 % of theoretical yield.

Challenges and advances in the heterologous expression of cellulolytic enzymes: a review

Second generation biofuel development is increasingly reliant on the recombinant expression of cellulases. Designing or identifying successful expression systems is thus of preeminent importance to industrial progress in the field. Recombinant production of cellulases has been performed using a wide range of expression systems in bacteria, yeasts and plants. In a number of these systems, particularly when using bacteria and plants, significant challenges have been experienced in expressing full-length proteins or proteins at high yield. Further difficulties have been encountered in designing recombinant systems for surface-display of cellulases and for use in consolidated bioprocessing in bacteria and yeast. For establishing cellulase expression in plants, various strategies are utilized to overcome problems, such as the auto-hydrolysis of developing plant cell walls. In this review, we investigate the major challenges, as well as the major advances made to date in the recombinant expression of cellulases across the commonly used bacterial, plant and yeast systems. We review some of the critical aspects to be considered for industrial-scale cellulase production.