Inulinase hyperproduction by Kluyveromyces marxianus through codon optimization, selection of the promoter, and high-cell-density fermentation for efficient inulin hydrolysis

Enhanced expression of glycolysis regulators KmGcr1p and KmGcr2p in Kluyveromyces marxianus: An efficient strategy for high-temperature ethanol production from inulin

Bioethanol production from non-food biomass has emerged as a sustainable alternative to satisfy future energy demands. Kluyveromyces marxianus stands out as a potential consolidated bioprocessing (CBP) strain for high-temperature ethanol production from inulin. Nevertheless, enhancing its fermentation efficiency remains crucial. Here, we characterized its glycolysis regulator KmGcr2p and demonstrated that KmGcr2p boosts the expression of target genes controlled by another glycolysis regulator, KmGcr1p, through their interaction. Furthermore, we engineered the strain Ogcr1 + 2 through co-overexpressing KmGCR1 and KmGCR2, leading to a 55.8 % increase in inulinase activity, improved growth at 37 °C to 45 °C and under 10 % ethanol, and enhanced ethanol production at 42 °C by 36.0 % from inulin and 39.5 % from Jerusalem artichoke tuber flour. Our results highlight that co-overexpression of glycolysis regulators KmGcr1p and KmGcr2p can simultaneously enhance inulin saccharification, thermotolerance, ethanol tolerance, and ethanol production, presenting a promising and feasible strategy for high-temperature CBP ethanol production from inulin and inulin-rich feedstocks.

Transfer of disulfide bond formation modules via yeast artificial chromosomes promotes the expression of heterologous proteins in Kluyveromyces marxianus

Kluyveromyces marxianus is a food-safe yeast with great potential for producing heterologous proteins. Improving the yield in K. marxianus remains a challenge and incorporating large-scale functional modules poses a technical obstacle in engineering. To address these issues, linear and circular yeast artificial chromosomes of K. marxianus (KmYACs) were constructed and loaded with disulfide bond formation modules from Pichia pastoris or K. marxianus. These modules contained up to seven genes with a maximum size of 15 kb. KmYACs carried telomeres either from K. marxianus or Tetrahymena. KmYACs were transferred successfully into K. marxianus and stably propagated without affecting the normal growth of the host, regardless of the type of telomeres and configurations of KmYACs. KmYACs increased the overall expression levels of disulfide bond formation genes and significantly enhanced the yield of various heterologous proteins. In high-density fermentation, the use of KmYACs resulted in a glucoamylase yield of 16.8 g/l, the highest reported level to date in K. marxianus. Transcriptomic and metabolomic analysis of cells containing KmYACs suggested increased flavin adenine dinucleotide biosynthesis, enhanced flux entering the tricarboxylic acid cycle, and a preferred demand for lysine and arginine as features of cells overexpressing heterologous proteins. Consistently, supplementing lysine or arginine further improved the yield. Therefore, KmYAC provides a powerful platform for manipulating large modules with enormous potential for industrial applications and fundamental research. Transferring the disulfide bond formation module via YACs proves to be an efficient strategy for improving the yield of heterologous proteins, and this strategy may be applied to optimize other microbial cell factories.

Kluyveromyces as promising yeast cell factories for industrial bioproduction: From bio-functional design to applications

As the two most widely used Kluyveromyces yeast, Kluyveromyces marxianus and K. lactis have gained increasing attention as microbial chassis in biocatalysts, biomanufacturing and the utilization of low-cost raw materials owing to their high suitability to these applications. However, due to slow progress in the development of molecular genetic manipulation tools and synthetic biology strategies, Kluyveromyces yeast cell factories as biological manufacturing platforms have not been fully developed. In this review, we provide a comprehensive overview of the attractive characteristics and applications of Kluyveromyces cell factories, with special emphasis on the development of molecular genetic manipulation tools and systems engineering strategies for synthetic biology. In addition, future avenues in the development of Kluyveromyces cell factories for the utilization of simple carbon compounds as substrates, the dynamic regulation of metabolic pathways, and for rapid directed evolution of robust strains are proposed. We expect that more synthetic systems, synthetic biology tools and metabolic engineering strategies will adapt to and optimize for Kluyveromyces cell factories to achieve green biofabrication of multiple products with higher efficiency.

Production, purification, and characterization of inulinase from Streptomyces anulatus

Inulinase is an enzyme that catalyzes inulin to d-fructose. This enzyme can be extracted from plants, but it is difficult to obtain it in large quantities, so its production cost is high. Therefore, microbial inulinase has great potential for industrial needs. In the last decade, there have been very few reports on actinobacterial inulinases, especially on purification and characterization of inulinase process extraction. This study aims to select actinomycetes that possess high inulinase activity from the soil. To screen inulinase-producing bacteria, modified Czapex-Dox agar supplemented with 1% inulin powder was used. The most effective isolate was Streptomyces sp. EFBO8, morphological and genotypic identification methods, confirmed that the strain is Streptomyces anulatus and that its nucleotide sequence has been deposited in GenBank under accession number OQ073700. To optimize inulinase production, kinetics were performed by using S. anulatus strain, which proved to be most productive with a value of 24,024 EU/mL. The enzyme was purified from the culture filtrate by precipitation with ammonium sulfate (NH₄ )₂ SO₄ , followed by column chromatography Sephadex (G-50) separation. Purified protein has a molecular mass of 3331.83 Da.

Rhizopus oryzae Inulinase Production and Characterization with Application in Chicory Root Saccharification

The objective of this study was to create a fermentation process for the production of inulinase, an important enzyme with numerous applications in the food and pharmaceutical industries, using low-cost agricultural waste as substrates for Rhizopus oryzae NRRL 3563. High titer inulinase production in chicory roots by Rhizopus oryzae in a submerged culture was accomplished using a statistical experimental design. A two-level Plackett–Burman design followed by a three-level Box–Behnken design producing a high inulinase titer of 1085.11 U/mL, 2.83-fold the maximum level, was obtained in the screening experiment. The optimal levels were as follows: chicory root, 10 g/L; NaNO3, 5 g/L; and KCl, 0.2 g/L. The produced inulinase enzyme was purified using 70% ammonium sulfate precipitation and ultra-filtration causing 3.63-fold purification with 60% activity recovery. The enzyme had a molecular weight of approximately 130 KDa. The purified enzyme showed optimum activity at 50 °C and pH 6.0. The pH stability range was three to six and the temperature stability was up 70 °C. The purified inulinase could hydrolyze inulin and sucrose, but not cellobiose or soluble starch. Km and Vmax for inulin were determined to be 0.8 mg/mL and 50,000 U/mg, respectively. The two-level Plackett–Burman design was applied followed by a Box–Behnken model for optimization of fermentation conditions. Accordingly, the optimal combination of fermentation was a reaction time of seven hours, a temperature of 60 °C, and an enzyme concentration of 40,000 U/mL, which resulted in a 58.07% saccharification yield. The characteristics of the enzyme and its kinetic parameters suggested that it was highly effective in the fermentation of inulin and inulin-containing substrates. Additionally, it raises the potential of using inulinase enzymes in pharmaceutical and food industries.

Engineering of non-model eukaryotes for bioenergy and biochemical production

The prospect of leveraging naturally occurring phenotypes to overcome bottlenecks constraining the bioeconomy has marshalled increased exploration of nonconventional organisms. This review discusses the status of non-model eukaryotic species in bioproduction, the evaluation criteria for effectively matching a candidate host to a biosynthetic process, and the genetic engineering tools needed for host domestication. We present breakthroughs in genome editing and heterologous pathway design, delving into innovative spatiotemporal modulation strategies that potentiate more refined engineering capabilities. We cover current understanding of genetic instability and its ramifications for industrial scale-up, highlighting key factors and possible remedies. Finally, we propose future opportunities to expand the current collection of available hosts and provide guidance to benefit the broader bioeconomy.

Recent trends in the biotechnology of functional non-digestible oligosaccharides with prebiotic potential

Prebiotics as a part of dietary nutrition can play a crucial role in structuring the composition and metabolic function of intestinal microbiota and can thus help in managing a clinical scenario by preventing diseases and/or improving health. Among the different prebiotics, non-digestible carbohydrates are molecules that selectively enrich a typical class of bacteria with probiotic potential. This review summarizes the current knowledge about the different aspects of prebiotics, such as its production, characterization and purification by various techniques, and its link to novel product development at an industrial scale for wide-scale use in diverse range of health management applications. Furthermore, the path to effective valorization of agricultural residues in prebiotic production has been elucidated. This review also discusses the recent developments in application of genomic tools in the area of prebiotics for providing new insights into the taxonomic characterization of gut microorganisms, and exploring their functional metabolic pathways for enzyme synthesis. However, the information regarding the cumulative effect of prebiotics with beneficial bacteria, their colonization and its direct influence through altered metabolic profile is still getting established. The future of this area lies in the designing of clinical condition specific functional foods taking into consideration the host genotypes, thus facilitating the creation of balanced and required metabolome and enabling to maintain the healthy status of the host.

A review of yeast: High cell-density culture, molecular mechanisms of stress response and tolerance during fermentation

Yeast is widely used in the fermentation industry, and the major challenges in fermentation production system are high capital cost and low reaction rate. High cell-density culture is an effective method to increase the volumetric productivity of the fermentation process, thus making the fermentation process faster and more robust. During fermentation, yeast is subjected to various environmental stresses, including osmotic, ethanol, oxidation, and heat stress. To cope with these stresses, yeast cells need appropriate adaptive responses to acquire stress tolerances to prevent stress-induced cell damage. Since a single stressor can trigger multiple effects, both specific and nonspecific effects, general and specific stress responses are required to achieve comprehensive protection of cells. Since all these stresses disrupt protein structure, the upregulation of heat shock proteins and trehalose genes is induced when yeast cells are exposed to stress. A better understanding of the research status of yeast HCDC and its underlying response mechanism to various stresses during fermentation is essential for designing effective culture control strategies and improving the fermentation efficiency and stress resistance of yeast.

Bioprospecting Kluyveromyces marxianus as a Robust Host for Industrial Biotechnology

Kluyveromyces marxianus is an emerging non-conventional food-grade yeast that is generally isolated from diverse habitats, like kefir grain, fermented dairy products, sugar industry sewage, plants, and sisal leaves. A unique set of beneficial traits, such as fastest growth, thermotolerance, and broad substrate spectrum (i.e., hemi-cellulose hydrolysates, xylose, l-arabinose, d-mannose, galactose, maltose, sugar syrup molasses, cellobiose, and dairy industry) makes this yeast a particularly attractive host for applications in a variety of food and biotechnology industries. In contrast to Saccharomyces cerevisiae, most of the K. marxianus strains are apparently Crabtree-negative or having aerobic-respiring characteristics, and unlikely to endure aerobic alcoholic fermentation. This is a desirable phenotype for the large-scale biosynthesis of products associated with biomass formation because the formation of ethanol as an undesirable byproduct can be evaded under aerobic conditions. Herein, we discuss the current insight into the potential applications of K. marxianus as a robust yeast cell factory to produce various industrially pertinent enzymes, bioethanol, cell proteins, probiotic, fructose, and fructo-oligosaccharides, and vaccines, with excellent natural features. Moreover, the biotechnological improvement and development of new biotechnological tools, particularly CRISPR-Cas9-assisted precise genome editing in K. marxianus are delineated. Lastly, the ongoing challenges, concluding remarks, and future prospects for expanding the scope of K. marxianus utilization in modern biotechnology, food, feed, and pharmaceutical industries are also thoroughly vetted. In conclusion, it is critical to apprehend knowledge gaps around genes, metabolic pathways, key enzymes, and regulation for gaining a complete insight into the mechanism for producing relevant metabolites by K. marxianus.