Promoter and signal sequence from filamentous fungus can drive recombinant protein production in the yeast Kluyveromyces lactis

Precision cellular agriculture: The future role of recombinantly expressed protein as food

Cellular agriculture is a rapidly emerging field, within which cultured meat has attracted the majority of media attention in recent years. An equally promising area of cellular agriculture, and one that has produced far more actual food ingredients that have been incorporated into commercially available products, is the use of cellular hosts to produce soluble proteins, herein referred to as precision cellular agriculture (PCAg). In PCAg, specific animal- or plant-sourced proteins are expressed recombinantly in unicellular hosts-the majority of which are yeast-and harvested for food use. The numerous advantages of PCAg over traditional agriculture, including a smaller carbon footprint and more consistent products, have led to extensive research on its utility. This review is the first to survey proteins currently being expressed using PCAg for food purposes. A growing number of viable expression hosts and recent advances for increased protein yields and process optimization have led to its application for producing milk, egg, and muscle proteins; plant hemoglobin; sweet-tasting plant proteins; and ice-binding proteins. Current knowledge gaps present research opportunities for optimizing expression hosts, tailoring posttranslational modifications, and expanding the scope of proteins produced. Considerations for the expansion of PCAg and its implications on food regulation, society, ethics, and the environment are also discussed. Considering the current trajectory of PCAg, food proteins from any biological source can likely be expressed recombinantly and used as purified food ingredients to create novel and tailored food products.

Medium optimization for high mycelial soluble protein content of Ophiocordyceps sinensis using response surface methodology

Ophiocordyceps sinensis is widely utilized due to its pharmaceutical value. Mycelial protein forms a key active component of O. sinensis and determines the medicinal potential of fungus. Here, we describe the development of an optimized fermentation medium to obtain more mycelial soluble protein from O. sinensis using response surface methodology (RSM) and investigate the increased mycelial protein content using transcriptomics. The maximum mycelial protein content of 2.11% was obtained using a medium consisting of 20% beef broth, 0.10% peptone, 2% glucose, 0.15% yeast extract, 0.20% KH₂PO₄, and 0.02% MgSO₄. Transcriptome analysis identified 790 differentially expressed genes (DEGs), including 592 up-regulated genes and 198 down-regulated genes, optimisation resulted in more up-regulated genes. The main DEGs were enriched in metabolic pathways, ABC transporters, starch and sucrose metabolism, tyrosine metabolism, and glutathione metabolism. In addition, some DEGs associated with mycelial protein enhancement such as tyrosinase (TYR), glutathione S-transferase (GST), glutamine synthetase (glnA), and β-glucosidase may contribute to increased mycelial protein content. Real-time quantitative PCR (RT-qPCR) was used to confirm gene expression and the results support the accuracy of RNA-Seq and DEG analysis. This study provides an optimized fermentation method for enhancing the mycelial protein content of O. sinensis and a reference for the effective development of O. sinensis protein.

Recent advances in the development of Aspergillus for protein production

Aspergillus had been widely used in the industrial production of recombinant proteins. In addition to the safety and broad substrate utilization spectrum, its efficient post-translational modification and strong protein secretion capacity have significant advantages for developing an excellent protein-producing cell factory in industrial production. However, the difficulties in genetic manipulation of Aspergillus and varying expression levels of different heterologous proteins hampered its further development and application. Recently, the development of CRISPR genome editing and high-throughput screening platforms has facilitated the Aspergillus development of a wide range of modifications and applications. Meanwhile, multi-omics analysis and multiplexed genetic engineering have promoted effective knowledge mining. This paper provides a comprehensive and updated review of these advances, including high-throughput screening, genome editing, protein expression modules, and fermentation optimization. It also highlights and discusses the latest significant progress, aiming to provide a practical guide for implementing Aspergillus as an efficient protein-producing cell factory.

Customized yeast cell factories for biopharmaceuticals: from cell engineering to process scale up

The manufacture of recombinant therapeutics is a fastest-developing section of therapeutic pharmaceuticals and presently plays a significant role in disease management. Yeasts are established eukaryotic host for heterologous protein production and offer distinctive benefits in synthesising pharmaceutical recombinants. Yeasts are proficient of vigorous growth on inexpensive media, easy for gene manipulations, and are capable of adding post translational changes of eukaryotes. Saccharomyces cerevisiae is model yeast that has been applied as a main host for the manufacture of pharmaceuticals and is the major tool box for genetic studies; nevertheless, numerous other yeasts comprising Pichia pastoris, Kluyveromyces lactis, Hansenula polymorpha, and Yarrowia lipolytica have attained huge attention as non-conventional partners intended for the industrial manufacture of heterologous proteins. Here we review the advances in yeast gene manipulation tools and techniques for heterologous pharmaceutical protein synthesis. Application of secretory pathway engineering, glycosylation engineering strategies and fermentation scale-up strategies in customizing yeast cells for the synthesis of therapeutic proteins has been meticulously described.

Novel genetic tools that enable highly pure protein production in Trichoderma reesei

Trichoderma reesei is an established protein production host with high natural capacity to secrete enzymes. The lack of efficient genome engineering approaches and absence of robust constitutive gene expression systems limits exploitation of this organism in some protein production applications. Here we report engineering of T. reesei for high-level production of highly enriched lipase B of Candida antarctica (calB) using glucose as a carbon source. Multiplexed CRISPR/Cas9 in combination with the use of our recently established synthetic expression system (SES) enabled accelerated construction of strains, which produced high amounts of highly pure calB. Using SES, calB production levels in cellulase-inducing medium were comparable to the levels obtained by using the commonly employed inducible cbh1 promoter, where a wide spectrum of native enzymes were co-produced. Due to highly constitutive expression provided by the SES, it was possible to carry out the production in cellulase-repressing glucose medium leading to around 4 grams per liter of fully functional calB and simultaneous elimination of unwanted background enzymes.

Established and Upcoming Yeast Expression Systems

Yeast was the first microorganism used by mankind for biotransformation of feedstock that laid the foundations of industrial biotechnology. Long historical use, vast amount of data, and experience paved the way for Saccharomyces cerevisiae as a first yeast cell factory, and still it is an important expression platform as being the production host for several large volume products. Continuing special needs of each targeted product and different requirements of bioprocess operations have led to identification of different yeast expression systems. Modern bioprocess engineering and advances in omics technology, i.e., genomics, transcriptomics, proteomics, secretomics, and interactomics, allow the design of novel genetic tools with fine-tuned characteristics to be used for research and industrial applications. This chapter focuses on established and upcoming yeast expression platforms that have exceptional characteristics, such as the ability to utilize a broad range of carbon sources or remarkable resistance to various stress conditions. Besides the conventional yeast S. cerevisiae, established yeast expression systems including the methylotrophic yeasts Pichia pastoris and Hansenula polymorpha, the dimorphic yeasts Arxula adeninivorans and Yarrowia lipolytica, the lactose-utilizing yeast Kluyveromyces lactis, the fission yeast Schizosaccharomyces pombe, and upcoming yeast platforms, namely, Kluyveromyces marxianus, Candida utilis, and Zygosaccharomyces bailii, are compiled with special emphasis on their genetic toolbox for recombinant protein production.

Genetic and physiological basis for antibody production by Kluyveromyces marxianus

Kluyveromyces marxianus is a thermotolerant, crabtree-negative yeast, which preferentially directs metabolism (e.g., from the tricarboxylic acid cycle) to aerobic alcoholic fermentation. Thus K. marxianus has great potential for engineering to produce various materials under aerobic cultivation conditions. In this study, we engineered K. marxianus to produce and secrete a single-chain antibody (scFv), a product that is highly valuable but has historically proven difficult to generate at large scale. scFv production was obtained with strains carrying either plasmid-borne or genomically integrated constructs using various combinations of promoters (P_MDH1 or P_ACO1) and secretion signal peptides (KmINUss or Scα-MFss). As the wild-type K. marxianus secretes endogenous inulinase predominantly, the corresponding INU1 gene was disrupted using a Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)—associated protein (CRISPR–Cas9) system to re-direct resources to scFv production. Genomic integration was used to replace INU1 with sequences encoding a fusion of the INU1 signal peptide to scFv; the resulting construct yielded the highest scFv production among the strains tested. Optimization of growth conditions revealed that scFv production by this strain was enhanced by incubation at 30 °C in xylose medium containing 200 mM MgSO₄. These results together demonstrate that K. marxianus has the potential to serve as a host strain for antibody production.

Using a vector pool containing variable-strength promoters to optimize protein production in Yarrowia lipolytica

Background

The yeast Yarrowia lipolytica is an increasingly common biofactory. To enhance protein expression, several promoters have been developed, including the constitutive TEF promoter, the inducible POX2 promotor, and the hybrid hp4d promoter. Recently, new hp4d-inspired promoters have been created that couple various numbers of UAS1 tandem elements with the minimal LEU2 promoter or the TEF promoter. Three different protein-secretion signaling sequences can be used: preLip2, preXpr2, and preSuc2.

Results

To our knowledge, our study is the first to use a set of vectors with promoters of variable strength to produce proteins of industrial interest. We used the more conventional TEF and hp4d promoters along with five new hybrid promoters: 2UAS1-pTEF, 3UAS1-pTEF, 4UAS1-pTEF, 8UAS1-pTEF, and hp8d. We compared the production of RedStar2, glucoamylase, and xylanase C when strains were grown on three media. As expected, levels of RedStar2 and glucoamylase were greatest in the strain with the 8UAS1-pTEF promoter, which was stronger. However, surprisingly, the 2UAS1-pTEF promoter was associated with the greatest xylanase C production and activity. This finding underscored that stronger promoters are not always better when it comes to protein production. We therefore developed a method for easily identifying the best promoter for a given protein of interest. In this gateway method, genes for YFP and α-amylase were transferred into a pool of vectors containing different promoters and gene expression was then analyzed. We observed that, in most cases, protein production and activity were correlated with promoter strength, although this pattern was protein dependent.

Conclusions

Protein expression depends on more than just promoter strength. Indeed, promoter suitability appears to be protein dependent; in some cases, optimal expression and activity was obtained using a weaker promoter. We showed that using a vector pool containing promoters of variable strength can be a powerful tool for rapidly identifying the best producer for a given protein of interest.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0647-3) contains supplementary material, which is available to authorized users.