Various expression systems exist for recombinant protein production in bacteria, yeasts, insects, and mammalian cells. All of them have their drawbacks and advantages. Yeasts are interesting and versatile hosts caused by benefits such as growth speed, simple genetic manipulations, secretory expression, post-translational modification, scalable fermentation, high biomass concentrations, and safe, pathogen-free production [27,28]. There are two large yeast expression systems: methylotroph and non-methylotroph. Typical examples of non-methylotroph and methylotroph yeasts are Saccharomyces cerevisiae and Pichia pastoris.

Saccharomyces cerevisiae, known as baker’s yeast, was the first eukaryotic organism with a completely sequenced genome [29]. As said before, S. cerevisiae belongs to the non-methylotroph yeast group. It was initially developed as a replacement host for producing a recombinant protein that could not be expressed in bacterial cells [27,30]. The native resistance of S. cerevisae to low pH, high osmolality, and numerous inhibitors (acetic acid, furfural, vanillin, etc.) allows low-cost and facile fermentation procedures with high biomass concentrations under aerobic and anaerobic conditions, thereby enabling a higher yield of recombinant proteins [31]. Plentiful genetic tools are developed for expression in S. cerevisiae, such as recombinant protein expression controlled by strong constitutive promoters like TEF1 and GAP or inducible promoters like galactose-inducible GAL1 [32]. Unfortunately, this expression host has some disadvantages such as a low level of protein secretion, hyperglycosylation [33], and proteolytic degradation of expressed proteins. From a biotechnological point of view, this expression system is “generally recognized as safe” (GRAS) because it is nonpathogenic and has a history in the food and pharmaceutical industry [27].

With the intention of achieving a higher expression level, a few approaches were used, such as various fermentation conditions, optimization of the codon, strong promotors and terminators, and a multi-copy expression vector—Table 1 [27,34,35].

In 1992, Baetselier et al. confirmed that expressing up to 1.5 g/L using a suitable vector–host system was possible [38]. In this study, they used expression vectors pαGO1 and pSGO2, which contain an expression cassette of the regulated hybrid promoter ADH2-GAPDH, the α-factor or GOx signal sequence for secretion, the mature GOx cDNA, and the GAPDH terminator. The yeast strain GRF181 transformants of these plasmids were cultured on a YP medium with 8% sucrose [38]. The bidirectional inducible promoters can control recombinant expression in S. cerevisiae, galactose dehydrogenase 1 (GAL1), and UDP-glucose-epimerase (GAL10). For the expression induced by the GAL1 promoter, 1% galactose concentration was the most successful and was obtained at 32 U/mL [36]. It was also noted that indirect control of ethanol production in feedback controlled fed-batch processes could be accomplished via feeding carbon sources. Galactose feeding was utilized to control the pH of the culture, decrease ethanol production, and improve the quantity of GOx produced [37].

Termitomyces clypeatus CDH intracellular expression in S. cerevisiae was achieved by Banerjee et al. [41] in a relatively low but detectable degree of the expressed protein, 0.039 U/mg, with cellobiose as an electron donor [41]. Previous research showed that the secretion signal influences the level of cellobiose dehydrogenase expression. Hence, the native secretory leader sequence gave three times higher expression than a signal sequence of α-factor [39]. Also, in research conducted earlier in our laboratory, the ability of S. cerevisiae to produce cellobiose dehydrogenase was confirmed, but the yields of the expressed enzymes were not high [40]. The results of work [39,40], both using the native secretion signal of CDH, are very different due to the use of different yeast strains. In work [39], the protease-free S. cerevisiae BJ5465 strain was used that can give high amounts of protein after long fermentation times. In contrast, in work [40], researchers used the S. cerevisiae InvSc1 strain (Invitrogen, Waltham, MA, USA), which usually gives a maximum of 1 mg/mL of recombinant protein after 16 h of fermentation and is mostly used for directed evolution experiments. Most prior research has shown that S. cerevisiae is not a suitable host for high-yield cellobiose dehydrogenase production. Still, it is a great host choice for protein engineering techniques due to its higher transformation efficiency.

Zhao et al. obtained 5093 U/L of HRP via strain engineering, such as selecting an appropriate cis-regulatory module (CRM) and substituting a core promoter sequence (CPS) and terminator. The yield is significantly increased up to 330 times by replacing the α-factor signal peptide with another signal peptide for transport of HRP in the endoplasmic reticulum [42]. In this work, the authors concluded that improper combinations of pro-peptide and pre-peptide sequences can lead to the accumulation of recombinant HRP within the endoplasmic reticulum. Therefore, the author’s eight-propeptide variants of the α-factor signal peptide were tested to facilitate the export of HRP from the endoplasmic reticulum. To confirm the increased amount of expressed HRP, the enzyme was purified and deglycosylated using EndoH. Using this additional prepropeptide sequence engineering in a 5 L flask reactor, the authors obtained 13,506 U/L of the HRP.

Functional LAC expression in S. cerevisiae was described in the early nineties. Afterward, articles about the optimization of heterologous LAC expression were published [50]. Cassland et al. recognized several important factors affecting LAC expression: the cultivation temperature, the gene selected, and the selected S. cerevisiae strain [48,51]. Previous research showed that heterologous production of LAC can be upgraded using protein engineering methods, so mutated M. thermophila LAC showed 170-fold higher activity than the wild type [44]. In the 2013, a group of authors demonstrated the possibility of secretory production of initially intracellular LAC and considered aeration an important factor affecting LAC heterologous production [46]. Iimura et al. confirmed that aeration is an important factor besides inducer and copper concentration, so the LAC yield was nearly two times higher when the culture device was used. Aeration was accelerated (45 U/L in baffled flask and 80 U/L when the culture device was used) [45]. A recent study examined a few factors affecting LAC expression in S. cerevisiae. It concluded that expression depends on the gene source, used construct, temperature, pH value of cultivation media, and copper concentration. This research has provided evidence for adding alanine to maintain the pH value of cultivation media because it greatly impacts laccase expression. Also, they proved that lowering the temperature during expression from 30 to 20 °C yielded more than double the laccase activity in the identical cultivation period [49]. Several studies suggest that the secretion signal could greatly impact LAC expression in S. cerevisiae, so Aza et al. successfully used an improved α_9H2 signal sequence in their work [47,52]. As was the case in other enzymes expressed in yeasts, the structure of the carbohydrate component of the enzyme synthesized by yeast differs from the structure of carbohydrate component of the native enzyme. Usually, hyperglycosylation in yeast, especially in S. cerevisiae, occurs (up to 50% per mass) that can increase stability but also decrease the specific activity of the recombinant enzyme.

Pichia pastoris (recently renamed as Komagataella phaffii) has gained an important role in recombinant protein production in the past several decades. P. pastoris can use methanol as a sole carbon source, given the fact it belongs to methylotroph yeasts. Undemanding genetic manipulation, high cell culture density, the capability of secreting recombinant proteins into the cell culture medium, unexacting purification of secreted proteins, eukaryotic post-translational modification, and stability of genetic constructs make this host convenient for the recombinant expression of proteins [53,54]. Promoters that control the heterologous expression of proteins could be constitutive (glyceraldehyde-3-phosphate dehydrogenase and PGAP) or inducible (alcohol oxidase, AOX1, and AOX2) [55]. Considering the existence of PAOX1 and PAOX2 in this host genome, there are three possible phenotypes of P. pastoris, specifically Mut + (wild-type methanol utilization; both of the alcohol oxidase enzymes, Aox1p and Aox2p, are functional), Muts (slow methanol utilization; disrupted Aox1p and functional Aox2p), and Mut- (no methanol utilization; both Aox1p and Aox2p are disrupted) [29]. According to Walsh and Walsh (2022), P. pastoris takes a superior position regarding S. cerevisiae in the field of recombinant protein production; the reason for that probably lies in the tightly regulated expression of both the intracellular and extracellular recombinant protein, achieving high cell density caused by the aerobic process of respiration and glycosylation like in eukaryotic cells [28,56]. P. pastoris is “generally recognized as safe” (GRAS) by the Food and Drug Administration (FDA) and suitable for diverse biotechnological applications.

Several strategies can be applied to achieve a high yield of recombinant proteins. The strategies cover codon optimization, choice of suitable host strains and expression vectors, gene copy number, insertion of the gene of interest under the control of the strong promoter and appropriate signal sequence, and optimization of fermentation conditions (temperature, incubation period, agitation, carbon source, and concentration of inducer)—Table 2 [28,57,58]. The stability of integrated genes within yeast genomes without selection pressures is high, but this can still lead to 1% transformant loss after each cell division cycle.

The yield of recombinant protein production in P. pastoris depends on several factors, such as gene optimization and synthesis, plasmid construction, host strain, and fermentation conditions [75].

As reported by Qui et al. (2016), the highest activity of recombinantly produced GOx was obtained when the expression was carried out at 30 °C and the pH of the medium was 6 [59,60].

Methanol is used as a source of energy and carbon for recombinant protein production in P. pastoris as an expression system. As a result, the methanol content in the culture medium is a significant variable while producing GOx [61,62].

Apart from the mentioned fermentation conditions, codon optimization can influence protein expression. It has been shown that replacing low-usage codons (<15%) with high-usage codons can increase the expression yield. For example, high-level expression of P. notatum F4 GOx was enabled via the distribution of G + C codons and removal of AT-rich regions, and the newly designed gene was named god-m [76].

The construction of multi-copy or high-copy transformants, which increase the gene dosage for expression GOx in P. pastoris, represents good strategies for enlarging the yield of production enzymes. Recent works have demonstrated that, to construct recombinant strains containing multiple copies of the GOx gene, it is first necessary to build vectors containing two or three tandem copies of the GOx expression cassette, termed pPICZHisα2GOX and pPICZHisα-3GOX. The generation of vectors containing more than three copies of the GOx expression cassette was unsuccessful, probably due to vector size limitations. The best results are obtained for the secretory expression of GOx in a three-copy strain [77].

Research showed that the yield of expression of GOx can be regulated via the overexpression of the Hac1p, unfolded protein response regulator of chaperones. Yu et al. finally achieved an enzyme activity level of around 2125.3 U/mL in fermenter culture using basic process changes [77].

P. pastoris is established as a standard expression system for CDH. Bey et al. reported that cultivation mode impacts CDH expression; cultivation in a shake flask and a bioreactor produced 1176 U/L and 7800 U/L, respectively [63]. A higher yield of CDH is expected when multiple copy transformants are selected [63]. According to prior research, the duration of CDH expression depends on the CDH origin [39,64].

HRP expression in P. pastoris was achieved using the construct pPICZαB-HRP and, as an inducer, methanol. For better yields of that recombinant production, 1.0 mM vitamin B1, 1.0 mM δ-ALA, and 0.5 mL/l trace element mix (0.5 g/L MgCl2, 30 g/L FeCl₂·6H₂O, 1 g/L ZnCl₂·4H₂O, 0.2 g/L CoCl₂·6H₂O, 1 g/L Na₂MoO₄·2H₂O, 0.5 g/L CaCl₂·2H₂O, 1 g/L CuCl_2, and 0.2 g/L H₂BO₃) were added to growth medium at the point of induction [43]. One such carbon source given to the medium is 1% sorbitol. Casamino acids are used to stop protein breakdown [65]. Specific productivity (qp) of the recombinant P. pastoris strain was increased 5.5-fold via a dynamic feeding strategy, where the setpoint for the specific substrate uptake rate (qs) was increased stepwise until a predetermined maximum (qsmax) was achieved, in contrast to a traditional feed-forward strategy [78,79]. P. pastoris successfully secreted a specific fusion construct of HRP and SpG in bioreactor cultivations with 110 mg/L yields. Recombinant HRP yields from P. pastoris that have been previously reported are normally in the 10 mg/L range [66].

Different strategies can be applied to achieve higher yields or higher activity of recombinantly produced LAC in P. pastoris. Concrete data is presented in Table 2. Previous studies have shown that there are two main aspects of optimizing LAC production in P. pastoris and yeast in general: control at the level of recombinant gene construction and control of the parameters to obtain optimal cultivation [80]. Prior research recognized temperature, methanol concentrations, pH value during cultivation, and copper concentration as important factors affecting heterologous LAC expression. Hong et al. concluded that cultivation in shake flasks at low temperatures with a final concentration of methanol 0.5% improved laccase activity; also, they confirmed their observation via cultivation under controlled conditions in the fermenter [69]. As has previously been reported in the literature, the expression of T. versicolor LAC, lcc1 in P. pastoris, was enhanced if the pH was periodically altered to pH 6.0 during fermentation [81]. O’Callaghan et al. designed a medium for maintaining a constant pH value. They examined the impact of proteolytic and non-proteolytic P. pastoris strains and the effect of copper availability on the laccase expression. They did not observe significant differences between proteolytic and non-proteolytic strains, but adding alanine to maintain pH and appropriate copper concentration had a significant impact [70]. Other researchers discovered that, via the optimization of several parameters such as the initial pH, the final concentration of methanol as an inducing agent, medium volume, initial OD600, copper concentration, and peptone concentration in the medium (pH 7, 0.6% MeOH, 50 mL of medium, 0.5 mM Cu²⁺ and 4% peptone), researchers can obtain 4.4 times higher LAC activity compared to the initial medium. Besides that, they have also suggested that the native LAC secretion signal was superior to the secretion signal of the α-factor [71]. Difficulty detecting laccase associated with poor secretion using an α-factor secretion signal can be overcome using evolved α-factor preproleader [72]. According to Xu et al., the significance of the laccase expression factors took the following order: concentration of methanol added > initial pH > Cu²⁺ concentration > temperature [74]. A considerable body of literature promotes distinct optimal conditions for heterologous laccase expression. Ardila-Leal et al. statistically improved culture media for rPOXA 1B laccase production, expressed in Pichia pastoris containing pGAPZαA-LaccPost-Stop in a 10 L bioreactor [68]. They obtained 3159.93 U/L using ABTS as a substrate.

3. State-of-the-art technologies for increasing recombinant protein expression

In the articles mentioned above, optimization of fermentation was done by changing fermentation media composition, induction time, temperature optimization, etc. Still, there are also trials of increasing the fermentation yield of these enzymes by using state-of-the-art technologies such as precision fermentation [83], directed evolution [84], protein, and strain engineering [85], high-throughput screening methods based on in vitro compartmentalization [86], flow cytometry, and microfluidics.

3.1. Directed evolution, protein and strain engineering

Strain engineering for protein production can be performed using precision fermentation that combines synthetic biology, genetic engineering, and machine learning approaches. This is based on biofoundries that provide an integrated infrastructure for rapid construction, design and analysing genetically modified organisms [87]. The first step usually involves generating large host organism libraries by diverse genetic modifications like protease knock-out, cassette modifications, etc. Afterwards comes the screening process. Computational approaches such as deep learning based on artificial neural networks and analyzing genome sequences for predicting gene manipulations to enhance recombinant protein production have recently been used [88–90]. This approach can predict the production performance of well-studied organisms like S.cerevisiae [91], P. pastoris [92] and optimize metabolic flux via altering genes involved in the metabolic network [93]. Therefore, the machine learning approach is proven capable of recommending strain engineering strategies [93].

Adaptive laboratory evolution is another approach for improving microbial phenotypes in many organisms [94]. In this approach, microbes are cultured in a desired growth environment for an extended period, allowing natural selection to enrich mutant strains. Evolved strains are later characterized and their DNA sequenced to find adaptive mutations that enable phenotypic improvement.

Expression of recombinant proteins in S.cerevisiae, especially oxidoreductases, can be increased using synthetic biology methods by choosing suitable promotors, selectable markers, and plasmids. Further, an increase in enzyme production can also be enhanced by utilizing various secretion factors. For example, it can be increased dramatically by site-directed mutagenesis or directed evolution of secretion peptide recombinant protein production. For instance, protein engineering approaches were carried out by Aza et al. to facilitate the heterologous production of various laccases by S.cerevisiae that included best-evolved signal peptides, new N-glycosylation sites in the enzyme genes, and consensus enzyme design for enhancing protein folding and stability [95]. The introduction of N-glycosylation sites is case specific since it can lead to decreased activity but also can enhance protein folding and, therefore, the enzyme activity. Authors obtained mutated α-factor preproleader α_9H2 that enhanced LAC production in the yeast twofold. Using other above-mentioned protein engineering strategies, they obtained 37 mg/L of ascomycete LAC. The same authors in another publication designed improved universal signal peptide α_OPT by adding four mutations into the α_9H2 preproleader sequence [96].

30. pastoris was by Zhou et all. in 2023 used for the expression of GOx and by using screening of different signal peptides, introducing multiple copies of genes, and engineering vesicle trafficking hyperproducing strain G1Ese co-expressing trafficking components EES and SEC was obtained that could produce up to 7223 U/mL with 30.7 g/L of GOx that is 3.3 fold higher than the highest level reported so far [97]. It is also possible to engineer P. pastoris strain by coexpression of chaperons and protein disulfide isomerase in these yeast cells [98]. To increase secretory expression of heterologous proteins in P. pastoris Duan et all. screened endogenous signal peptides and protein folding factors. Their effects on the expression of three reporter proteins were tested and they were able to identify Msb2 signal peptide and Dan4 signal peptide that increase recombinant protein secretion 8 and 172 fold, respectively compared to alpha-mating pre-pro leader sequence in P. pastoris [99].

Ito et al. l., in their recent work, created a terminator catalog by testing 72 sequences of terminators from S. cerevisiae and P. pastoris and found that terminator RNA sequences from S. cerevisiae maintain function when transferred to P. pastoris [100]. They managed to fine-tune protein expression levels in metabolic engineering and synthetic biology in P. pastoris and enhance them 17-fold. In a similar work on RNAi expression tuning, Wang et all. found genes with functions in cellular metabolism, protein modification and degradation, and cell cycle that can significantly influence the expression level of proteins in S. cerevisiae [101].

One of the problems with expressing recombinant proteins in Pichia can be glycosylation, although its is a much bigger problem for S. cerevisiae and usually, glycosylation is necessary for eukaryotic proteins to be correctly folded and expressed. To solve this problem, strain glyco-engineering trials of Pichia were done to prevent hyperglycosylation and enable higher fermentation yield of recombinant peroxidases [102]. Different glycoengineered P. pastoris strains were developed, and the physiology and growth behaviors of Man5GlcNAc2 glycosylating P. pastoris strain in the controlled environment of a bioreactor was characterized using flow cytometry during expression of HRP C1A isoform of the enzyme. The HRP C1A isoform expressed in the novel glycoengineered Pichia strain had similar kinetic characteristics as the one expressed in the wild-type Pichia strain. Still, the thermal stability of the recombinant HRP was decreased due to the reduced glycosylation. Still, the recombinant enzyme formation rate in the novel strain increased from 0.77 U/gh to 1.05 U/gh during fermentation.

3.2. High-throughput screening methods

3.2.1. Flow cytometry

To follow the influence of various factors on protein production in P. pastoris, it is essential to be able to follow the physiological state of recombinant yeast cells. Hyka et al. quantified factors affecting the physiological state of recombinant P. pastoris Mut+ (methanol utilization-positive) by using a combination of staining with different fluorescent dyes and analyzing by flow cytometry [103]. The authors found that cell vitalities could range from 5% to 95% in high-cell-density cultures with strain-producing HRP, depending on the influence of various stresses such as recombinant protein expression, high cell density, and pH. This quantitative assessment of the individual cells' physiology using flow cytometry enables the implementation of innovative concepts in bioprocess development. This is especially important because the paradigm assumes a uniform cell population and does not differentiate between individual cells whose state can only be followed by single-cell analysis. The conclusion was that only part of the cell population contributes to the recombinant protein production, and the objective should be to maintain productive cells over a long period as long as possible.

Flow cytometry can also be used for following expression and correctly folding active proteins like cytochrome c peroxidase when recombinant protein is fused with a green fluorescent protein (GFP) [104].

3.2.2. Microfluidics

Since the screening phase and early process development based on microtiter plates and flasks still represent a bottleneck due to the high cost and time-consuming procedures, Totaro et al. developed a screening protocol for P. pastoris clone selection based on the multiplexed microfluidic device using 15 µL cultivation chambers that were able to operate in perfusion mode and monitor dissolved oxygen content in the culture in a non-invasive way [105]. Using a microfluidic platform, the authors identified the best producer clone after 12 h from inoculation and confirmed the results by lab-scale fermentation.

Microfluidics combined with flow cytometry was also used for high.-throughput droplet screening and genome sequencing analysis for improved amylase-producing A. oryzae strain [106]. This work, 450000 droplets were screened within two weeks, and a high-producing strain with 6.6 folds increased production was found.

3.2.3. In vitro compartmentalization

In vitro, compartmentalization is often used in protein engineering and can be made in polydisperse format for single-cell experiments, or it can be made in monodisperse format by microfluidics [107]. Microspheres made of soft materials are also used in protein engineering as an alternative to liquid compartments [108]. Both of these compartmentalization methods can be used to improve not only enzyme activity and stability but also production yield during fermentation, and usually, the best way to do so is to perform directed evolution experiments using strains for production.

To optimize recombinant protein production in yeasts (P. pastoris), droplet microfluidics can be used to encapsulate (compartmentalize) large genetic libraries of strains within biocompatible gel beads that are engineered to selectively retain any recombinant protein of interest by binding it via His tag usually used for labeling and purification, and afterward staining of secreted protein with fluorescent dyes [109]. This platform can be used broadly for various proteins, including oxidoreductases. As proof of principle, authors found P. pastoris strain that 5.7-fold increased recombinant cutinase production after screening more than 10⁶ genotypes.

Compartmentalization within double emulsion can also be used to optimize recombinant protein production instead of beads. In vitro, compartmentalization within a double emulsion of water-in-oil-in-water was done using microfluidics and fluorinated oil. The fluorescent immunosensor quench-body detected the secreted recombinant protein (fibroblast growth factor 9), and clones with high protein secretion were detected by fluorimetry [110]. This method also shortens the development period of industrial strains for recombinant protein production.

4. Conclusions

Optimization of culture conditions represents one of the most used techniques to overcome the problem of low yield since the composition of medium plays a significant role in the production of recombinant protein. Establishing optimal reaction conditions such as pH and temperature is one of the critical steps for a higher yield of recombinant expression.

It can be concluded that despite the problems with the expression of OXR in yeasts like S. cerevisiae and P. pastoris due to the necessity of adding transition metals (copper, iron) and metabolic precursors of FAD and heme during fermentation, there are various approaches to increase expression yield of these enzymes. Some of them are optimizing fermentation conditions, the codon usage, using strong promoters and terminators, and multi-copy expression vectors. P. pastoris usually gives higher expression yields of proteins with lesser glycosylation levels compared to S. cerevisiae, which usually gives smaller expression yields of recombinant proteins, very high glycosylation levels, and microheterogeneity of expressed proteins. Still, there are always exceptions depending on the specific recombinant protein and used yeast strain.

As we could see from the literature recently, there are also new possibilities for further increase in fermentation yield that explore cutting-edge technologies such as directed evolution, protein and strain engineering, high-throughput screening methods based on in vitro compartmentalization, flow cytometry, and microfluidics.