Skip to main content

Screening for functional IRESes using α-complementation system of β-galactosidase in Pichia pastoris

Abstract

Background

Pichia pastoris is becoming a promising chassis cell for metabolic engineering and synthetic biology after its whole genome and transcriptome sequenced. However, the current systems for multigene co-expression in P. pastoris are not efficient. The internal ribosome entry site (IRES) has an ability to recruit the ribosome to initiate protein synthesis by cap-independent translation manner. This study seeks to screen IRES sequences that are functional in P. pastoris, which will allow P. pastoris to express multiple proteins in a single mRNA and increase its efficacy as a platform for metabolic engineering and synthetic biology.

Results

In order to efficiently screen the IRES sequences, we first set out to create a screening system using LacZ gene. Due to the cryptic transcription of the LacZ gene, we established the α-complementation system of β-galactosidase in P. pastoris with the optimum length of the α-complementing peptide at ~ 92 amino acids. The optimal α-complementing peptide was then used as the second reporter to screen IRESes in the engineered GS115 expressing the corresponding ω-peptide. A total of 34 reported IRESes were screened. After ruling out all false positive or negative IRESes, only seven IRESes were functional in P. pastoris, which were from TEV, PVY, RhPV, TRV, KSHV, crTMV viruses and the 5′-UTR of the YAP1 gene of S. cerevisiae.

Conclusions

We showed here that α-complementation also works in P. pastoris and it can be used in a variety of in vivo studies. The functional IRESes screened in this study can be used to introduce multiple genes into P. pastoris via a prokaryotic-like polycistronic manner, which provided new efficient tools for metabolic engineering and synthetic biology researches in P. pastoris.

Background

Pichia pastoris (today re-classified into the genus Komagataella), a methylotrophic yeast, has become an important industrial microorganism for the production of heterologous proteins due to its rapid growth, high-density fermentation, simple genetic manipulation and capacity of posttranslational modification [1]. The simple genetic organization (such as haploid and lack of introns on most genes), no overflow metabolism and the methanol assimilation pathway of P. pastoris determine its potential as a chassis strain for metabolic engineering and synthetic biology which has already attracted a lot of research interest soon after the whole genome and transcriptome sequencing of P. pastoris [2,3,4,5,6,7].

In metabolic engineering and synthetic biology, the production of synthetic molecules often involves integration of multiple genes or even entire metabolic pathways into the host. For example, in order to realize secretion of a human glycoprotein from P. pastoris, a total of 14 genes on the human glycosylation pathways were integrated into the yeast genome [8]. In the production of riboflavin, a total of six key genes in the riboflavin biosynthesis pathway were integrated into P. pastoris genome, which effectively increased the yield of riboflavin [9]. However, the expression of entire heterologous pathways is technically challenging in P. pastoris. Therefore, how to better solve co-expression of multiple genes is important for P. pastoris to become a highly efficient platform for the application of metabolic engineering and synthetic biology.

The current common approach to express multiple genes in P. pastoris is to construct multiple expression vectors (each vector with one target gene) or multiple expression cassettes in an expression vector (each cassette consisting of a promoter, a target gene and a terminator) [10,11,12]. The method for expressing multiple genes by multiple vectors requires some vectors and selectable markers together with repeated rounds of transformation and screening during genetic manipulation, which greatly increases the difficulty of successful genetic engineering. Using multiple expression cassettes in one expression vector to express multiple genes increases the chance of homologous recombination due to the use of too many identical promoter and terminator sequences and often leads to genetic instability [13].

Some viruses infecting eukaryotic cells can use the unique mRNA sequences on their untranslated regions (UTRs) called internal ribosome entry sites (IRESes) to directly recruit ribosomes to start cap-independent internal initiation for their protein synthesis [14]. The IRES elements were firstly observed in polio virus and encephalomyocarditis virus mRNAs [15, 16]. The cap-independent internal initiation translation was found not only in virus mRNAs but also in the UTRs of some eukaryotic mRNAs [17, 18]. The properties of IRES elements recruiting translational machinery to initiate protein synthesis by passing the requirement for the 7-methyl-guanosine cap at the 5′-end of the mRNA and its associated protein factors allow the construction of a bicistronic or polycistronic expression system to express multiple protein products using a single promoter and terminator in a single plasmid [19,20,21]. It has been reported that the drawbacks of double transformation and selection can be avoided by using an IRES to construct bicistronic vector [18]. Therefore, IRES may provide an effective approach for multiple gene expression in P. pastoris.

Some studies demonstrated that the yeast Saccharomyces cerevisiae has a potential to use IRES elements to initiate the translation [22,23,24,25], suggesting that IRES elements also are active in lower eukaryotes like yeast. Moreover, the 5′-UTR of GPR1 mRNA from S. cerevisiae was demonstrated to possess IRES activity [18]. After sequencing the P. pastoris transcriptome, Liang S et al. analyzed the 5′-UTR of 914 genes and first identified that the 5′-UTRs of GCN2 and KOG1 may contain functional IRESes [4]. These studies suggested that P. pastoris also has the potential to initiate the translation by cap-independent internal initiation. Many IRESes from viral RNA and cellular 5′-UTR functioning in S. cerevisiae, insects, plants or animals have been identified since the first IRES was discovered in 1988. They were well summarized in the review by Baird et al. [14]. It is still unknown whether the cellular protein synthesis apparatus in P. pastoris can efficiently handle these IRESes from other species, especially viruses. In this paper, we used a bicistronic reporter system with EGFP as the first reporter and α-peptide of β-galactosidase as the second reporter to screen 29 viral IRESes and five cellular IRESes from S. cerevisiae to find out functional IRESes in P. pastoris.

Results

Cryptic transcription of the LacZ gene in P. pastoris

Escherichia coli β-galactosidase [EC 3.2.1.23] is capable of decomposing X-gal (a colorless soluble compound) to form a galactose and a substituted indole that spontaneously dimerizes to give an insoluble, blue product. The microorganism expressing β-galactosidase forms blue colonies on the solid medium bearing X-gal, which makes β-galactosidase a convenient and effective reporter in microbial research [26]. Based on this property of β-galactosidase, we planned to use β-galactosidase as a reporter in bicistronic system to indicate the function of IRESes in P. pastoris. Several researchers have reported that cryptic promoters in plasmid backbones or reporter genes are able to drive transcription of reporter genes to generate unwanted aberrant transcripts [27,28,29]. If the reporter gene in reporter constructs can be transcribed by cryptic promoter in plasmid backbone or reporter gene itself, it will reduce the reliability of the experimental results especially in screening for functional IRESes. Therefore, we first verified whether the LacZ gene can be transcribed by possible cryptic promoter in plasmid backbone or reporter LacZ gene in P. pastoris. The promoter driving the expression of LacZ gene in the vector was removed to construct a promoterless vector pPICZA-Lac(-P) (Fig. 1a). The pPICZA-Lac(-P), positive vector pPICZA-LacZ and negative vector pPICZA were transformed into P. pastoris GS115, respectively. We found that the background activities of β-galactosidase were detected in GS115 with the transformation of pPICZA-Lac(-P) (Fig. 1b, c), indicating that there may be a cryptic promoter in plasmid backbone or LacZ gene to drive LacZ gene expression in P. pastoris.

Fig. 1
figure1

Background activity of LacZ gene in P. pastoris. a Schematic diagram of expression vectors with or without AOX1 promoter. b Analysis of enzymatic activity of β-galactosidase on BMMY plates containing X-Gal. The vector pPICZA-LacZ that the transcription of LacZ gene is driven by AOX1 promoter was used as positive control, and empty vector pPICZA was used as negative control. c Quantitative analysis of enzymatic activity of β-galactosidase

α-complementation of β-galactosidase in P. pastoris

Based on our results, screening for a functional IRESes directly using the full-length LacZ gene is not practical due to the cryptic transcription of LacZ gene in P. pastoris. As is known, the β-galactosidase is required to form a homotetramer to acquire enzymatic activity, and the formation of the homotetramer depends on the amino acid sequence of so-called α-peptide or α-donor at the N-terminus of β-galactosidase. If α-peptide is removed from the full-length enzyme, the remaining amino acid sequence (so-called ω-peptide or α-acceptor) does not form tetramers and has no enzymatic activity [30]. In an in vitro experiment, the activity of β-galactosidase could be restored in the presence of both the N-terminal α-peptide and the C-terminal ω-peptide, a phenomenon known as α-complementation, which has been used in bacteria and mammals [31,32,33]. If the α-complementation of β-galactosidase can be established in P. pastoris, it may solve the problem of cryptic transcription of LacZ gene through a bicistronic vector system. In order to establish an efficient α-complementation system, the expression vectors with α-peptide and ω-peptide of different lengths were constructed (Fig. 2a), and the corresponding vectors containing encoding sequences of α-peptide and ω-peptide were co-transformed into P. pastoris. The α-peptide with a length of 1–92 amino acids had the best complementary effect, and its enzymatic activity could reach about 65% of the full-length β-galactosidase activity (Fig. 2b, c). The size of the bicistronic vectors was particularly important in this study because 34 IRESes would be cloned into the bicistronic vectors and transformed into P. pastoris, the ligation and cloning efficiencies of which usually drop with the increase in vector size. Therefore, we decided to integrate the DNA sequence encoding ω-peptide which has the larger molecular weight into the P. pastoris’s genome to construct a transgenic strain expressing ω-peptide and clone the DNA sequence encoding the α-peptide as the second reporter gene inserted behind the IRESes sequence in the bicistronic vector. The encoding sequence of the α-peptide bearing 1–92 amino acids was then used as a reporter gene in the bicistronic vector for functional IRESes screening in the following studies.

Fig. 2
figure2

Development of the α-complementation of β-galactosidase in P. pastoris. a Schematic diagram of vectors containing α-peptides and ω-peptides with different lengths. b Detection of β-galactosidase activity on plates containing X-gal. Empty vector pAO815 and pPICZA as negative controls; full-length LacZ gene (LacZ WT) as a positive control. c The relative activities of β-galactosidase in the α-complementation systems with different lengths of α-peptide and ω-peptide. Normalization was performed with full-length β-galactosidase (LacZ WT) activity at 100%

Screening for functional IRESes in P. pastoris

To screen functional IRESes in P. pastoris, 34 IRES sequences that are functional in plants, mammals or S. cerevisiae were selected, 30 of which came from viruses and four from the 5′-UTR region of S. cerevisiae’s genes (Tables 1, 2 and Additional file 1). The 34 IRES sequences were cloned into the bicistronic vectors between the first reporter (EGFP) and the second reporter (α-peptide (1–92aa) of β-galactosidase). The encoding sequence of β-galactosidase ω-peptide was cloned into another vector for the construction of a transgenic strain GS115-LacZΔ (1–92) expressing ω-peptide (Fig. 3a). The 34 bicistronic vectors were separately transformed into GS115-LacZΔ (1–92), and the function of every IRES in P. pastoris was examined by detecting β-galactosidase activity. The β-galactosidase activities were only detected in 7 out of the 34 transformed strains, the IRES sequences in which came from TEV, PVY, RhPV, TRV, KSHV, crTMV viruses and the 5′-UTR of the YAP1 gene of S. cerevisiae (Fig. 3b, c). Of note, the transgene expression was often affected by integration location, transgene silencing, transgene loss, etc. [34,35,36]. Although the β-galactosidase activities were not detected in the other 27 transformed strains, it is possible that it was caused by transgene silencing or loss, rather than lack of IRES activity. To eliminate the false negative possibilities, the protein expression of the first reporter EGFP was examined by western blot. The EGFP proteins were all expressed in the 27 IRESes, which further confirmed that these 27 IRESes had no functional activity in P. pastoris (Additional file 2: Figure S1A). Among the seven functional IRESes, their β-galactosidase activities were different. Studies have shown that copy number of transgenes affected their expression in P. pastoris [37, 38]. To make sure that the difference of IRES activities was not caused by copy number difference of transgenes, relative copy numbers of the α-peptide sequence were examined by genomic real-time PCR [39]. There was no significant difference in the copy numbers of the seven IRESes (Additional file 2: Figure S1B), indicating that the differences of β-galactosidase activity are caused by translation efficiencies driven by different IRES sequences in P. pastoris.

Table 1 Viral IRES information involved in this study
Table 2 Gene 5′-UTR information involved in this study
Fig. 3
figure3

Screening for functional IRESes in P. pastoris. a Schematic diagram of the plasmid vectors. b Screening on the X-gal plate for functional IRESes in P. pastoris. Three different colonies were shown for each IRES. c Quantitative detection of β-galactosidase activity for seven functional IRESes in P. pastoris. The strains transformed with empty vector were used as negative control (NC)

Translational activity of the IRESes is not influenced by read-through, cryptic transcription or splicing

To further confirm the activity of the seven IRES sequences, several potential false positive possibilities need to be ruled out. If the ribosomes were not stopped at the stop codon of the first reporter and were read through the bicistronic mRNAs to the second reporter during translation, fusion proteins of EGFP and β-galactosidase α-peptide (1–92aa) would be produced (Fig. 4a). The fusion proteins could also function in α-complementation of β-galactosidase, resulting in a false positive result. If fusion proteins of EGFP and β-galactosidase α-peptide (1–92aa) were produced, they would be larger than EGFP (26.9 KD) and detected by western blotting. The anti-EGFP antibody was used to examine the fusion proteins of seven transgenic strains with β-galactosidase activity. No fusion proteins were detected in all seven cases (Fig. 4b).

Fig. 4
figure4

Exclusion of read-through of bicistronic mRNA. a Schematic diagram of proteins produced by non-read-through and read-through of bicistronic mRNA. b The fusion protein produced by read-through of bicistronic mRNA was excluded by western blot

The analysis of the genome sequences of P. pastoris showed that there are 5313 coding genes, of which 633 genes contained introns, indicating that P. pastoris has the ability for intron processing [40]. If there was a cryptic splicing site between the EGFP and LacZ (1–92) sequences in the bicistronic mRNA, the mRNA could be spliced by the splicing apparatus of P. pastoris to produce a monocistronic mRNA in which the IRES sequence was removed. In the monocistronic mRNA, the translation of the β-galactosidase α-peptide (1–92) would not be driven by the IRES in cap-independent translation but by cap-dependent translation (Fig. 5a). To exclude the possible occurrence of cryptic splicing in the bicistronic mRNAs, three pairs of overlapping primers (Gup and Gdown; Iup and Idown; Lup and Ldown) on the EGFP, IRES and LacZ (1–92) sequences were designed and used to detect mRNAs by RT-PCR. All three PCR products were correctly amplified, and the size of the products was the same as the expected size in all seven cases, indicating that there is no evidence for cryptic splicing or any kind of mRNA shortening in the bicistronic mRNAs (Fig. 5b).

Fig. 5
figure5

Detection of cryptic splicing in bicistronic mRNA by RT-PCR. a Schematic diagram of cryptic splicing and primer design. b Detection of RT-PCR products on agarose gel. NC, PCR negative control reaction without template. , reactions without or with reverse transcriptase, respectively

It is also possible that the expression of the reporter located in the second position is driven by cryptic promoter harbored in IRES sequence, but not the real activity of IRES [41, 42]. The internal initiation activities of IRESes observed in this study may be due to the cryptic promoters (Fig. 6a). To test whether a cryptic promoter was present in the IRES, the promoterless vectors without the AOX1 promoter were used (Fig. 6b). All seven IRESes (TEV, PVY, TRV, RhPV, KSHV crTMV and 5′-UTR of YAP1) could not induce the expression of LacZ (1–92aa) gene in the promoterless constructs (Fig. 6c), eliminating the possibility of a cryptic promoter within IRESes.

Fig. 6
figure6

Detection of cryptic promoter using promoterless vector. a Schematic diagram of producing LacZ (1–92) transcript with 5′ cap by a cryptic promoter harbor in IRES sequence. b Schematic diagram of promoterless vector removed the AOX1 promoter. c Detection of expression of the second reporter LacZ (1–92) with or without AOX1 promoter

Discussion

β-Galactosidase coding by LacZ gene from E. coli is very popular nowadays as a useful reporter in the research of microorganism due to its ability to hydrolyze the substrate X-gal to form blue colonies which is appropriate for screening. In this study, more than 30 IRES sequences coming from viruses and 5′-UTR of genes were examined in P. pastoris. Several published researches have reported that cryptic promoters or cryptic splicing sites present in plasmid backbone or reporter genes could generate unwanted aberrant transcripts which produce artifactual results including tests for IRES function [18, 27, 28]. In this study, we used promoterless vector to test possible aberrant transcript of LacZ gene in P. pastoris before IRES function was analyzed. The results clearly demonstrated that the strains transformed with promoterless vectors with LacZ gene possess β-galactosidase activity, indicating there probably could be cryptic promoter activity within the backbone of vector and/or reporter LacZ. It was reported that firefly luciferase gene from the common North American firefly photinus pyralis, another widely used reporter gene, also possesses a cryptic promoter activity that is detectable both in the budding yeast S. cerevisiae and in mammalian cells [27]. According to these findings, researchers must be aware of the unexpected transcription from cryptic or unusual sites bearing in the backbone of plasmid or reporter genes when the reporter system is employed to analyze cis-regulatory elements for the purposes of transcription or translation. Experiments carried out in microorganism are prone to be affected by cryptic transcription because they use shorter and simpler elements to initiate transcription compared to higher eukaryotes.

The α-complementation of β-galactosidase was firstly discovered by Jacob and Monod [32]. After that, α-complementation has been proved to function in vivo in bacteria, S. cerevisiae and in mammalian cells [33, 43, 44]. In this study, we successfully developed the α-complementation system of β-galactosidase in P. pastoris, where only successful mating cells have β-galactosidase activity when α-peptide and ω-peptide are expressed separately in cells of the opposite mating type. This system can be used as a marker for a variety of in vivo studies in P. pastoris, such as (i) protein folding and assembly; (ii) protein–protein interactions; (iii) protein trafficking, where only co-compartmentalization shall produce the α-complementation; (iv) processing of cleavage sites by proteases; and (v) easy monitoring of mating in P. pastoris. Thus, we believe that this system will become the basis of many experiments and applications in P. pastoris systems.

In this study, we used the α-peptide of β-galactosidase with the optimal length (1–92 amino acids) as the second reporter in bicistronic reporter vector to screen functional IRESes in P. pastoris. On total, seven IRESes from viruses of TEV, PVY, TRV, RhPV, KSHV crTMV and 5′-UTR of YAP1 gene were found to internally initiate expression of the second reporter in P. pastoris from the 34 selected IRESes. IRESes of TEV and PVY are more active than the other IRESes. In the yeast S. cerevisiae, the 5′ UTRs of TFIID, HAP4, p150 (also called TIF4631) and YAP1 genes were reported with the ability to initiate internal translation [45,46,47]. The 5′ UTRs of TFIID, HAP4, p150 and YAP1 were examined for the activity of IRES in P. pastoris, and only the 5′ UTR of YAP1 showed the ability to initiate internal translation. Our result indicated that the mechanism of cap-independent translation between S. cerevisiae and P. pastoris is different. The IRES from EMCV was reported to drive the translation of the second reporter, bacterial hygromycin B phosphotransferase (hph), as internal initiation element in P. pastoris [48]. However, we did not detect the activity of EMCV-IRES using our reporter system.

There are two modes of translation initiation: cap-dependent and cap-independent initiation of protein translation. In cap-independent initiation, the presence of the m7G structure at the 5′ terminus of the mRNA is not required. IRES has the ability to directly recruit ribosomes to initiate protein translation by forming special structures. Due to the property, IRESes are often used to express more than one gene in a dicistronic or polycistronic manner under a promoter control from one vector by prokaryotic-like polycistronic expression system. These IRESes screened in this study can be used not only in metabolic engineering and synthetic biology, which often required the expression of entire heterologous pathways, but also as models for studying cap-independent initiation of protein synthesis in P. pastoris.

Conclusions

In this study, we found that LacZ gene has background activity in P. pastoris. In order to eliminate the background activity of LacZ gene, we successfully developed the α-complementation system of β-galactosidase in P. pastoris. Co-expression of α- and ω-peptides recovers the enzymatic activity that is absent in the single components. The optimum length of the α-complementing peptide is ~ 92 amino acids. This α-complementation system provides useful tool for future in vivo studies in P. pastoris including protein folding and assembly, protein–protein interactions, protein trafficking, processing of cleavage sites by proteases and monitoring cell mating. The α-peptide (1–92aa) was then used as the second reporter in bicistronic vector to screen functional IRESes in P. pastoris. A total of seven IRESes from viruses of TEV, PVY, TRV, RhPV, KSHV crTMV and 5′-UTR of YAP1 gene were found to be functional in P. pastoris from the 34 selected IRESes. The two IRESes from TEV and PVY viruses are the most active ones. These functional IRESes can be used to introduce multiple genes into P. pastoris by a prokaryotic-like polycistronic manner, which are convenient for researches on metabolic engineering and synthetic biology using P. pastoris.

Materials and methods

Strains

Pichia pastoris GS115 is the host cell for expression, and Escherichia coli (E. coli) DH5α is the cloning host cell for genetic manipulation.

Plasmids

To carry out α-complementary of β-galactosidase in P. pastoris, a series of vectors were constructed. The LacZ gene was firstly amplified from pAd/CMV/V5-GW/LacZ and cloned into pPICZA at EcoRI site for construction of pPICZA-LacZ. N-terminal α-peptide encoding sequences with different lengths (encoding 1 to 33, 1 to 41, 1 to 92, 1 to 142 and 1 to 200 amino acids) and corresponding C-terminal ω-peptide sequences (encoding 34 to 1029, 42 to 1029, 93 to 1029 and 201 to 1029 amino acids) of β-galactosidase were amplified from plasmid pPICZA-LacZ using primers listed in Additional file 2: Table S1 and inserted into expression vectors pAO815 and pPICZA at EcoR I using a ClonExpress® II One Step Cloning Kit (Vazyme Biotech; Cat no. C112), respectively.

To screen functional IRES elements in P. pastoris, EGFP gene and LacZ (1–92) encoding 1 to 92 amino acids of β-galactosidase were used as the first and second cistrons, respectively. pPICZA plasmid was used to construct the dicistronic reporter vector. The EGFP gene and LacZ (1–92) were amplified from plasmid pEGFP-N1 and pPICZA-LacZ, respectively. The two fragments were assembled into one fragment using overlapping extension PCR (OE-PCR) method. A SnaBI site was introduced between EGFP and LacZ (1–92), which was used to clone IRES sequences into the dicistronic reporter vector. The assembled fragment EGFP-LacZ (1–92) was cloned into EcoRI site of pAO815 to form plasmid pAO815-EGFP-LacZ (1–92). All IRES elements in this study were synthesized with flanking ACGAGCTGTACAAGTAATAC in 5′ end and ACGACGGGATCTATCATTAC in 3′ end by Sangon Biotech (Shanghai) Co., Ltd., and subcloned into the SnaBI site of pAO815-EGFP-LacZ (1–92) to form the plasmid pAO815-EGFP-IRES-LacZ (1–92) using a ClonExpress® II One Step Cloning Kit.

Electroporation of P. pastoris

The P. pastoris GS115 cells were grown on a YPD plate (1% yeast extract, 2% tryptone, 2% dextrose and 1.5% agar) to isolate single colonies. A single colony of GS115 was picked from YPD plate and incubated at 30 °C overnight. 0.1 ml of the overnight culture was incubated in 100 ml fresh medium in a 500-ml flask to OD600 ≈ 1.5 before preparing competent cells. The competent cells were prepared with 1 M sorbitol solution according to Pichia Expression Kit Instruction Manual. The purified plasmid DNA was digested with restriction enzyme recommended by instruction manual to obtain linear plasmid DNA. The competent cells were mixed with 10 μg linear plasmid DNA and then add them to a 0.2 cm electroporation cuvette which was incubated about 5 min on the ice and placed in Bio-Rad Gene Pulser (Bio-Rad, USA) to electroporate with 25 vF, 200 Ω. Pre-chilled 1 M sorbitol was added immediately to the electroporation cuvette after pulsing, and the cells were transferred to a sterile 1.5-ml tube. After incubating at 30 °C for 1 h, the transformed cells were spread on MD (2% dextrose, 1.34% yeast nitrogen base, 4 × 10−5 % biotin and 1.5% agar) plates. The plates were incubated at 30 °C for 2–3 days until colonies appear.

Expression of the reporters in P. pastoris

Colonies of the successfully transformed P. pastoris cells were picked and incubated in a shaking incubator at 220 rpm in BMGY (1% yeast extract, 2% tryptone, 1.34% YNB, 1% glycerol, 100 mM potassium phosphate (pH 6.0) and 4 × 10−5% biotin) medium for about 24 h at 30 °C until the OD600 reached 2–5. After centrifugation at 3000 rpm for 5 min at room temperature, the supernatant was removed, and the cells were resuspended in BMMY (1% yeast extract, 2% tryptone, 1.34% YNB, 1% methanol, 100 mM potassium phosphate (pH 6.0) and 4 × 10−5% biotin) medium to OD600 ≈ 1 and incubated under the same conditions for 3 days to induce expression of the reporters. After induction, cells were harvested for further experimental studies.

Western blot

Harvested cells were washed once with 1-ml 1 M sorbitol, and the cells were resuspended by adding 100 μl breaking buffer (50 mM sodium phosphate, pH 7.4, 1 mM PMSF, 1 mM EDTA and 5% glycerol). An equal volume of acid-washed glass beads (Sigma; Cat no. G8772) was added to the resuspension. The mixture was vortexed for 30 s and then immediately placed on ice for 30 s. This operation was repeated eight times. The cell lysate was transferred to a new tube after centrifuging at 16,000 rpm for 10 min at 4 °C. Protein concentration was quantified by using Pierce™ BCA Protein Assay Kit (Thermo; Cat no. 23227) and then boiled and denatured at 95 °C for 5 min. For western blot analysis, the 30 μg samples were separated on 10% SDS-PAGE, and protein bands were transferred to Hybond-C nitrocellulose membrane (Amersham Bioscience, Little Chalfont, UK) through electroblotting. The membranes were blocked with 5% fat-free milk and probed overnight at 4 °C with primary antibody, against EGFP (Proteintech, China, Cat no. 50430-2-AP), and IRDye 800CW-conjugated goat anti-rabbit secondary antibodies (LI–COR Biosciences, Lincoln, NE, USA; cat. no. C60607–15) were used as the secondary antibody at 1:1000 dilutions. The signals were detected and measured using LICOR Odyssey system (LI–COR, Nebraska, USA).

Assay for β-galactosidase activity

For qualitative analysis of β-galactosidase activity, BMMY plates containing 200 μg/ml of X-Gal were prepared. Yeast transformants were transferred into BMMY plates with X-Gal from YPD plates using sterile toothpicks, and BMMY plates were grown for about 3 days at 30 °C until the blue colonies appeared.

For quantitative analysis of β-galactosidase activity, single colonies of transformants from YPD plates were grown at 30 °C for 24 h in 5 ml of BMGY. Cells were harvested and transferred into 5 ml of BMMY to grow at 30 °C until an optical density at 600 nm of about 1.0 was reached. Cells were harvested by centrifugation and washed using 1.0-ml sterile dH2O. After washing, cells were pelleted again and resuspended in breaking buffer (100 mM Tris–HCl, 1 mM dithiothreitol, 20% glycerol, pH 8.0). Glass beads were added into the tube with the cells in breaking buffer. Cell lysis was performed by vortexing six times at top speed in 15-s bursts (chilling on ice between bursts). The extract was clarified by centrifugation, and total protein concentration was determined by Bradford assay Pierce™ BCA Protein Assay Kit. Forty micrograms of total proteins was added to 500 μl Z buffer. In total, 200 μl of ONPG (4 mg/ml) was added to initiate the reaction at 28 °C. The reaction was stopped by adding Na2CO3 solution. Absorbance was determined at 420 nm. The results were normalized against protein concentration and incubation time.

RT-PCR

Total RNA was isolated from P. pastoris cells using the Yeast RNA Kit (Omega; cat. no. R6870). The cDNA was obtained by reverse transcription of total RNA according to the instructions of the GoScript™ Reverse Transcription Mix, Oligo (dT) kit (Promega; cat. no. A2790). The RT-PCR reaction system was prepared using a 2× M5 HiPer Taq PCR mix (Mei5bio; cat. no. MF001-01), and RT-PCR was performed in a SimpliAmp Thermal Cycler (Applied biosystems, USA). The primers used in RT-PCR are shown in Additional file 2: Table S1.

Availability of data and materials

The data supporting the conclusions of this article are included with the article and its additional file.

Abbreviations

IRES:

internal ribosome entry site

UTR:

untranslated region

EGFP:

enhanced green fluorescent protein

X-gal:

5-bromo-4-chloro-3-indolyl β-d-galactoside

OE-PCR:

overlapping extension PCR

ONPG:

2-nitrophenyl β-d-galactopyranoside

TEV:

Tobacco etch virus

PVY:

Potato virus Y

RhPV:

Rhopalosiphum padi

TRV:

Triatoma virus

KSHV:

Kaposi-sarcoma-associated herpesvirus

crTMV:

Tobacco mosaic virus

References

  1. 1.

    Ahmad M, Hirz M, Pichler H, Schwab H. Protein expression in Pichia pastoris: recent achievements and perspectives for heterologous protein production. Appl Microbiol Biotechnol. 2014;98(12):5301–17.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  2. 2.

    Gasser B, Mattanovich D. A yeast for all seasons—is Pichia pastoris a suitable chassis organism for future bioproduction? FEMS Microbiol Lett. 2018;365(17):fyn181.

    Article  CAS  Google Scholar 

  3. 3.

    Wagner JM, Alper HS. Synthetic biology and molecular genetics in non-conventional yeasts: current tools and future advances. Fungal Genet Biol. 2016;89:126–36.

    CAS  PubMed  Article  Google Scholar 

  4. 4.

    Liang S, Wang B, Pan L, Ye Y, He M, Han S, Zheng S, Wang X, Lin Y. Comprehensive structural annotation of Pichia pastoris transcriptome and the response to various carbon sources using deep paired-end RNA sequencing. BMC genomics. 2012;13:738.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  5. 5.

    Renuse S, Madugundu AK, Kumar P, Nair BG, Gowda H, Prasad TS, Pandey A. Proteomic analysis and genome annotation of Pichia pastoris, a recombinant protein expression host. Proteomics. 2014;14(23–24):2769–79.

    CAS  PubMed  Article  Google Scholar 

  6. 6.

    Yang Z, Zhang Z. Production of (2R, 3R)-2,3-butanediol using engineered Pichia pastoris: strain construction, characterization and fermentation. Biotechnol Biofuels. 2018;11:35.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  7. 7.

    Siripong W, Wolf P, Kusumoputri TP, Downes JJ, Kocharin K, Tanapongpipat S, Runguphan W. Metabolic engineering of Pichia pastoris for production of isobutanol and isobutyl acetate. Biotechnol Biofuels. 2018;11:1.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  8. 8.

    Hamilton SR, Davidson RC, Sethuraman N, Nett JH, Jiang Y, Rios S, Bobrowicz P, Stadheim TA, Li H, Choi BK, et al. Humanization of yeast to produce complex terminally sialylated glycoproteins. Science. 2006;313(5792):1441–3.

    CAS  PubMed  Article  Google Scholar 

  9. 9.

    Marx H, Mattanovich D, Sauer M. Overexpression of the riboflavin biosynthetic pathway in Pichia pastoris. Microb Cell Fact. 2008;7:23.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  10. 10.

    Gasser B, Sauer M, Maurer M, Stadlmayr G, Mattanovich D. Transcriptomics-based identification of novel factors enhancing heterologous protein secretion in yeasts. Appl Environ Microbiol. 2007;73(20):6499–507.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  11. 11.

    Gasser B, Maurer M, Gach J, Kunert R, Mattanovich D. Engineering of Pichia pastoris for improved production of antibody fragments. Biotechnol Bioeng. 2006;94(2):353–61.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  12. 12.

    Araya-Garay JM, Feijoo-Siota L, Rosa-dos-Santos F, Veiga-Crespo P, Villa TG. Construction of new Pichia pastoris X-33 strains for production of lycopene and beta-carotene. Appl Microbiol Biotechnol. 2012;93(6):2483–92.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  13. 13.

    Vogl T, Sturmberger L, Kickenweiz T, Wasmayer R, Schmid C, Hatzl AM, Gerstmann MA, Pitzer J, Wagner M, Thallinger GG, et al. A toolbox of diverse promoters related to methanol utilization: functionally verified parts for heterologous pathway expression in Pichia pastoris. ACS synthetic biology. 2016;5(2):172–86.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  14. 14.

    Baird SD, Turcotte M, Korneluk RG, Holcik M. Searching for IRES. RNA. 2006;12(10):1755–85.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  15. 15.

    Jang SK, Krausslich HG, Nicklin MJ, Duke GM, Palmenberg AC, Wimmer E. A segment of the 5′ nontranslated region of encephalomyocarditis virus RNA directs internal entry of ribosomes during in vitro translation. J Virol. 1988;62(8):2636–43.

    CAS  PubMed  PubMed Central  Google Scholar 

  16. 16.

    Pelletier J, Sonenberg N. Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA. Nature. 1988;334(6180):320–5.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  17. 17.

    Macejak DG, Sarnow P. Internal initiation of translation mediated by the 5′ leader of a cellular mRNA. Nature. 1991;353(6339):90–4.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  18. 18.

    Liang S, Lin Y, Li C, Ye Y. Internal ribosome entry site mediates protein synthesis in yeast Pichia pastoris. Biotechnol Lett. 2012;34(5):957–64.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  19. 19.

    Morgan RA, Couture L, Elroy-Stein O, Ragheb J, Moss B, Anderson WF. Retroviral vectors containing putative internal ribosome entry sites: development of a polycistronic gene transfer system and applications to human gene therapy. Nucleic Acids Res. 1992;20(6):1293–9.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  20. 20.

    Chen WS, Chang YC, Chen YJ, Chen YJ, Teng CY, Wang CH, Wu TY. Development of a prokaryotic-like polycistronic baculovirus expression vector by the linkage of two internal ribosome entry sites. J Virol Methods. 2009;159(2):152–9.

    CAS  PubMed  Article  Google Scholar 

  21. 21.

    Huang Y, Zhen R, Jiang M, Yang J, Yang Y, Huang Z, Lin Y. Development of all-in-one multicistronic Tet-O n lentiviral vectors for inducible co-expression of two transgenes. Biotechnol Appl Biochem. 2015;62(1):48–54.

    CAS  PubMed  Article  Google Scholar 

  22. 22.

    Rosenfeld AB, Racaniello VR. Components of the multifactor complex needed for internal initiation by the IRES of hepatitis C virus in Saccharomyces cerevisiae. RNA Biol. 2010;7(5):596–605.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  23. 23.

    Coordes B, Brunger KM, Burger K, Soufi B, Horenk J, Eick D, Olsen JV, Strasser K. Ctk1 function is necessary for full translation initiation activity in Saccharomyces cerevisiae. Eukaryot Cell. 2015;14(1):86–95.

    PubMed  Article  CAS  Google Scholar 

  24. 24.

    Hertz MI, Thompson SR. In vivo functional analysis of the Dicistroviridae intergenic region internal ribosome entry sites. Nucleic Acids Res. 2011;39(16):7276–88.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  25. 25.

    Landry DM, Hertz MI, Thompson SR. RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs. Genes Dev. 2009;23(23):2753–64.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  26. 26.

    Macgregor GR, Nolan GP, Fiering S, Roederer M, Herzenberg LA. Use of Escherichia coli (E. coli) LacZ (beta-Galactosidase) as a reporter gene. Methods Mol Biol. 1991;7:217–35.

    CAS  PubMed  Google Scholar 

  27. 27.

    Vopalensky V, Masek T, Horvath O, Vicenova B, Mokrejs M, Pospisek M. Firefly luciferase gene contains a cryptic promoter. RNA. 2008;14(9):1720–9.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  28. 28.

    Rosfjord E, Lamb K, Rizzino A. Cryptic promoter activity within the backbone of a plasmid commonly used to prepare promoter/reporter gene constructs. In vitro Cell Dev Biol Anim. 1994;30a(7):477–81.

    CAS  PubMed  Article  Google Scholar 

  29. 29.

    Boshart M, Kluppel M, Schmidt A, Schutz G, Luckow B. Reporter constructs with low background activity utilizing the cat gene. Gene. 1992;110(1):129–30.

    CAS  PubMed  Article  Google Scholar 

  30. 30.

    Jacobson RH, Zhang XJ, DuBose RF, Matthews BW. Three-dimensional structure of beta-galactosidase from E. coli. Nature. 1994;369(6483):761–6.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  31. 31.

    Gallagher CN, Roth NJ, Huber RE. A rapid method for the purification of large amounts of an alpha-complementing peptide derived from beta-galactosidase (E. coli). Prep Biochem. 1994;24(3–4):297–304.

    CAS  PubMed  PubMed Central  Google Scholar 

  32. 32.

    Ullmann A, Jacob F, Monod J. Characterization by in vitro complementation of a peptide corresponding to an operator-proximal segment of the beta-galactosidase structural gene of Escherichia coli. J Mol Biol. 1967;24(2):339–43.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  33. 33.

    Moosmann P, Rusconi S. Alpha complementation of LacZ in mammalian cells. Nucleic Acids Res. 1996;24(6):1171–2.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  34. 34.

    Flagfeldt DB, Siewers V, Huang L, Nielsen J. Characterization of chromosomal integration sites for heterologous gene expression in Saccharomyces cerevisiae. Yeast. 2009;26(10):545–51.

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  35. 35.

    Markstein M, Pitsouli C, Villalta C, Celniker SE, Perrimon N. Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes. Nat Genet. 2008;40(4):476–83.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  36. 36.

    Choi HW, Lemaux PG, Cho MJ. Long-term stability of transgene expression driven by barley endosperm-specific hordein promoters in transgenic barley. Plant Cell Rep. 2003;21(11):1108–20.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  37. 37.

    Wang QH, Gao LL, Liang HC, Gong T, Yang JL, Zhu P. Research advances of the influence factors of high level expression of recombinant protein in Pichia pastoris. Acta pharmaceutica Sinica. 2014;49(12):1644–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  38. 38.

    Jiao L, Zhou Q, Su Z, Xu L, Yan Y. High-level extracellular production of Rhizopus oryzae lipase in Pichia pastoris via a strategy combining optimization of gene-copy number with co-expression of ERAD-related proteins. Protein Expr Purif. 2018;147:1–12.

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  39. 39.

    Huang Y, Zhen B, Lin Y, Cai Y, Lin Z, Deng C, Zhang Y. Expression of codon optimized human bone morphogenetic protein 4 in Pichia pastoris. Biotechnol Appl Biochem. 2014;61(2):175–83.

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  40. 40.

    De Schutter K, Lin YC, Tiels P, Van Hecke A, Glinka S, Weber-Lehmann J, Rouze P, Van de Peer Y, Callewaert N. Genome sequence of the recombinant protein production host Pichia pastoris. Nat Biotechnol. 2009;27(6):561–6.

    PubMed  Article  CAS  Google Scholar 

  41. 41.

    Hecht K, Bailey JE, Minas W. Polycistronic gene expression in yeast versus cryptic promoter elements. FEMS Yeast Res. 2002;2(2):215–24.

    CAS  PubMed  Article  Google Scholar 

  42. 42.

    Wang Z, Weaver M, Magnuson NS. Cryptic promoter activity in the DNA sequence corresponding to the pim-1 5′-UTR. Nucleic Acids Res. 2005;33(7):2248–58.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  43. 43.

    Welply JK, Fowler AV, Zabin I. beta-Galactosidase alpha-complementation. Effect of single amino acid substitutions. J Biol Chem. 1981;256(13):6811–6.

    CAS  PubMed  Google Scholar 

  44. 44.

    Abbas-Terki T, Picard D. Alpha-complemented beta-galactosidase. An in vivo model substrate for the molecular chaperone heat-shock protein 90 in yeast. Eur J Biochem. 1999;266(2):517–23.

    CAS  PubMed  Article  Google Scholar 

  45. 45.

    Iizuka N, Najita L, Franzusoff A, Sarnow P. Cap-dependent and cap-independent translation by internal initiation of mRNAs in cell extracts prepared from Saccharomyces cerevisiae. Mol Cell Biol. 1994;14(11):7322–30.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  46. 46.

    Zhou W, Edelman GM, Mauro VP. Transcript leader regions of two Saccharomyces cerevisiae mRNAs contain internal ribosome entry sites that function in living cells. Proc Natl Acad Sci USA. 2001;98(4):1531–6.

    CAS  PubMed  Article  Google Scholar 

  47. 47.

    Edwards SR, Wandless TJ. Dicistronic regulation of fluorescent proteins in the budding yeast Saccharomyces cerevisiae. Yeast. 2010;27(4):229–36.

    CAS  PubMed  PubMed Central  Google Scholar 

  48. 48.

    Xu L, Gang W, Wang W, Lv X, Yan A. Development of a prokaryotic-like polycistronic expression system based on a virus-originated internal ribosome entry site (IRES) in industrial eukaryotic microorganisms. Rsc Adv. 2014;4(93):51615–8.

    CAS  Article  Google Scholar 

Download references

Acknowledgements

Not applicable.

Funding

This project is financed by the Natural Science Foundation of Fujian Province (2016J01146) and the Scientific Research Innovation Team Construction Program of Fujian Normal University (IRTL1702).

Author information

Affiliations

Authors

Contributions

YH and YL conceived and designed the experiments. YZ and YH performed the majority of the laboratory work. SL and TL completed the α-complementation of β-galactosidase. JW constructed plasmids. YH and SL wrote the manuscript. YL revised the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Yide Huang or Yao Lin.

Ethics declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Huang, Y., Zhang, Y., Li, S. et al. Screening for functional IRESes using α-complementation system of β-galactosidase in Pichia pastoris. Biotechnol Biofuels 12, 300 (2019). https://doi.org/10.1186/s13068-019-1640-3

Download citation

Keywords

  • Pichia pastoris
  • IRES
  • β-Galactosidase
  • α-Complementation
  • Multigene co-expression