Heterologous Expression of Bovine Prochymosin in Pichia pastoris GS115

Document Type: Short Paper


1 National Institute of Genetic Engineering and Biotechnology, Tehran, IR Iran and Departments of Biology, Faculty of Microbiology, Alzahra University, Tehran, IR Iran

2 National Institute of Genetic Engineering and Biotechnology, Tehran, IR Iran

3 Departments of Biology, Faculty of Microbiology, Alzahra University, Tehran, IR Iran


Objectives: In present research we evaluate the expression of this critical enzyme in a eukaryotic system for future use in cheese industry.
Materials and Methods: We have cloned bovine prochymosin gene in methylotrophic yeast, P. pastoris, using pPIC9K as an expression vector. The recombinant plasmid was transformed into the host by electroporation, and it was expressed in optimum con‌ditions (temperature 29oC, 200 rpm, 2% methanol for induction, and 5 days of incuba‌tion). Transcription and expression of the recombinant prochymosin was evaluated by the reverse transcription polymerase chain reaction (RT-PCR), sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis as well as western blotting and enzyme-linked immunosorbent assay (ELISA).
Results: In optimum conditions, only a low level of this heterologous protein was de‌tected using ELISA method and subsequently confirmed by RT-PCR.
Conclusions: Since it has been reported that P. pastoris is an appropriate host for the ex‌pression of recombinant proteins, a low level of expression of prochymosin in this host should be explored in our future research.


1. Background

Chymosin is an aspartic proteinase (EC that is responsible for the coagulation of milk in the fourth stomach of unweaned calves (1). This enzyme (35.6 kDa) is secreted by the cells of the gastric mucosa as an inactive precursor, known as prochymosin (40.8 kDa). In the acid­ic conditions of the lumen, it is subsequently converted to chymosin, by autocatalytic cleavage of the 42-amino acid N-terminal prosequence (2). Chymosin is used exten­sively in cheese production because of specific cleavage of κ-casein, at the Phe105 – Met106 bond. Due to a short­age of calf stomachs, it is possible to clone the gene for calf chymosin in appropriate vectors and express them in different hosts including E. coli, (Chy-Max, Pfizer, Milwau­kee, USA), Kluyveromyces lactis (Maxiren, Gist-Brocades, Delft, Holland) and Aspergillus niger var. awamori (Chy­mogen, Genencor, Palo Alto, CA, USA) (3). The methylotro­phic yeast Pichia pastoris is suitable for the expression of eukaryotic proteins. P. pastoris has numerous advantages of higher eukaryotic expression systems, but the ease of its genetic manipulation is similar to E. coli and S. cerevi­siae. The other advantage of P. pastoris is that the ultra­high cell densities are easily achieved at minimal costs (4, 5). The P. pastoris expression system has been used successfully for the production of different recombinant heterologous proteins, such as A. awamori glucoamylase, Aspergillus oryzae Tannase, Rhizopus oryzae lipase, E. coli L-galactosidase, dengue virus structural protein, human granulocyte-colony stimulating factor and human eo­sinophil peroxidase (6, 7). In most cases, the alcohol oxi­dase I promoter (PAOXI) was used for the expression of heterologous genes, and vectors integrate into the Pichia genome. PAOXI is completely repressed when cells have used glucose as carbon source, and induced in the pres­ence of methanol (4).

2. Objectives

Ahmadian et al. (1) have shown that the expression of recombinant prochymosin in E.coli system was accept­able, but the formation of inclusion bodies and the neces­sity for refolding and activation of the produced enzyme, caused to evaluate the expression of this important en­zyme in a eukaryotic system for meet the dairy industry’s needs.

3. Materials and Methods

In the present study, the bovine prochymosin gene, was cloned in pPIC9K, at NotI-SnaBI site, under the control of alcohol oxidase I promoter (PAOXI) and with Saccharo­myces cerevisiae alpha factors (α-MF) to secrete proteins into the medium. The recombinant plasmid (pPIC9K/Prochymosin) was transformed into E. coli strain TOP10 for amplification of plasmid. Approximately 10 μg of re­combinant expression plasmid was linearized with SacΙ. Transformation of P. pastoris strain GS115 was made using electroporation following manufacturer’s recommenda­tions (Invitrogen) by a Gene Pulser (Bio-Rad) using 80 µg of competent cells. The recombinant GS115 strain was cul­tured on Yeast Extract Peptone Dextrose (YPD) Medium plus 2% agar. The strain GS115 has a mutation in the his­tidinol dehydrogenase gene (his4) that prevents it from synthesizing histidine. The expression plasmid carries the HIS4 gene that complements his4 in this host, so the transformed cells are selected for their ability to grow on a histidine-deficient medium (Minimal Dextrose or MD: 1.34% yeast nitrogen base without amino acids, 4×10-5 % bio­tin, 2% dextrose and 2% agar) by incubation at 28 - 30°C for 4 days. PCR amplification was used to verify the prochy­mosin gene integration into the AOX1 locus in the chro­mosome of the transformed P. pastoris. For PCR amplifi­cation, the reactions were carried out in a GeneAmp PCR system 9700 (PE Applied Biosystems) with conditions of denaturation at 94o C for 3 min; 30 cycles for amplifica­tion (at 94oC / 60 sec, 53oC / 60 sec, and 72oC / 150 sec); and the final extension at 72oC for 300 sec. The reaction mix­ture contained 0.2 mM of each primers (F primer 5′-AOX1:  5´-GACTGGTTCCAATTGACAAGC-3´; and R primer 3′-AOX1: 5′-GCAAATGGCATTCTGACATCC-3´), 2 mM MgCl2, 2.5 U of PFU DNA polymerase (Fermentas) and extracted genome of recombinant pichia strains as a template. Gene inser­tion events at the AOX1 (GS115) loci arise from a single crossover event between the loci and any of the three AOX1 regions on the vector. These events result in the in­sertion of one or more copies of the vector upstream or downstream of the AOX1. The phenotype of such a trans­formant is His+ Mut+ that can utilize methanol quickly. For confirmation of gene insertion, two different PCR products from two clones were selected and their nucleo­tide sequences were determined (MWG, Germany). The pPIC9K vector contains bacterial kanamycin gene that confers resistance to geneticin in P. pastoris. Because of the genetic linkage between the kanamycin gene and the “expression cassette”, a single copy of pPIC9K integrated into the Pichia genome confers ~ 0.25 mg.mL-1 resistance to geneticin. Multiple integrated copies of pPIC9K can in­crease the geneticin resistance level from 0.5 mg.mL-1 (1 - 2 copies) up to 4 mg.mL-1 (7 - 12 copies). Protein expression may upsurge as a result of the gene dosage effect; it in­volves growing colonies in microtiter plates until all col­onies reach to the same density. The colonies were then spotted on the YPD-geneticin plates (in different concen­trations of geneticin: 0.25, 0.5, 1.0, and 2.0 mg.mL-1) and scored for geneticin resistancy. For expression of the re­combinant protein, selected colonies were inoculated into 10 mL Buffered Minimal Glycerol-complex (BMGY) Medium (1% (w/v) yeast extract, 2% (w/v) peptone, 0.1M phosphate buffer (pH 6.0), 1.34% yeast nitrogen base, 4×10-5 % biotin and 1% (v/v) glycerol), and were incubated at 28°C in a shaker incubator at 180 rpm until it reached A600 of 2-6 as per the manufacturer’s recommendation. The cells were harvested by centrifugation and resus­pended in 50 mL of Buffered Minimal Methanol-complex (BMMY) Medium (the same as BMGY except that glycerol was replaced by 2% v/v Methanol), to A600 of 1.0 in a 250 mL conical flask. Incubation was continued at 29°C in a shaker incubator at 200 rpm with the addition of meth­anol every 24 hours to achieve a concentration of 2% to sustain the induction for 5 days (based on our optimiza­tion experiments). Samples with high copy numbers of the prochymosin gene were analyzed for transcription of the prochymosin gene. RNA was extracted from the dis­rupted cells according to the RNAfast protocol following the manufacturer’s recommendation. Isolated RNA was used as the template in reverse transcription reaction. First strand cDNA synthesis was performed using Revert AidTM First Strand cDNA Synthesis Kit (Fermentase). The cDNA produced was used as a template for amplification by PCR. After every induction, recombinant proteins se­creted into the medium, were precipitated using ammo­nium sulphate and 80% TCA solutions. Protein samples were dialyzed against a solution of 100mM Tris-Hcl pH 8.0 for removing the salts. The solution was loaded onto Ni-NTA column for purifying 6XHis-tagged proteins. The protein samples were separated by electrophoresis on a 12% SDS-PAGE gel. The expression of prochymosin was determined using a monoclonal anti-6Xhis-tag antibody (Serotec, USA) as a first antibody (2 µg.mL-1) and a 1:2000 dilution of polyclonal rabbit anti-mouse immunoglobu­lin/HRP (Roche, Germany) as a second through western blotting. Finally, protein samples were visualized using DAB/H2O2 chromogen-substrate solution. Expression of the recombinant prochymosin was also confirmed by Enzyme Linked Immunosorbent Assay (ELISA) using an­ti-prochymosin polyclonal antibody as a first antibody (of 1/500 in PBS) and a polyclonal rabbit anti-mouse im­munoglobulin/HRP (diluted 1:2000 in PBS) as a second. Finally, protein samples were visualized using freshly prepared chromogen-substrate mixture (ABTS/H2O2). The positive results are shown as green color, but we used ELI­SA-reader (for reading absorption in 405 nm) for quanti­tative evaluation.

4. Results

To confirm the transformation of recombinant plasmid (pPIC9K/ the approximately 1100 bp fragment of bovine prochymosin gene which fused to six histidine tag at its 3’ end) in E. coli strain TOP10, we have used digest check as described in Figure 1. In results of PCR experiments, two expected bands (a 1.5 kb and another 2.2 kb) were detected (Figure 2A). The results of sequencing showed that recombinant prochymosin is the same as Bos taurus chymosin precursor (mRNA, complete cds) present in the gene bank (Accession number: FJ768675.1), and also the one which was previously cloned and sequenced by Ah­madian et al. (1). In our studies only a few high-geneticin resistant colonies were observed (colonies number 3, 6, 7, 8, 14, and 24), which were smaller in sizes than low-geneti­cin resistant colonies but their morphology were similar. Colony number 6, which has grown on 2 mg.mL-1 geneti­cin, was selected for expression of recombinant protein in a shake flask; and colony number 10 for comparison. The expression of precipitated 40 kDa protein (prochy­mosin) from the supernatant of growing medium of the colony number 6 was detected only with ELISA analysis as a green color with A405 = 0.051 with an average of three repeats. The low level of expression was below the limit of detection sensitivity of Western blotting. The colony number 10 didn’t show any detectable expression of tar­get protein.  The result of RT-PCR analysis was same as the PCR amplification of target gene as described previously (2 bands), and confirms the result of ELISA analysis (Fig­ure 2B).

5. Discussion

Hence, in optimum conditions for the expression of prochymosin gene in P. pastoris, only a low level of re­combinant protein was detected using ELISA method and subsequently confirmed by RT-PCR. Although it has been reported that P. pastoris represents an appropriate host for the expression of recombinant proteins, the low level of expression in this host could be attributed to several factors. These potential impediments include, the lack of consistency of codon usage of the bovine and pichia (8), copy number of the gene (9), the efficiency and strength of promoters (10), efficiency of translation signals (11) and signal peptides (12), processing and folding in the en­doplasmic reticulum and Golgi apparatus (13), environ­mental factors of expression (14), extracellular secretion (15), and protein turnover by proteolysis (16, 17). As the re­combinant, colony number 6 is high geneticin resistant (which grown on 2 mg/mL of this Antibiotic), the copy number of the gene was not restrictive for recombinant protein production. We have used some protease inhibi­tors such as EDTA (5 mM) to reduce proteolysis in pro­duction process. Therefore, it remains to be determined which of these factors resulted in the enhancement of prochymosin production existing in the machinery of P. pastoris. The fermentation can be easily scaled up to achieve greater level of expression. Meanwhile, the pa­rameters influencing the growth and protein produc­tivity of P. pastoris (such as pH, aeration, carbon and ni­trogen source feed rate) can be controlled. According to some reports, the expression level could be increased by growing the recombinant Pichia in a fermentor, as the higher cell density could improve the production rate of prochymosin. In the fermentor, 3 - 5 times higher tran­scription levels can be obtained as a consequence of the controlled methanol concentration (18). Additionally, it is shown that codon optimization of prochymosin gene can further improve the expression level (8, 19).


The authors thank the National Institute of Genetic En­gineering and Biotechnology (NIGEB) of Iran for support and funding. We would like to thank Dr. Mehdi Sham­sAra, faculty member at the NIGEB for his useful com­ments and Mr. Mostafa Keshavarz for his experimental assistance during the course of this research.

Authors’ Contribution

Gholamreza Ahmadian was corresponding author. Sara Sadr Mohammad Beigi wrote the manuscript and is guarantor. Sara Sadr Mohammad Beigi and Fatemeh Ramezani equal contributed to the development of the protocol, abstracted data, and repaired the manuscript. Soheila Ghandili and Mohammadreza Soudi were techni­cal assistant and advisor respectively.

Financial Disclosure

We have no financial interests related to the material in the manuscript.

Funding/ Support

This project was supported by grant No.432 from Na­tional Institute of Genetic Engineering and Biotechnol­ogy, Tehran, I.R. Iran.

1.      Fox PF, McSweeney PLH. Rennets: their role in milk coagulation and cheese ripening. In: Law BA, editor. Microbiol Biochem Cheese and Fermented Milk J. London: Blackie Academic and Professional; 1999. p. 1-49.

2.      Foltmann B. Prochymosin and chymosin (prorennin and ren­nin). In: E. G, Perlmann LL, editors. Met  Enzymol: Academic Press; 1970. p. 421-36.

3.      Badiefar L, Ahmadian G, Asgarani E, Ghandili S, Salek Esfahani M, Khodabandeh M. Optimization of conditions for expression and activation of a splice variant of prochymosin lacking exon 6 in Escherichia coli. Int J Dairy Tech. 2009;62(2):265-71.

4.      Ahn J, Hong J, Lee H, Park M, Lee E, Kim C, et al. Translation elon­gation factor 1-alpha gene from Pichia pastoris: molecular clon­ing, sequence, and use of its promoter. Appl Microbiol Biotechnol. 2007;74(3):601-8.

5.      Skoko N, Argamante B, Grujicic NK, Tisminetzky SG, Glisin V, Lju­bijankic G. Expression and characterization of human interfer­on-beta1 in the methylotrophic yeast Pichia pastoris. Biotechnol Appl Biochem. 2003;38(Pt 3):257-65.

6.      Saeedinia A, Shamsara M, Bahrami A, Zeinoddini M, Naseeri-Khalili MA, Mohammadi R, et al. Heterologous expression of hu­man granulocyte-colony stimulating factor in Pichia pastoris. Biotechnol J. 2008;7(3):569-73.

7.      Ciaccio C, Gambacurta A, De Sanctis G, Spagnolo D, Sakarikou C, Petrella G, et al. rhEPO (recombinant human eosinophil peroxi­dase): expression in Pichia pastoris and biochemical character­ization. Biochem J. 2006;395(2):295-301.

8.      Outchkourov NS, Stiekema WJ, Jongsma MA. Optimization of the expression of equistatin in Pichia pastoris. Protein Expr Purif. 2002;24(1):18-24.

9.      Vassileva A, Chugh DA, Swaminathan S, Khanna N. Effect of copy number on the expression levels of hepatitis B surface antigen in the methylotrophic yeast Pichia pastoris. Protein Expr Purif. 2001;21(1):71-80.

10.   Sears IB, O’Connor J, Rossanese OW, Glick BS. A versatile set of vectors for constitutive and regulated gene expression in Pichia pastoris. Yeast. 1998;14(8):783-90.

11.   Cavener DR, Ray SC. Eukaryotic start and stop translation sites. Nucleic Acids Res. 1991;19(12):3185-92.

12.   Raemaekers RJ, de Muro L, Gatehouse JA, Fordham-Skelton AP. Functional phytohemagglutinin (PHA) and Galanthus nivalis agglutinin (GNA) expressed in Pichia pastoris correct N-terminal processing and secretion of heterologous proteins expressed us­ing the PHA-E signal peptide. Eur J Biochem. 1999;265(1):394-403.

13.   Kowalski JM, Parekh RN, Mao J, Wittrup KD. Protein folding sta­bility can determine the efficiency of escape from endoplasmic reticulum quality control. J Biol Chem. 1998;273(31):19453-8.

14.   Villatte F, Hussein AS, Bachmann TT, Schmid RD. Expression level of heterologous proteins in Pichia pastoris is influenced by flask design. Appl Microbiol Biotechnol. 2001;55(4):463-5.

15.   Rossini D, Porro D, Brambilla L, Venturini M, Ranzi BM, Vanoni M, et al. In Saccharomyces cerevisiae, protein secretion into the growth medium depends on environmental factors. Yeast. 1993;9(1):77-84.

16.   Cregg JM, Cereghino JL, Shi J, Higgins DR. Recombinant protein expression in Pichia pastoris. Mol Biotechnol. 2000;16(1):23-52.

17.   Zahri S, Zamani MR, Motallebi M, Sadeghi M. Cloning and charac­terization of cbhII gene from Trichoderma parceramosum and its expression in Pichia pastoris. IranJ Biotech. 2005;3(4):204-15.

18.   Cereghino JL, Cregg JM. Heterologous protein expression in the methylotrophic yeast Pichia pastoris. FEMS Microbiol Rev. 2000;24(1):45-66.

19.   Feng Z, Zhang L, Han X, Zhang Y. Codon optimization of the calf prochymosin gene and its expression in Kluyveromyces lactis. World J Microb  Biotech. 2010;26(5):895-901.