Current Opinion in Biotechnology Vol. 6, No. 5, October 1995 Advances in the use of Pichia pastoris for high-level gene expression [Review article] Mike Romanos Current Opinion in Biotechnology 1995, 6:527-533. |
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In the past few years, the Pichia pastoris expression system has rapidly achieved much wider use thanks to increasing awareness of the early successes and to its sale in kit form by Invitrogen (San Diego, USA). From being a specialist system, used primarily by yeast groups in biotechnology companies, it is now a mainstream expression host used alongside Escherichia coli, Saccharomyces cerevisiae, and baculovirus. This was clear from the diverse interests of delegates at a recent Pichia meeting (San Diego, USA, 1994) organized by Invitrogen.
Pichia is an industrial methylotrophic yeast initially chosen for production of single-cell protein because of its ability to grow to very high cell density in simple defined media. From this basis, a highly efficient expression system was designed using the methanol-inducible alcohol oxidase 1 (AOX1) promoter and vectors that integrate into the Pichiagenome [1]. Several examples show that Pichia can routinely achieve percentage yields (540% of cell protein) much higher than baker's yeast, and often equivalent to E. coli or baculovirus [1][2]. Additionally, scale-up of Pichia culture to high cell density is simple and has resulted in enormous yields on a volumetric basis (e.g. >12 gl-1 for tetanus toxin fragment C [3] and >3 gl-1 secreted human serum albumin [HSA] [4]).
Although most Pichia expression vectors are very similar, different strategies can be employed because a selection of host phenotypes and chromosomal sites of integration is available. This gives greater scope for optimizing expression, but has caused some confusion, particularly among users unfamiliar with yeast genetics. In this review, I attempt to clarify the choices that are available and give suggestions as to when they should be used. I also discuss some of the most recent developments and results with the Pichia system, and provide an update on some of the many Pichia-derived products in commercial development or about to reach the market.
Pichia has the following main advantages: first, extremely high yields of intracellular proteins; second, very high levels of secretion into an almost protein-free medium; third, ease of fermentation to high cell density; and fourth, genetic stability and scale-up without loss of yield. It is proving valuable in producing large amounts of protein for analytical studies; one interesting recent application is in efficient in vivo isotopic labelling of proteins for NMR [5]. The system is almost certainly the simplest of any to scale up, a feature that makes it very attractive for rapid production of biological products for clinical trials.
Fig. 1.Two typical Pichia expression vectors, pPIC3 and pPIC3K.(a) Vector pPIC3 comprises a 5' AOX1 region including promoter, cloning site polylinker, AOX1 terminator (AOX1t), HIS4marker, 3' AOX1 region and ampicillin-resistance marker (Ap). (b) Vector pPIC3K, in addition to the above, contains the kanamycin-resistance (kanr) marker for G418 selection of multicopy transformants. |
Like any other expression system, however, Pichia is no panacea, and examples of low yields or failure of expression are also accumulating, though many remain unpublished. Probably the commonest problem encountered is proteolysis of secreted polypeptides [1], though a number of ways of overcoming this have become available. Another common problem is inefficient secretion of complex foreign proteins (e.g. HIV-1 gp120 [6]). Despite many examples of yields in the grammes per litre range, heterologous secretion is more demanding than intracellular expression and not guaranteed to work. Finally, some genes do not give any detectable protein, often because yeast transcriptional terminators result in truncated mRNA. The problem was first described for the highly AT-rich tetanus toxin gene in S. cerevisiae and solved by gene synthesis to increase the GC content [2]. The same problem has been seen in Pichia and solved in the same way (e.g. with the Bacillus sphaericus Bsp2 insecticidal toxin [P1] and with HIV-1 Env [6]). It is noteworthy that the Env DNA, which is not AT-rich, is efficiently transcribed in S. cerevisiae.
As Pichia has no stable episomal vectors, integrating vectors are employed. All use HIS4 as a selectable marker and have the same general organization, as exemplified by pPIC3 (Fig. 1). Some of the most useful vectors and their properties are listed in Table 1. The most commonly used host strain is GS115 (his4), but the more recently available protease-deficient strains (e.g. SMD1168;his4, pep4) are finding increasing use in reducing proteolytic cleavage of secreted proteins. KM71 (his4, aox1) and other strains that have an inactive AOX1 gene, are fundamentally different in that they grow very slowly on methanol as a carbon source, for example, during induction (i.e. they have a Muts phenotype, rather than the Mut+ phenotype of GS115).
Table 1. Pichia expression vectors. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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*The cloning site is not unique, thus three-way ligations are used. [a] K Sreekrishna, K Kropps, personal communication. (For further details contact K Sreekrishna, Marion Merrell Dow Inc, 2110 East Galbraith Road, PO Box 156300, Cincinnati, Ohio 45215, USA.) |
Expression vectors are directed to integrate into the Pichiagenome in one of two ways, depending on where the DNA is cut before transformation (see Table 2). Digestion to give a DNA fragment with homology to AOX1 at both ends leads to replacement of genomic AOX1 by the fragment (i.e. transplacement) and generates a Muts recombinant strain. Linearization of the vector, by cutting either 5' to the AOX1 promoter or within the HIS4 marker, directs integration of the plasmid at the homologous sites in the genome. The Mut phenotype of the latter type of transformant is dictated by the host strain used.
Table 2. Types of Pichia transformant. | |||||||||||||||||||||||||||||||||||
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*These sites are common to all vectors and can be used generally, unless present in the foreign gene. The vector pHIL-D2 has NotI sites in place of BglII and can be used when the foreign gene contains BglII sites. This problem does not often occur in small-scale cultures. |
Some unexpected features of Pichia transformations increase the number of types of transformant and thus the potential for confusion. With integration at AOX1 or HIS4, multicopy transformants (up to 10) can arise from repeated recombination events. On the other hand, transplacement would be expected to yield only single-copy Muts transformants; however, a detailed analysis has revealed three sources of heterogeneity among the transformants [3]. First, a high proportion of 'transformants' contain no vector, express no foreign protein and probably represent his4gene conversions. Second, only 530% are true transplacements (Muts), the remainder have integrations at AOX1 or HIS4 and are Mut+. Finally, 110% of Mutstransformants have up to 30 integrated copies of the transplacing fragment as tandem head to tail repeats that probably arise by a mechanism involving in vivo ligation [3]. The Mut+ population also contains multicopy clones. Although transplacement usually requires the laborious sphaeroplast transformation technique because of low frequencies, it yields a highly divergent population of transformants, which is useful for detailed optimization studies. Also, it seems to be the only way of obtaining very high copy number transformants.
In some of the earliest studies, expression of -galactosidase and hepatitis B surface antigen was not improved by increasing vector copy number [7][8]. In numerous subsequent examples, however, the isolation of multicopy integrants has resulted in dramatically higher yields [3][9][10][11]. In a detailed study of tetanus toxin fragment C, our group [3] showed that expression was correlated with copy number (114 copies), whereas site of integration and Mut phenotype had, at most, only a minor effect on yield. This is perhaps surprising because the Mut phenotype affects both the growth rate during induction and the accumulation of large amounts of endogenous alcohol oxidase. Muts strains may yield a higher proportion of correctly folded product in situations where folding is rate-limiting (e.g. in the case of hepatitis B surface antigen [8]).
The extremely high level of alcohol oxidase (530%) expressed from AOX1in induced wild-type Pichia had suggested that one copy of an AOX1 expression vector would produce maximal mRNA levels. In a recent paper, mRNA levels were analyzed from a series of transformants containing increasing copy numbers (112) of an HIV-1 Env expression vector [12]. The Env mRNA level increased progressively with copy number up to the maximum number tested; at a single copy of the vector, it was two- to threefold less than AOX1 mRNA, but with greater than three copies it exceeded AOX1 mRNA. A progressive increase was also seen with fragment C, suggesting that transcription is, in general, limiting in Pichiacontaining only a single copy of the vector and that it is sensible to routinely maximize copy number. Despite this, other factors, such as protein stability, must have a major effect because final yields of different proteins vary greatly, even with multicopy clones. For example, 12 copies of Env vector yielded 2.5% of total cell protein, whereas 14 copies of fragment C vector yielded 27%.
Aside from gene dosage, a critical factor that has long been recognized to affect induction efficiency is aeration ofPichia cultures. This results from the tendency of cultures, especially Mut+ strains, to become oxygen-limited in shake-flask inductions, and it probably explains the consistently large increase (e.g. 510-fold) in yield that is observed when switching to fermenters.
Many users have been attracted to Pichia by the very high reported levels of protein secretion in high-density cultures, such that the product can comprise >80% of the protein in the medium. Yet, secretion is complex and is dependent not only on factors such as gene dosage and Mut phenotype, but also on other factors that affect the yield and quality of product (e.g. signal sequence, processing, proteolysis and glycosylation).
Perhaps the most contentious issue, as demonstrated by the lively debate at the recent meeting on Pichia in San Diego, is Mut phenotype. Because secretory vesicles in S. cerevisiae localize to the bud, it had been widely believed that secretion could only occur in dividing cells. Secretion of mouse -amylase fromS. cerevisiae has, however, been shown to be as efficient in non-dividing as dividing cells [13]. The group at SIBIA Inc (La Jolla, California) had favoured Mut+ strains and have used these in many examples of high-level secretion (e.g. epidermal growth factor [EGF], insulin-like growth factor-1 [IGF-1], aprotinin, etc. [14] [P2] [P3]). Even so, results with HSA [4] and murine EGF [15] demonstrate that Muts strains can also yield high levels. Many more recent successful examples utilize either Mut+ or Muts strains.
In the case of gene dosage, agreement is absolute that an optimal, rather than maximal, copy number is usually required. In many cases, secretion efficiency has been improved with several vector copies [P2][P3]. Examples also exist where the maximum copy number tested was optimal (e.g. with murine EGF [15]). With bovine lysozyme, however, increasing the copy number from one to three reduced the level of secreted product [16], and for HIV gp120, a copy number of greater than one reduced secretion and increased accumulation of intracellular products [6]. It would appear that less efficiently secreted proteins are likely to block the secretory pathway at higher expression levels.
Several foreign proteins have been efficiently secreted using their native signal peptide (e.g. HSA, where a strain containing three copies of the gene, expressed from a modifiedAOX2 promoter, gave a staggering yield of 10 gl-1 [4][P4]). With bacterial -amylase, however, the yield using a yeast signal was two-to threefold higher [17], and in general, yeast signals are more likely to be successful [2]. Secretion of EGF and murine EGF using the S. cerevisiae -factor leader was shown to be highly efficient, and analysis of the product showed authentic processing at the Kex2 endopeptidase cleavage site [15][P2]. The vectors pPIC9 and pPIC9K, which contain the -factor leader sequence with convenient cloning sites [12], have recently become available from Invitrogen and are now widely used. Recent successful examples using the -factor leader include the following: single-chain Fv antibody fragments [18]; a 9 kDa thrombomodulin fragment [19]; blood factor XII [19]; a fragment of amyloid -protein [20]; oncostatin M (SJ McAndrew et al., abstract, Current Topics in Gene Expression Systems: Pichia pastoris, San Diego, USA, October 1994) coffee-bean -galactosidase (A Zhu, LF Kimball, Current Topics in Gene Expression Systems: Pichia pastoris, San Diego, USA, October 1994), and cathepsin B (JS Mort et al., abstract, Current Topics in Gene Expression Systems: Pichia pastoris, San Diego, October 1994). An alternative signal sequence, that of the Pichiaacid phosphatase 1 (PHO1) gene, is used in the vector pHIL-S1, which is also available from Invitrogen.
Studies using S. cerevisiae have shown that the particular yeast signal peptide used can affect efficiency of secretion [2]. Recently, a synthetic hybrid signal based on Pho1, with an additional 19 residues, including a Kex2 cleavage site, has been found to improve secretion of tick anticoagulant protein and some other proteins two- to threefold in Pichia [5]. Even so, it is not clear that general rules concerning the signal peptide can be applied to any protein.
The problem of proteolytic instability in the medium has been encountered with several proteins secreted from Pichia. It has been seen in shake flasks, but usually appears to be far worse in fermenters, because of the higher concentration of proteases or the different medium used. Three different approaches have been used successfully to overcome proteolysis [1]: adding amino acid or peptide supplements to the growth medium, buffering the pH of the medium to a value where degradation is reduced (e.g. pH 3), or using protease-deficient host strains. In the case of IGF-1, no protein was produced unless the medium was buffered to pH 3, but a 50% increase was then achieved using a pep4 strain grown in a medium buffered to pH 3 [P3].
S. cerevisiae has been avoided as a host for the development of human therapeutic glycoproteins because yeast-derived glycoproteins are antigenic and frequently hyperglycosylated (i.e. they contain extensive outer chain mannose units [50 to 150 residues] that can mask function). Pichia-derived invertase is, however, not hyperglycosylated and has an outer-chain length of 814 units, compared with >50 in S. cerevisiae[21]. BulkPichia glycoprotein was found to be less frequently hyperglycosylated, to have a shorter outer-chain length (<30 residues), and to lack the highly antigenic terminal 1,3-mannose linkages present in S. cerevisiae [22][23]. Nevertheless, it should be emphasized that glycosylation in Pichia and that in mammals is not identical, and it is not known how antigenicPichia glycoproteins are or how the pharmacological properties of heterologous products might be affected.
For the development of vaccines, totally authentic glycosylation may be unnecessary, provided the proteins elicit a protective immune response. Even so, results with two viral glycoproteins, HIV1 gp120 and EpsteinBarr virus gp350, were not promising. HIV-1 gp120 was hyperglycosylated [6], whereas gp350 was less highly glycosylated than the S. cerevisiae-derived material (CA Scorer, personal communication), but neither of these proteins was recognized by antibodies raised against the native protein. In contrast, the Bm86 cattle tick membrane glycoprotein, secreted using the invertase signal peptide, was not hyperglycosylated and formed immunogenic particles which partially protected cattle against challenge [24].
For intracellular expression, it would seem reasonable to isolate transformants with maximum vector copy number. A G418-selection protocol using vectors containing the Tn903 kanr gene (e.g. pPIC3K) has recently been described [12]. Using this procedure, multicopy clones (510 copies) can be isolated, even following electroporation, which had been thought to yield only single-copy transformants. This greatly simplifies the rapid isolation of multicopy clones and may be considered the method of choice for general laboratory use. In practice, this method works best using the KM71 strain and SacI-digested vector because of the higher transformation frequencies that are attainable. Where very high copy numbers (1030) are required, however, it then appears that transplacement using the sphaeroplast transformation method must be used. Transformants can subsequently be screened for high copy number 'jackpot clones', either Muts or Mut+, using a rapid DNA dot-blot method [11]. Precise copy numbers should be determined using quantitative DNA dot blots [3].
For secretion, initial studies could be carried out with single-copy transformants, but it would be preferable to start with a series with different copy numbers. Such a series could be created in several ways. A range of multicopy transformants, isolated by G418-selection [12] or DNA dot blot [11], could be analyzed for copy number [3]. An alternative method developed by SIBIA is to utilize a plasmid that can be used to generate multi-cassette vectors with up to eight copies in vitro [1][16]. This method has the disadvantage that several DNA cloning steps are required, but the advantage that the copy number is determined before transformation. Any of these approaches can be carried out in either Mut+ or Muts strains for comparison.
An alternative empirical approach to optimization has been used for tick anticoagulant protein [5]. Transplacement was used to generate a heterogeneous pool of transformants and the level of secreted product from 91 Muts and Mut+ clones was tested in inductions in microtitre plates. Eleven transformants were further evaluated in shake-flask inductions and one chosen for fermenter optimization, giving a a final product level of 1.7 gl-1 of product. This method could be used in other cases where a simple method exists for quantitating the product.
Pichia transformants are generally tested in fermenters as soon as possible because shake-flask inductions are sub-optimal. Mut+and Muts strains each have their advantages: Mut+ strains are less likely to become poisoned by methanol, whereas Muts strains are less likely to become oxygen-limited. Although a matter of debate, reports exist of induction using Muts that is equally rapid (48 h) as that using Mut+ strains [3][10][11][15]. Because the increase in yield in going from shake-flask to fermenter inductions is not always predictable [11], it may be prudent to select several transformants before proceeding to detailed fermenter optimization.
The number of different proteins being expressed in Pichia is expanding rapidly, and results from ongoing studies will increase our knowledge of the capabilities and limitations of this expression system. The more wide adoption of Pichia, however, will require additional refinements (e.g. more auxotrophic and mutant strains, alternative selection markers, a drug-selection system that shows greater dose-dependence than G418, vectors for simultaneous expression of two proteins and alternative promoters to AOX1). These refinements, many of which should be available shortly, will enable the Pichia system to gain some of the flexibility of S. cerevisiae.
Pichia is already widely accepted as an important biotechnological host organism, and we are now at the exciting stage of observing products moving through to clinical trials and beyond. IGF-1 and HSA should soon be marketed products for the treatment of amylotrophic lateral sclerosis and as a serum replacement, respectively. Numerous cytokines, vaccines and other biological products are under development, and a Cuban group has developed a hepatitis B vaccine that is currently being sold in South America.
I would like to thank my colleagues in the field, especially Jeff Clare, Koti Sreekrishna, Jim Cregg, Rich Buckholz, David Higgins, Mick Hunter and Bennet Cohen, for continually sharing information with me.