Transcriptional control of gene expression in Pichia pastoris by manipulation of terminators.

Controlling gene expression is often the foremost goal of most biological endeavors like the production of industrial enzymes and expression of heterologous metabolic pathway genes. The components of the entire "expression cassette" exert control on net protein output. This control is primarily achieved through altering the promoter driving expression and by changing the copy number of the gene. However, there are only a few recent studies on terminators. Terminators are essential components in expression cassettes that influence the 3' end processing of mRNA, mRNA stability, and translational efficiency, which can modulate protein production. In Pichia pastoris (Komagataella phaffi), little attention has been paid to the selection of terminator regions in efforts to increase heterologous gene expression. To explore the potential application of the terminator regions on increased secretory production of Candida antarctica lipase B (CALB), we assessed the ability of three different classes of terminator regions: (1) terminator regions of methanol oxidation pathway genes of P. pastoris; (2) terminator regions of well-expressed and housekeeping genes of P. pastoris; and (3) terminators of other yeast genes like Saccharomyces cerevisiae. The terminator of dihydroxyacetone synthase (DHAS TT), a high expressing gene in the methanol utilization pathway, shows inducible CALB expression levels similar to the AOX1 terminator (AOX1 TT) under the control of AOX1 promoter and threefold higher in constitutive expression of CALB under the control of GAP promoter. The Calb transcript abundance was also found to correlate with protein expression. Furthermore, mRNA half-life determination showed a direct correlation between the stability of transcripts and increased transcription rate. Together, our results emphasize that enhancing transcript stability using the correct choice of transcription terminators (TT) will help in developing robust production strains suitable for scale-up.Key points• Influence of transcription terminators on Calb gene expression• Modulation of gene expression by enhancing transcript stability.

Compact Cell Settlers for Perfusion Cultures of Microbial (and Mammalian) Cells.

As microbial secretory expression systems have become well developed for microbial yeast cells, such as Saccharomyces cerevisiae and Pichia pastoris, it is advantageous to develop high cell density continuous perfusion cultures of microbial yeast cells to retain the live and productive yeast cells inside the perfusion bioreactor while removing the dead cells and cell debris along with the secreted product protein in the harvest stream. While the previously demonstrated inclined or lamellar settlers can be used for such perfusion bioreactors for microbial cells, the size and footprint requirements of such inefficiently scaled up devices can be quite large in comparison to the bioreactor size. Faced with this constraint, we have now developed novel, patent-pending compact cell settlers that can be used more efficiently with microbial perfusion bioreactors to achieve high cell densities and bioreactor productivities. Reproducible results from numerous month-long perfusion culture experiments using these devices attached to the 5 L perfusion bioreactor demonstrate very high cell densities due to substantial sedimentation of the larger live yeast cells which are returned to the bioreactor, while the harvest stream from the top of these cell settlers is a significantly clarified liquid, containing less than 30% and more typically less than 10% of the bioreactor cell concentration. Size of cells in the harvest is smaller than that of the cells in the bioreactor. Accumulated protein collected from the harvest and rate of protein accumulation is significantly (> 6x) higher than the protein produced in repeated fed-batch cultures over the same culture duration. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:913-922, 2017.

Effect of molecular chaperones on the expression of Candida antarctica lipase B in Pichia pastoris.

One of the reasons for limited heterologous protein secretion in Pichia pastoris is the suboptimal folding conditions inside the cell. The Hsp70 and Hsp40 chaperone families in the cytoplasm or the ER regulate the folding and secretion of heterologous proteins. Here, we have studied the effect of chaperones Ydj1p, Ssa1p, Sec63p and Kar2p on the secretory expression of Candida antarctica lipase B (CalB) protein. Expression of CalB in P. pastoris resulted in the induction of Kar2p secretion into the medium surpassing the retrieval capacity of the cell. Individual overexpression of Ydj1p, Ssa1p and Sec63p in recombinant P. pastoris increased CalB expression level by 1.6-, 1.4- and 1.4-fold respectively compared to the control strain harboring only the CalB gene. However, overexpression of Kar2p had a negative effect on the expression of CalB. Moreover, Western blot analysis indicated accumulation and secretion of Kar2p in the ER, Golgi and extracellular medium in the chaperone coexpression strains. When expressed in combinations such as Ydj1p-Ssa1p, Ydj1p-Sec63p, Kar2p-Ssa1p, Kar2p-Sec63p, the expression level of CalB was increased by 2.5-, 1.5-, 1.5- and 1.5-fold respectively. Contrastingly, the Kar2p-Ydj1p combination resulted in decreased CalB secretion in the supernatant. From these results, we conclude that overexpression of Kar2p is not required for the secretion of CalB. Also, our work confirmed the synergistic effect of Ssa1p and Ydj1p chaperones in the expression of CalB.

Improved secretion of Candida antarctica lipase B with its native signal peptide in Pichia pastoris.

Secretion efficiency of the 85-amino acid Sacchromyces cerevisiae alpha signal peptide and the 25-amino acid Candida antarctica lipase B signal (nsB) peptide were compared. Three reporter proteins used for the study are C. antarctica lipase A (CalA), lipase B (CalB) and hGMCSF. The copy number of recombinant α-CalB and nsB-CalB clones was determined by qPCR and clones with equivalent gene copies were used for comparative analysis. About threefold increased CalB production corresponding to an activity of 480 U ml(-1) was obtained with its native signal peptide, whereas with the alpha signal peptide the maximum activity was 160 U ml(-1). Also, CalB was secreted as a mature protein with native N-terminus when fused to its own signal peptide, while unprocessed CalB with N-terminal extension was detected with the alpha signal peptide. Real time PCR analysis of CalB strains indicated that the difference in protein expression was not at the transcriptional level. The nsB signal sequence was also effective in secreting CalA enzyme and its secretion efficiency was on par with the alpha signal sequence. Further, hGMCSF fused inframe with the nsB signal peptide was also efficiently secreted into the medium. These results indicate that the nsB signal peptide can be a better alternative to alpha signal peptide for heterologous protein expression in Pichia pastoris.