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. 2020 Nov;104(22):9785-9800.
doi: 10.1007/s00253-020-10937-w. Epub 2020 Oct 6.

Impact of overproduced heterologous protein characteristics on physiological response in Yarrowia lipolytica steady-state-maintained continuous cultures

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Impact of overproduced heterologous protein characteristics on physiological response in Yarrowia lipolytica steady-state-maintained continuous cultures

Paulina Korpys-Woźniak et al. Appl Microbiol Biotechnol. 2020 Nov.

Abstract

Overproduction of recombinant secretory proteins triggers numerous physiological perturbations. Depending on a given heterologous protein characteristics, the producer cell is faced with different challenges which lead to varying responses in terms of its physiology and the _target protein production rate. In the present study, we used steady-state-maintained Yarrowia lipolytica cells to investigate the impact of different heterologous proteins on the physiological behavior of the host cells. Such an approach allowed to uncouple the impact of the overproduction of a particular protein from the phenomena that result from growth phase or are caused by the heterogeneity of the analyzed populations. Altogether, eight variants of recombinant strains, individually overproducing heterologous proteins of varying molecular weight (27-65 kDa) and reporting activity (enzymatic and fluorescent) were subjected to chemostat cultivations. The steady-state-maintained cells were analyzed in terms of the substrate utilization, biomass and metabolites production, as well as the reporter protein synthesis. Simplified distribution of carbon and nitrogen between the respective products, as well as expression analysis of the heterologous genes were conducted. The here-obtained data suggest that using a more transcriptionally active promoter results in channeling more C flux towards the _target protein, giving significantly higher specific amounts and production rates of the _target polypeptide, at the cost of biomass accumulation, and with no significant impact on the polyols production. The extent of the reporter protein's post-translational modifications, i.e., the number of disulfide bonds and glycosylation pattern, strongly impacts the synthesis process. Specific responses in terms of the protein formation kinetics, the gene expression levels, and transcript-to-protein linearity were observed.Key Points• Eight expression systems, producing different reporter proteins were analyzed.• The cells were maintained in steady-state by continuous chemostat culturing.• Protein- and promoter-specific effects were observed.

Keywords: Chemostat; Heterologous protein; Overexpression; Overproduction; Recombinant strain; Secretion; Steady state.

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Conflict of interest statement

The authors declare that they have no competing interestsEthics approval

N/A

Figures

Fig. 1
Fig. 1
Cloning vectors used in this study. a YLEX commercial cloning system-based vectors. b Golden Gate assembly-based vectors. The GGVA was assembled using a set of 4-nt overhangs indicated in the scheme (A, B, C, D, X, E, F, and M). Abbreviations: Ins, regions for non-homologous recombination (GGVA) or directing integration with pBR-docking platform (YLEX); M, selection marker LEU2/URA3; P, promoter 4UAS-pTEF/hp4d; SP, signal peptide (derived from spYALI0B03564g for GGA or XPR2 gene for YLEX-based expression); G, _target gene (one of the three SoA/TlG/YFP devoid of their native SP); T, terminator tLip2/tXpr2; ori, bacterial origin of replication; AmpR, bacterial selection marker. The expression cassettes were digested with NotI restriction endonuclease prior to transformation
Fig. 2
Fig. 2
Glycerol consumption, concentration of major small molecular weight metabolites, biomass, secretory protein production (scTlG/scSoA), and yellow fluorescence (inYFP/scYFP) during steady-state chemostat cultivations of Po1g- and Po1h-derived Yarrowia lipolytica strains. x-axis: strains. y-axis: a concentration of glycerol (GLY) in [g L−1], b concentration of erythritol (ERY) in [g L−1], c concentration of mannitol (MAN) in [g L−1], d biomass accumulation: dry cell weight (DCW) in [gDCW L−1], e TlG activity in culture medium in [GAU L−1], f SoA activity in culture medium in [AAU L−1], g YFP fluorescence of Po1g_inYFP/Po1h_inYFP recombinant strains in the cellular pellet and culture medium in [kRFU], h YFP fluorescence of Po1g_scYFP/Po1h_scYFP recombinant strains in the cellular pellet and culture medium in [kRFU]. Error bars indicate ±SD from at least biological duplicates in two technical replicates. N/D, non-detected
Fig. 3
Fig. 3
Simplified carbon and nitrogen distribution between the products. C and N amounts were determined based on either elementary analysis or chemical formulas. Total of C and N in all the considered products was defined as 100%. Error bars indicate ±SD from at least biological duplicates in two technical replicates
Fig. 4
Fig. 4
Relative expression levels of the heterologous genes encoding the reporter proteins in steady-state chemostat cultivations of Y. lipolytica recombinant strains. x-axis, reporter genes (scSoA, scTlG, inYFP, and scYFP); y-axis, LOG10RQ - Relative Quantitation values obtained in RTqPCR transformed logarithmically for more convenient presentation. Red: Po1h-derived Y. lipolytica strains. Blue: Po1g-derived Y. lipolytica strains. Transcript levels were determined by RTqPCR, from at least biological duplicates in two technical replicates

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