Improving the expression of a heterologous protein by genome shuffling in Kluyveromyces marxianus.

Genome shuffling is an efficient way to pool advantageous traits during positive selections of industrial microorganisms. In this study, for the first time, the effectiveness of genome shuffling to improve yielding of heterologous proteins was investigated in Kluyveromyces marxianus (KM), a promising yeast host. After two rounds of mating and screening, a novel KM strain, D, was obtained which displayed a 5-fold increase of expression level of a heterologous protein comparing to its parental strains. A range of alleles linked with improved yielding were well preserved from a parental strain T1/E to D, including one mutant allele of MTC6 known to attenuate autophagy. The results reflected an efficient pooling of advantageous alleles in our screen. Transcriptional analysis of D, revealed that mRNA levels of genes implicated in protein folding, including those of AHA1, DNAJB13, and YGR250C, were significantly elevated, suggesting potential roles of these genes in promoting the expression of heterologous proteins. Our study not only indicates the applicability of genome shuffling in the optimization of KM host strains but also provided valuable clues to clarify the mechanisms underlying the high yielding of heterologous proteins.