Most inducible expression systems suffer from growth defects, leaky basal induction, and inhomogeneous expression levels within a host cell population. These difficulties are most prominent with the overproduction of membrane proteins that are toxic to host cells. Here, we developed an Escherichia coli inducible expression system for membrane protein production based on titrated expression of a mutant lac repressor (mLacI). Performance of the mLacI inducible system was evaluated in conjunction with commonly used lac operator-based expression vectors using a T7 or tac promoter. Remarkably, expression of a target gene can be titrated by the dose-dependent addition of l-rhamnose, and the expression levels were homogeneous in the cell population. The developed system was successfully applied to overexpress three membrane proteins that were otherwise difficult to produce in E. coli. This gene expression control system can be easily applied to a broad range of existing protein expression systems and should be useful in constructing genetic circuits that require precise output signals.

The thermotolerant methylotrophic yeast Hansenula polymorpha is able to grow at elevated temperature up to 48 °C as one of a few yeast strains which are naturally capable of alcoholic fermentation of xylose, a pentose sugar abundant in lignocellulosic biomass. However, the current level of ethanol production from xylose by H. polymorpha is still very low compared to those of other xylose-fermenting strains. Therefore, it is necessary to analyze and remodel the xylose metabolism in H. polymorpha at the whole genome level to identify and overcome these limits. In the present study, the transcriptomes of H. polymorpha grown on xylose were compared with those of glucose-grown cells under both aerobic and microaerobic conditions. Approximately, two percent of H. polymorpha genes were either up- or down-regulated by more than two-fold during the growth on xylose. The majority of the up-regulated genes were involved in metabolism. Some genes involved in xylose metabolism, such as XYL1, XYL2, and TAL1 were also up-regulated, despite the fact that the differences in their induction level were only about three-fold. On the other hand, the majority of the down-regulated genes were involved in metabolism and cellular transport. Interestingly, some genes involved in glycolysis and ethanol fermentation were also repressed during growth on xylose, suggesting that these genes are good targets for engineering H. polymorpha to improve xylose fermentation.

The thermotolerant methylotrophic yeast Hansenula polymorpha is attracting interest as a potential strain for the production of recombinant proteins and biofuels. However, only limited numbers of genome engineering tools are currently available for H. polymorpha. In the present study, we identified the HpPOL3 gene encoding the catalytic subunit of DNA polymerase δ of H. polymorpha and mutated the sequence encoding conserved amino acid residues that are important for its proofreading 3'-->5' exonuclease activity. The resulting HpPOL3* gene encoding the error-prone proofreading-deficient DNA polymerase δ was cloned under a methanol oxidase promoter to construct the mutator plasmid pHIF8, which also contains additional elements for site-specific chromosomal integration, selection, and excision. In a H. polymorpha mutator strain chromosomally integrated with pHIF8, a URA3(-) mutant resistant to 5-fluoroorotic acid was generated at a 50-fold higher frequency than in the wild-type strain, due to the dominant negative expression of HpPOL3*. Moreover, after obtaining the desired mutant, the mutator allele was readily removed from the chromosome by homologous recombination to avoid the uncontrolled accumulation of additional mutations. Our mutator system, which depends on the accumulation of random mutations that are incorporated during DNA replication, will be useful to generate strains with mutant phenotypes, especially those related to unknown or multiple genes on the chromosome.