Development of CRISPR/Cas9-Based Genome Editing Tools for Polyploid Yeast Cyberlindnera jadinii and Its Application in Engineering Heterologous Steroid-Producing Strains.

In this study, a suite of efficient CRISPR/Cas9 tools was developed to overcome the genetic manipulation challenges posed by the polyploid genome of industrial yeast Cyberlindnera jadinii. The developed CRISPR/Cas9 system can achieve a 100% single-gene knockdown efficiency in strain NBRC0988. Moreover, the integration of a single exogenous gene into the target locus using a 50 bp homology arm achieved near-100% efficiency. The efficiency of simultaneous integration of three genes into the chromosome is strongly influenced by the length of the homology arm, with the highest integration efficiency of 62.5% obtained when selecting a homology arm of about 500 bp. By utilizing the CRISPR/Cas system, this study demonstrated the potential of C. jadinii in producing heterologous sterols. Through shake-flask fermentation, the engineered strains produced 92.1 and 81.8 mg/L of campesterol and cholesterol, respectively. Furthermore, the production levels of these two sterols were further enhanced through high-cell-density fed-batch fermentation in a 5 L bioreactor. The highest titer of campesterol reached 807 mg/L [biomass OD600 = 294, productivity of 6.73 mg/(L·h)]. The titer of cholesterol reached 1.52 g/L [biomass OD600 = 380, productivity of 9.06 mg/(L·h)], marking the first gram-scale production of steroidal compounds in C. jadinii.

Non-coding RNAs and related molecules associated with form-deprivation myopia in mice.

The role of miRNAs and its regulatory mechanism in myopia are indeterminate. Our study aimed to investigate potential myopia-associated non-coding RNAs and related molecules by performing a comprehensive bioinformatic analysis of miRNA expression profile of mice with form-deprivation myopia (FDM). Differentially expressed miRNAs in two raw microarray data sets (GSE58124 and GSE84220) from Gene Expression Omnibus (GEO) database were comprehensively analysed using GEO2R. Target genes were predicted using miRDB and enriched with Metascape online tool. Protein-protein interaction (PPI) networks were constructed utilizing STRING and Cytoscape. Significant differentially expressed miRNAs were validated by real-time polymerase chain reaction (qRT-PCR) using RNA extracted from monocular FDM ocular tissues. As result, we identified three upregulated miRNAs (mmu-miR-1936, mmu-miR-338-5p, and mmu-miR-673-3p) significantly associated with myopia in the two microarray data sets (p < 0.05 and |Log (Fold Change) |>1). GO functional analysis suggested these three miRNAs were targeted in genes mostly enriched in morphogenesis and developmental growth of retinal tissues. Enrichment analysis revealed top eight transcription factors, including PAX6 and Smad3, related to myopia. Ten hub genes, including Rbx1, Fbxl3, Fbxo27, Fbxl7, Fbxo4, Cul3, Cul2, Klhl5, Fbxl16 and Klhl42, associated with ubiquitin conjugation were identified. qRT-PCR confirmed the increased expression of mmu-miR-1936 and mmu-miR-338-5p (p < 0.05), but no statistical difference was observed in mmu-miR-673-3p expression in myopic retinas. Our findings indicated mmu-miR-1936, mmu-miR-338-5p and mmu-miR-673-3p upregulation may be associated with myopia development via post-transcriptional gene regulation, and identified potential molecules that could be further explored in future studies of the mechanism in myopia.