Improving homology-directed repair by small molecule agents for genetic engineering in unconventional yeast? -- Learning from the engineering of mammalian systems

TL;DR

This paper reviews small molecule agents that enhance homologous recombination in unconventional yeasts, drawing lessons from mammalian systems to improve genome editing efficiency in these less-studied hosts.

Contribution

It consolidates knowledge of small molecules used to improve HR in mammalian cells and explores their potential application in yeast engineering.

Findings

Few chemicals have been applied to yeast genome editing.

Available assays can screen for yeast-specific HR-enhancing agents.

Conserved proteins suggest cross-species applicability of small molecules.

Abstract

The ability to precisely edit genomes by deleting or adding genetic information enables the study of biological functions and the building of efficient cell factories. In many unconventional yeasts, such as promising new hosts for cell factory design but also human pathogenic yeasts and food spoilers, this progress has been limited by the fact that most yeasts favor non-homologous end joining (NHEJ) over homologous recombination (HR) as DNA repair mechanism, impairing genetic access to these hosts. In mammalian cells, small molecules that either inhibit proteins involved in NHEJ, enhance protein function in HR, or molecules that arrest the cell cycle in HR-dominant phases are regarded as promising agents for the simple and transient increase of HR-mediated genome editing without the need for a priori host engineering. Only a few of these chemicals have been applied to the engineering of yeast although the targeted proteins are mostly conserved; making chemical agents a yet underexplored area in enhancing yeast engineering. Here, we consolidate knowledge of available small molecules that have been used to improve HR efficiency in mammalian cells and the few ones that have been used in yeast. We include available high throughput (HTP)-compatible NHEJ/HR quantification assays that could be used to screen for and isolate yeast-specific inhibitors.