ABSTRACT: Abstract: Chemogenomic fitness assays were combined with a transcriptome analysis to understand both the mode of action and the mechanisms of resistance to Chitosan oligosaccharides (COS). COS are deacetylated chitin compounds, with antimicrobial properties, that are presumed to act by disrupting the cell membrane. The fitness assays identified 39 yeast deletion strains sensitive to COS and 21 suppressors of COS sensitivity. The genes identified encode membrane proteins and members of the protein degradation/ proteosome pathway. The transcriptomes of wild-type and five suppressor strains overexpressing ARL1, BCK2, ERG24, MSG5, or RBA50, were analyzed in the presence and absence of COS. The COS-induced transcriptional response is distinct from previously described environmental stress responses (i.e. thermal, salt, osmotic and oxidative stress) and furthermore, treatment with environmental stressors does not provide resistance to COS. Some of the up-regulated transcripts in the suppressor overexpressing strains exposed to COS included genes involved in transcription, cell cycle, stress response and the RAS signal transduction pathway. Down-regulated transcripts included those encoding protein folding components, and respiratory chain proteins. Overexpression of the ARL1 gene, a member of the Ras superfamily that regulates membrane trafficking, provides protection against COS-induced cell membrane permeability and damage. We found that the ARL1 COS-resistant over-expression strain was as sensitive to amphotericin B, fluconazole and terbinafine as the wild-type (vector control). The gene targets of COS identified in this study suggest that COSM-bM-^@M-^Ys mechanism of action is different from other commonly studied fungicides, suggesting that COS may be an effective fungicide for drug-resistant fungal pathogens. We selected the 5 overexpressing strains based on the characteristics of the genes. ARL1, encoding a GTPase and is involved in membrane trafficking, was selected since it was observed in the HIP-HOP assay as a sensitive homozygous deletion strain and in the MSP assay as multicopy suppressor. The rest of selected overexpressing strains were BCK2 and MSG5, involved in cell integrity pathways, ERG24 in ergosterol synthesis, and RBA50 in transcription. BCK2 is a Ser-Thr rich protein with protein kinase C activity that acts in signal transduction. Overexpression of BCK2 can rescue defects in yeast cwh43M-NM-^T, which displays several cell wall defects [29]. BCK2 overexpression also can suppress a cell lysis defect of mpk1M-NM-^T and pck1M-NM-^T [30]. MSG5 is also involved in signal transduction. This gene encodes a protein phosphatase involved in cell cycle control through the dephosphorylation of MAPK and is indispensable for restricting the signaling by the cell integrity pathway in yeast [31]. The inhibition of MAPK signaling leads to inhibition of cell differentiation and cell division [32]. The functions of ARL1 and ERG24 and their potential roles in chitosan resistance will be described in more detail in the Discussion. To gain a further understanding on the mode of action and mechanisms of resistance to COS, we performed a transcriptome analysis of the above mentioned five overexpressing strains known to increase resistance to COS-5.44. Each overexpressing strain and the wild type (vector control) were treated with COS-5.44 and RNAs isolated from both treated and untreated cells. The RNAs were converted to labeled cDNA and hybridized to NimbleGen expression microarrays (see Methods). Three cDNA biological replicates either with or without a 60 minutes exposure to COS-5.44 for each of the five overexpressing strains as well as an untransformed wild type BY4743 cells (vector control; for a total of 36 samples) were hybridized to NimbleGen 4X72k microarrays (Roche NimbleGen, Inc. Design ID A6186-00-01, TI4932 60mer expr X4).
