Multiplex PCR and Southern blot analysis further confirmed that all albino transformants tested were true car2 null mutants (Figure 4B). The albino phenotype was directly caused by the deletion of CAR2 because the phenotype was completely restored when re-integrating a wild type gene fragment (Additional file 1). Whereas the targeted deletion frequency for CAR2 was estimated to be 10.5% in WT, it was increased to 75.3% in the ∆ku70e background, a more than 7-fold improvement.

Dramatically increased gene deletion frequencies were also observed at both STE20 and URA3 loci (Table 2), with the deletions verified by Southern blot and phenotypic analyses (Figure 5). Figure 4 Phenotypic and genotypic characterization of pKOCAR2 find more transformants. (A) A transformation plate showing both red and albino transformants, with black arrow heads marking some albino transformants. (B) Southern blot results using the 5′ flanking sequence of CAR2 as a probe. Genomic DNA was digested with PvuI and a band shift from 5.0 kb (WT) to 3.0 kb indicates successful deletion of CAR2 gene. Figure 5 Targeted deletion of STE20 and URA3 genes. (A) and (D) Illustration of gene deletion constructs; (B) and (E): Southern blots

Tipifarnib using probes shown in (A) and (D); (C) Colony phenotype of WT and ∆ste20 strains mated with R. toruloides ATCC 10788; (F) Growth phenotype of WT and ∆ura3 strains derived from 10-fold serially diluted cells. The latter showed resistance to 5-FOA (1 g/L) – a substrate that can be converted to a toxic intermediate by the URA3-encoded enzyme [27]. Effect of homology sequence length on deletion frequency To understand the effects of homology sequence length on gene deletion frequency, pKOCAR2 was modified to have various lengths of homology sequence, ranging from 50 to 1500 bp (Additional file 2). The minimum homology length

necessary for CAR2 deletion in WT was at least 250 bp with a gene deletion frequency of 0.7%, while only 100 bp was sufficient in the ∆ku70e strain, which gave gene deletion frequency of approximately 20%. Homology length of at least 1 kb was required to achieve gene deletion frequency of more than 90% using the ∆ku70e strain Parvulin (Table 3). Table 3 Effects of homologous sequence length on CAR2 deletion frequency Homology length (bp) Gene deletion frequencya Improvement (folds) WT ∆ku70e 50 0 (780) 0 (8) – 100 0 (620) 21.4% (14) – 250 0.7% (1668) 30.3% (33) 43.3 500 11.2% (2124) 67.0% (778) 6 750 10.5% (6152) 75.3% (885) 7.2 1000 30.4% (2280) 91.7% (2196) 3 1500 20.5% (2730) 91.0% (4304) 4.4 Note: aNumber in parenthesis indicate number of transformants screened. Sensitivity of KU70 deficient mutant to DNA damaging agents Deficiency in Ku complex encoding genes have been linked to elevated sensitivity to DNA-damaging agents due to the defects in DNA repair [12]. As expected, the ∆ku70 strain displayed higher susceptibility to DNA damage induced by methyl methane sulfonate (MMS) and exposure to ultraviolet (UV) radiation compared to WT.