Project description:Replicate cultres of Saccharomyces cerevisiae strain VL3 (a commercial wine strain) were inititaed with and without the the co-inoculation of a second yeast species, Pichia kluyveri (PKKR1). In addition replicate cultures of Pichia kluyveri were initiated. The media for all cultures was sterile Sauvignon blanc grape juice. Triplicates of each treatment were destructively harvested at days 2, 9 and 16 of fermentation and RNA extracted. RNA from S. cerevisiae could not be preferentially extracted from co-ferments. P. kluyveri genome has not been sequenced and so homology to S. cerevisiae probes on the array could not be accurately estimated. We extracted RNA from the P. kluyveri single ferments and hybridised them to the S. cerevisiae arrays to control for this. These species diverged over 100 MYA, and we did not observe abundant homology by way of cross hybridisation. The mean probe intensity for P. kluyveri cDNA was 17-fold lower than for S. cerevisiae, but some probes reported reasonable signal. The intensity distribution of these probes fit a log-normal distribution (P<0.01). 97% of the distribution fell below one-thirtieth of the S. cerevisiae maximum intensity: the remaining 3%, comprising 429 probes, potentially have reasonable homology to P. kluyveri cDNA and we removed these from all analyses. Please see associated additional file 'removePKKR1.r' R code to achieve this.
Project description:To understand the Sef1-dependent gene expression in Lachancea kluyveri under both fermentative and respiratory conditions, we perfomred the genome-wide gene expression profiling for the log-phase cells of Lachancea kluyveri wild type and sef1 deletion mutant under both YPD and YPGly conditions.
Project description:To understand the iron-responsive gene expression in Lachancea kluyveri under high and low iron conditions, we perfomred the genome-wide gene expression profiling for the log-phase cells of Lachancea kluyveri wild type, sef1 deletion, aft1 deletion and sef1aft1 double deletion mutants under the YPD+400mM ferrous iron and YPD+ 200 mM BPS conditions.
