Maintained by an eIF4E gene copy on a pVT-URA3 plasmid.

Maintained by an eIF4E gene copy on a pVT-URA3 plasmid. Plasmids were amplified and isolated from E. coli strain XL2blue. Site-directed mutagenesis to produce the required mutation in the open-reading frame of eIF4E was performed on pCEN16-eIF4E plasmid (oligonucleotide pairs are listed in Table S4; [19]). Plasmids with mutated forms were transformed into RH2585 DeIF4E::KanX ,pVTU-eIF4E. and cells were selected on synthetic media (SD: 0.67 Yeast Nitrogen Base, 2 Dextrose, 2 agar, 20 mg/mL Histidine). Plasmids were shuffled by using 5-FOA (fluoro oroctic acid) and selecting for the loss due to segregation of URA3 plasmids [20]. Diploid mutant eIF4E strains were Epigenetic Reader Domain obtained by crossing haploid cell lines to the opposite mating type RH2586 DeIF4E::KanX ,pVT-URA3 eIF4E. and positively selecting for ura3- clones on 5-FOA.LacZ-assay from ExtractsLacZ-assays of RH2585 DeIF4E::KanX ,pCEN16-eIF4E wt/ mutation. strains transformed with the plasmid yep355 Flo11LacZ (promoter region and 59UTR of Flo11 fused to the LacZ reporter gene; a generous gift of G. Fink, Whitehead Institute for Biomedical Research, MA) [24] were performed. Total cell extracts were obtained by treating cells resuspended in 0.1 M TrisHCl pH 8.0, 10 Glycerol, 1 mM DTT with chilled glass beads and protein Epigenetic Reader Domain concentrations were determined [23]. LacZ-assays were performed at 28uC with o-nitrophenyl-?D-galactoside (ONPG) as substrate; 1 ?Galactosidase Unit corresponds to 1 nmol hydrolysed ONPG per minute and mg protein.Quantitative RT-PCRTotal RNA isolation from yeast cells (transformed with the plasmid Flo11-LacZ) was done according to a slightly modified phenol:chloroform extraction protocol as described in the Molecular Cloning Laboratory Manual by Sambrook, Fritsch and Maniatis (1990). To eliminate genomic DNA contamination, DNase I treatment was performed (Roche, No. 04 716 728 001) and RNA concentrations determined (A260/A280). RNA was reverse-transcribed using MultiScribeTM Reverse Transcriptase and Random Hexamers (Applied Biosystems). Oligonucleotides for quantification of LacZ expression (or Act1 and Fba1 as stable reference genes) were designed to amplify PCR products of 70 to 150 bp [25]. For best specificity of oligonucleotides, a BLAST analysis of the S. cerevisiae genome was performed as well as an analysis to avoid secondary structures or self- and cross-dimers using Primer Express 3.0 (Applied Biosystems). The complete set of oligonucleotides used in this study is listed in table S4. Real-time PCR was performed in MicroAmpH optical 384-well reaction plates (10 mL reaction volume). Fast SYBRH Green Master Mix was mixed with oligonucleotide pairs 24786787 (0.9 mM final concentration) and 10, 2.5 or 0.625 ng cDNA were used per well. Assays were conducted in triplicates and a non-template-control was also incorporated for each oligonucleotide pair. Samples were analyzed via the 2DDCt method [26] with an Applied Biosystem ViiATM 7 PCR machine and melting-curve data were collected. alactosidase activity Units were normalized according to determined Flo11-LacZ mRNA levels.Phenotype InvestigationTo test for adhesion, haploid cells were streaked out on YPD plates, incubated for 2 days at 30u or 35uC and washed with a gentle stream of water. Pseudohyphenation was tested on nitrogen limited SLAD50 plates (50 mM ammonium sulphate, 0.17 Yeast Nitrogen Base without ammonium sulfate, 2 Dextrose, 2 agar, 5 mg/mL uracil and histidine). Cells were streaked out and incubated for 3 days at.Maintained by an eIF4E gene copy on a pVT-URA3 plasmid. Plasmids were amplified and isolated from E. coli strain XL2blue. Site-directed mutagenesis to produce the required mutation in the open-reading frame of eIF4E was performed on pCEN16-eIF4E plasmid (oligonucleotide pairs are listed in Table S4; [19]). Plasmids with mutated forms were transformed into RH2585 DeIF4E::KanX ,pVTU-eIF4E. and cells were selected on synthetic media (SD: 0.67 Yeast Nitrogen Base, 2 Dextrose, 2 agar, 20 mg/mL Histidine). Plasmids were shuffled by using 5-FOA (fluoro oroctic acid) and selecting for the loss due to segregation of URA3 plasmids [20]. Diploid mutant eIF4E strains were obtained by crossing haploid cell lines to the opposite mating type RH2586 DeIF4E::KanX ,pVT-URA3 eIF4E. and positively selecting for ura3- clones on 5-FOA.LacZ-assay from ExtractsLacZ-assays of RH2585 DeIF4E::KanX ,pCEN16-eIF4E wt/ mutation. strains transformed with the plasmid yep355 Flo11LacZ (promoter region and 59UTR of Flo11 fused to the LacZ reporter gene; a generous gift of G. Fink, Whitehead Institute for Biomedical Research, MA) [24] were performed. Total cell extracts were obtained by treating cells resuspended in 0.1 M TrisHCl pH 8.0, 10 Glycerol, 1 mM DTT with chilled glass beads and protein concentrations were determined [23]. LacZ-assays were performed at 28uC with o-nitrophenyl-?D-galactoside (ONPG) as substrate; 1 ?Galactosidase Unit corresponds to 1 nmol hydrolysed ONPG per minute and mg protein.Quantitative RT-PCRTotal RNA isolation from yeast cells (transformed with the plasmid Flo11-LacZ) was done according to a slightly modified phenol:chloroform extraction protocol as described in the Molecular Cloning Laboratory Manual by Sambrook, Fritsch and Maniatis (1990). To eliminate genomic DNA contamination, DNase I treatment was performed (Roche, No. 04 716 728 001) and RNA concentrations determined (A260/A280). RNA was reverse-transcribed using MultiScribeTM Reverse Transcriptase and Random Hexamers (Applied Biosystems). Oligonucleotides for quantification of LacZ expression (or Act1 and Fba1 as stable reference genes) were designed to amplify PCR products of 70 to 150 bp [25]. For best specificity of oligonucleotides, a BLAST analysis of the S. cerevisiae genome was performed as well as an analysis to avoid secondary structures or self- and cross-dimers using Primer Express 3.0 (Applied Biosystems). The complete set of oligonucleotides used in this study is listed in table S4. Real-time PCR was performed in MicroAmpH optical 384-well reaction plates (10 mL reaction volume). Fast SYBRH Green Master Mix was mixed with oligonucleotide pairs 24786787 (0.9 mM final concentration) and 10, 2.5 or 0.625 ng cDNA were used per well. Assays were conducted in triplicates and a non-template-control was also incorporated for each oligonucleotide pair. Samples were analyzed via the 2DDCt method [26] with an Applied Biosystem ViiATM 7 PCR machine and melting-curve data were collected. alactosidase activity Units were normalized according to determined Flo11-LacZ mRNA levels.Phenotype InvestigationTo test for adhesion, haploid cells were streaked out on YPD plates, incubated for 2 days at 30u or 35uC and washed with a gentle stream of water. Pseudohyphenation was tested on nitrogen limited SLAD50 plates (50 mM ammonium sulphate, 0.17 Yeast Nitrogen Base without ammonium sulfate, 2 Dextrose, 2 agar, 5 mg/mL uracil and histidine). Cells were streaked out and incubated for 3 days at.