Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling by array of yeast with homozygous YDR307W and YHL042W deletions

ABSTRACT: Saccharomyces cerevisiae strains carrying homozygous deletions of YDR307W and YHL042W genes and the wild-type strain (control) from a genetic background of BY4743 were used to elucidate the genome-wide transcriptional response to the deletion of YDR307W and YHL042W genes. Strains were cultivated in YPD medium in flasks with continuous shaking at 30C and 180 rpm. Samples for transcriptional profiling were collected at the mid-exponential phase of growth at an OD range of 0.85-0.95, immediately frozen in liquid nitrogen and stored at -80C until RNA isolation. All experiments were carried out in triplicates.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Ceyda Kasavi

PROVIDER: E-MTAB-2415 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The global regulator, H-NS, controls genes related to stress response, biofilm formation, and virulence expression by recognizing the curved DNA and silences gene transcription acquired from lateral gene transfer. Here, we rewired H-NS to control biofilm formation using protein engineering. One H-NS variant, H-NS K57N was obtained to reduce biofilm formation 10-fold compared to H-NS wild-type. Whole-transcriptome analysis (BW25113 hha hns / pCA24N-hns K57N vs. BW25113 hha hns / pCA24N-hns) revealed that H-NS K57N represses biofilm formation through the interactinon with other nucleoid proteins, Cnu and StpA. Remarkably, H-NS K57N enhanced the excision of defective prophage Rac while H-NS wild-type represses it, and H-NS controlled only Rac excision among E. coli prophages. These results imply that the repression of Rac excision is one of the silencing manner for foreign genes by H-NS. Also, the prophage excision not only led to the change of biofilm formation but also resulted in cell lysis through the expression of toxin protein HokD with reduced viability, which are important for cell physiology in response to the change of environmental conditions. Hence, H-NS regulatory system may be evolved easily with specialized functions in terms of biofilm formation, prophage control, and cell lysis. For the whole transcriptome study of BW25113 hha hns / pCA24N-hns K57N versus BW25113 hha hns / pCA24N-hns, cells were grown in 250 mL LB containing 1 mM IPTG for 7 h with 10 g of glass wool (Corning Glass Works, Corning, N.Y.) in 1 L Erlenmeyer flasks to form a robust biofilm. Biofilm cells were obtained by rinsing and sonicating the glass wool in sterile 0.85% NaCl solution at 0Â°C, and RNALater bufferÂ® (Applied Biosystems, Foster City, CA) was added for RNA stabilization and protection during the RNA preparation steps. Total RNA was isolated from biofilm cells. The E. coli GeneChip Genome 2.0 array (Affymetrix, Lot# 4059655) containing 10,208 probe sets for four E. coli strains (MG1655, CFT073, O157:H7-Sakai, and O157:H7-EDL933) was used for DNA microarray. cDNA synthesis, fragmentation, and hybridizations were performed.

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Transcription profiling by array of yeast with homozygous YDR307W and YHL042W deletions

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