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Series GSE75004 Query DataSets for GSE75004
Status Public on Jun 30, 2018
Title Translation elongation mediated quality control of integral membrane protein synthesis
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by high throughput sequencing
Other
Summary Saccharomyces cerevisiae has been engineered to utilize cellobiose, which are prevalent in plant cell wall, by introducing a cellodextrin transporter gene (cdt-1) and an intracellular β-glucosidase gene (codon-optimized gh1-1) from Neurospora crassa. We previously found that codon-optimization of GH1-1 improved fermentation rates under aerobic and anaerobic conditions. However, we found that the codon-optimized version of the CDT-1 transporter (here denoted OPT for the mRNA) resulted in reduced cellobiose uptake and slower growth in cellobiose by S. cerevisiae relative to the transporter with Neurospora-derived coding sequence (hereafter NC for the mRNA). We performed ribosome profiling and RNA deep sequencing of cells expressing NC and OPT grown at mid-exponential phases, respectively. Differences in ribosome occupancy on NC and OPT transcripts suggested increased rates of translation elongation of the N-terminal sequence of OPT in contrast to NC, which may be responsible for the slow-growth phenotype of cells expressing OPT.
 
Overall design Examine ribosome footprints and mRNA abundance in biological replicates of S. cerevisiae strains expressing a cellodextrin transporter gene (cdt-1) and the codon-optimized version of cdt-1, respecitively
 
Contributor(s) Acosta-Sampson L, Döring K, Lin Y, Yu VY, Bukau B, Kramer G, Cate JD
Citation(s) 28972146
Submission date Nov 13, 2015
Last update date Jul 18, 2021
Contact name Ligia Acosta-Sampson
E-mail(s) lacostasampson@berkeley.edu
Phone 510-666-2559
Organization name UC Berkeley
Department MCB/EBI
Lab Jamie H.D. Cate
Street address 2151 Berkeley Way, Room 320, MC 5230
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platforms (1)
GPL9377 Illumina Genome Analyzer II (Saccharomyces cerevisiae)
Samples (12)
GSM1940305 JCLIA001A
GSM1940306 JCLIA001B
GSM1940307 JCLIA001C
Relations
BioProject PRJNA302167
SRA SRP066187

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Supplementary file Size Download File type/resource
GSE75004_RAW.tar 15.0 Mb (http)(custom) TAR (of WIG)
GSE75004_The_transcriptome_profiles-lacostasampson.xlsx 660.6 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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