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| Status |
Public on May 25, 2011 |
| Title |
Relative expression profiling of ycdC knockout strain secreting HlyA protein |
| Platform organism |
Escherichia coli |
| Sample organism |
Escherichia coli K-12 |
| Experiment type |
Expression profiling by array
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| Summary |
The most important approach to the development of platform organisms for recombinant protein production relies on random mutagenesis and phenotypic selection. Complex phenotypes, including those associated with significant elevated expression and secretion of heterologous proteins, are the result of multiple genomic mutations. Using next generation sequencing, a parent and derivative hypersecreter strain (B41) of Escherichia coli were sequenced with an average coverage of 52.8X and 55X, respectively. A new base-pair calling program, revealed a single nucleotide polymorphism in the B41 genome at position 1,074,787, resulting in translation termination near the N-terminus of a transcriptional regulator protein, RutR, coded by the ycdC gene. We verified the hypersecretion phenotype in a ycdC::Tn5 mutant and observed a 3.4-fold increase in active hemolysin secretion, consistent with the increase observed in B41. mRNA expression profiling showed decreased expression of tRNA-synthetases and some amino acid transporters in the ycdC::Tn5 mutant. This study demonstrates that power of next generation sequencing to characterize mutants leading to successful metabolic engineering strategies for strain improvement.
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| Overall design |
6 samples were analyzed with three biological replicates for each strain. Hly-ycdC+ is the control strain.
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| Contributor(s) |
Gupta P, Lee KH |
| Citation(s) |
22505047 |
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| Submission date |
May 12, 2011 |
| Last update date |
Mar 08, 2019 |
| Contact name |
Kelvin H. Lee |
| E-mail(s) |
khl@udel.edu
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| Organization name |
University of Delaware
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| Department |
Biotechnology Institute
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| Street address |
15 Innovation Way
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| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19711 |
| Country |
USA |
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| Platforms (1) |
| GPL3154 |
[E_coli_2] Affymetrix E. coli Genome 2.0 Array |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA140275 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE29266_RAW.tar |
5.4 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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