Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes.

TitleMulti-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes.
Publication TypeJournal Article
Year of Publication2016
AuthorsMonk JM, Koza A, Campodonico MA, Machado D, Seoane JMiguel, Palsson BO, Herrgard MJ, Feist AM
JournalCell Syst
PubMed Date09/2016
ISSN2405-4712
Abstract

Escherichia coli strains are widely used in academic research and biotechnology. New technologies for quantifying strain-specific differences and their underlying contributing factors promise greater understanding of how these differences significantly impact physiology, synthetic biology, metabolic engineering, and process design. Here, we quantified strain-specific differences in seven widely used strains of E. coli (BL21, C, Crooks, DH5a, K-12 MG1655, K-12 W3110, and W) using genomics, phenomics, transcriptomics, and genome-scale modeling. Metabolic physiology and gene expression varied widely with downstream implications for productivity, product yield, and titer. These differences could be linked to differential regulatory structure. Analyzing high-flux reactions and expression of encoding genes resulted in a correlated and quantitative link between these sets, with strain-specific caveats. Integrated modeling revealed that certain strains are better suited to produce given compounds or express desired constructs considering native expression states of pathways that enable high-production phenotypes. This study yields a framework for quantitatively comparing strains in a species with implications for strain selection.

Alternate JournalCell Syst
PubMed ID27667363
Cover Image: 

Location

Location

417 Powell-Focht Bioengineering Hall

9500 Gilman Drive La Jolla, CA 92093-0412

Contact Us

Contact Us

In Silico Lab:  858-822-1144

Wet Lab:  858-246-1625

FAX:   858-822-3120

Website Concerns: sbrgit@ucsd.edu

User Login