Genome-Wide Quantification of the Effect of Gene Overexpression on Escherichia coli Growth

Hao Chen; Sumana Venkat; Jessica Wilson; Paige McGuire; Abigail L Chang; Qinglei Gan; Chenguang Fan

doi:10.3390/genes9080414

Genome-Wide Quantification of the Effect of Gene Overexpression on Escherichia coli Growth

Genes (Basel). 2018 Aug 16;9(8):414. doi: 10.3390/genes9080414.

Authors

Hao Chen¹, Sumana Venkat², Jessica Wilson³, Paige McGuire⁴, Abigail L Chang⁵, Qinglei Gan⁶, Chenguang Fan^{7

8}

Affiliations

¹ Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA. hc019@uark.edu.
² Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA. sv009@uark.edu.
³ Department of Chemistry, University of Arkansas, Fort Smith, AR 72913, USA. jwilso18@g.uafs.edu.
⁴ Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA. plmcguir@uark.edu.
⁵ Fayetteville High School, Fayetteville, AR 72701, USA. a.chang@g.fayar.net.
⁶ Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA. qingleig@uark.edu.
⁷ Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA. cf021@uark.edu.
⁸ Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA. cf021@uark.edu.

Abstract

Recombinant protein production plays an essential role in both biological studies and pharmaceutical production. Escherichia coli is one of the most favorable hosts for this purpose. Although a number of strategies for optimizing protein production have been developed, the effect of gene overexpression on host cell growth has been much less studied. Here, we performed high-throughput tests on the E. coli a complete set of E. coli K-12 ORF archive (ASKA) collection to quantify the effects of overexpressing individual E. coli genes on its growth. The results indicated that overexpressing membrane-associated proteins or proteins with high abundances of branched-chain amino acids tended to impair cell growth, the latter of which could be remedied by amino acid supplementation. Through this study, we expect to provide an index for a fast pre-study estimate of host cell growth in order to choose proper rescuing approaches when working with different proteins.

Keywords: ASKA collection; Escherichia coli; branched-chain amino acids; codon bias; gene ontology; gene overexpression; growth effect; recombinant protein production.