Genomics and Proteomics

Applied Microbiology and Biotechnology

, Volume 68, Issue 4, pp 518-532

First online:

Gene expression analysis of Escherichia coli grown in miniaturized bioreactor platforms for high-throughput analysis of growth and genomic data

  • Paolo BoccazziAffiliated withDepartment of Biology and Health Sciences and Technology, Massachusetts Institute of Technology Email author 
  • , Andrea ZanzottoAffiliated withDepartment of Chemical Engineering, Massachusetts Institute of Technology
  • , Nicolas SzitaAffiliated withDepartment of Chemical Engineering, Massachusetts Institute of Technology
  • , Sanchita BhattacharyaAffiliated withBioMicro Center, Department of Biology, Massachusetts Institute of Technology
  • , Klavs F. JensenAffiliated withDepartment of Chemical Engineering, Massachusetts Institute of Technology
  • , Anthony J. SinskeyAffiliated withDepartment of Biology and Health Sciences and Technology, Massachusetts Institute of Technology

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Abstract

Combining high-throughput growth physiology and global gene expression data analysis is of significant value for integrating metabolism and genomics. We compared global gene expression using 500 ng of total RNA from Escherichia coli cultures grown in rich or defined minimal media in a miniaturized 50-μl bioreactor. The microbioreactor was fabricated out of poly(dimethylsiloxane) (PDMS) and glass and equipped to provide on-line, optical measurements. cDNA labeling for microarray hybridizations was performed with the GeniconRLS system. From these experiments, we found that the expression of 232 genes increased significantly in cells grown in minimum medium, including genes involved in amino acid biosynthesis and central metabolism. The expression of 275 genes was significantly elevated in cells grown in rich medium, including genes involved in the translational and motility apparatuses. In general, these changes in gene expression levels were similar to those observed in 1,000-fold larger cultures. The increasing rate at which complete genomic sequences of microorganisms are becoming available offers an unprecedented opportunity for investigating these organisms. Our results from microscale cultures using just 500 ng of total RNA indicate that high-throughput integration of growth physiology and genomics will be possible with novel biochemical platforms and improved detection technologies.