Systems Biotechnology: Combined in Silico and Omics Analyses for the Improvement of Microorganisms for Industrial Applications - Systems Biology: Networks, Models, and Applications - page 199

can be exploited in understanding cellular physiology and metabolism,
and consequently developing improved organisms [35]. There have been
several successful examples of combining two or more high-throughput
x-omic studies for analyzing and engineering cellular metabolism, and
these are described below as case studies [16,30,36-38].

CASE STUDY 1: COMBINED ANALYSIS OF TRANSCRIPTOME AND PROTEOME OF
E. coli CELLS DURING HIGH CELL DENSITY CULTURE

E. coli has been the workhorse for the production of various bio-
products including recombinant proteins. In order to increase the
concentration and volumetric productivity of a desired product such
as recombinant protein, high cell density culture (HCDC) is often car-
ried out. However, it is often observed that the specific productivity,
defined as gram product per gram dry cell weight (DCW) per hour,
decreases as cell density increases. In order to understand the phys-
iological changes occurring as cell density increases, combined
transcriptome and proteome analyses were carried out during the
HCDC of E. coli W3110 [30]. As shown in figure 7.3, cells were grown
exponentially at a specific growth rate of 0.14 h −1 to 74 g DCW/l
using a chemically defined medium. Sample were taken at the cell
concentrations of 0.13 (S1), 0.88 (S2), 3.5 (S3), 12.7 (S4), 24 (S5), 40 (S6),
52 (S7), 62 (S8), 72 (S9), and 74 (S10) g DCW/l. For transcriptome
profiling, the cDNA made from S1 was labeled with Cy3 while all the
others were labeled with Cy5. Also, proteome analyses were carried

Figure 7.3 Time profiles of the concentrations of cell ( and ; the filled circles

are sampling points), glucose ( ), acetic acid ( ), lactic acid( ), and phosphate
( ) during the high cell density fed-batch fermentation of E. coli W3110. In the
batch phase, the specific growth rate was 0.49 h −1 . During the fed-batch period,
the specific growth rate was controlled at 0.14 h −1 by exponential feeding.

Reproduced with permission from Yoon et al. [30].