Systems Biotechnology: Combined in Silico and Omics Analyses for the Improvement of Microorganisms for Industrial Applications - Systems Biology: Networks, Models, and Applications - page 200

out for the same samples taken during the cultivation (S1-S10). It was
found that the expression of genes of TCA cycle enzymes, NADH
dehydrogenase, and ATPase was upregulated during the exponential
fed-batch period and downregulated afterwards. The expression of
chaperone genes was upregulated as cell density increased, suggesting
that cells experience stress during the HCDC. Expression of phosphate
starvation genes was most strongly upregulated toward the end of
cultivation, suggesting possible phosphate limitation at this point.
The most interesting finding was that the expression of most amino
acid biosynthesis genes was downregulated as cell density increased.
This finding immediately answers why the specific productivity of
recombinant protein is reduced during the HCDC. Even though the
results of transcriptome and proteome profiling were similar, there
were still a number of genes showing different profiles. At this time,
we do not know how to extract more information from these dis-
crepancies, and therefore it will be one of the important tasks in the
future. Instead, the “expression map,” which are transcriptome and
proteome profiles mapped onto the metabolic pathway network, was
proposed (figure 7.4). This expression map can provide a global snap-
shot of metabolic and physiological changes under evaluation. In the
earlier example of using transcriptome profiling results for increasing
IGF-I f production by recombinant E. coli [29], the target gene prsA could
be successfully selected from many candidates and amplified based
on the finding of broad downregulation of amino acid biosynthetic
enzymes observed from the expression map of E. coli during the HCDC.
These results prove the usefulness of having such an expression map.
There have recently been several more examples of combined
x-omic analysis for strain characterization and engineering. Lee et al. [37]
compared the transcriptome and proteome profiles of E. coli
W3110 and its L -threonine-overproducing mutant strain. Among the
4290 genes, 54 genes exhibited meaningfully differential gene expres-
sion. Further analysis of nucleotide sequences of some of these genes
revealed that mutations in the thrA and ilvA genes were responsible for
L -threonine production and the physiological changes in the mutant
strain. There has recently been a report on the combined analysis of the
genome and fluxome toward understanding the metabolic characteris-
tics of a relatively unknown microorganism. The approaches taken in
this study are summarized in the following case study.
CASE STUDY 2: COMBINED ANALYSIS OF GENOME AND FLUXOME FOR THE
ELUCIDATION OF UNKNOWN METABOLIC CHARACTERISTICS
Mannheimia succiniciproducens , which is able to produce large amounts
of succinic acid along with other acids, was isolated from the rumen
of Korean cows [39]. In order to engineer the metabolic pathways
for enhanced succinic acid production, it is essential to understand the
metabolic characteristics of this bacterium under various conditions.