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at the two molecular levels of cellular function. Some observations were consistent
between the transcriptional and metabolic level, indicating regulation of the relevant
response mechanisms at the transcriptional level, which are then by consequence re-
flected at the metabolic level too. For example, Cramer et al. ( 2007 ) and Gong et al.
(Gong et al. 2005 ) reported that the proline accumulation after salinity treatment
was consistent with the observed increase in the abundance of transcripts encod-
ing enzymes in the proline biosynthesis pathway (Cramer et al. 2007 ; Gong et al.
2005 ). However, other results at the metabolic level would not have been directly
predictable if only the transcriptomic information had been available, indicating thus
regulatory mechanisms that are active at the metabolic level. There are also pro-
cesses that are not directly involved in metabolism and cannot thus be directly ob-
servable through the metabolic profiles, but only through the transcriptomic profiles,
like photosynthesis, ethylene signaling, and others. Integrated omic analyses at mul-
tiple molecular levels are thus required for the comprehensive understanding of all
physiological changes due to a particular stress.
3.5 Omic Analyses of Elevated CO 2 Stress on Plants
The effect of the elevated CO 2 concentration in the growth environment of the
plants has been extensively studied with both physiological and high-throughput
biomolecular analysis studies at the transcriptional, protein, and metabolic levels,
mainly in the context of long-term (i.e., 1–2 weeklong) adaptation to high CO 2 en-
vironments. The main reason for these studies has been to investigate how the plants
will change their physiology in response to the greenhouse effect. Li et al. ( 2008 )
conducted a free-air CO 2 enrichment (FACE) experiment to study the metabolic and
transcriptional effects of elevated CO 2 (i.e., 550 ppm) in the growth environment of
two A. thaliana ecotypes. At the metabolic level, they observed an increase in the
concentration of sugars, like maltose, glucose, fructose, and galactose, and of TCA
cycle organic acid intermediates, along with a decrease in the levels of most amino
acids, with the exception of the aromatic amino acids tryptophan and phenylalanine,
the concentration of which increased under elevated CO 2. In accordance with the
metabolomic results, transcriptomic analysis indicated an increase in the concen-
trations of transcripts related to the cell wall formation and metabolic processes
like the glycolysis, the TCA cycle, and the anthocyanin and flavonoid biosynthesis.
Moreover, transcripts related to the amino acid biosynthesis were downregulated or
did not change, with the exception of those involved in the tryptophan and phenyl-
alanine biosynthesis. The abundance of transcripts related to photosynthesis, like
the photosystem I and II subunits, as well as Calvin cycle enzymes, was reduced
in plants treated with elevated CO 2 for long durations. The amount of transcripts
encoding chloroplast-localized proteins unrelated to light capture and fixation func-
tions also declined significantly. The authors suggested that these changes reflect ni-
trogen deprivation. Increased photosynthetic CO 2 fixation altered the apparent C:N
balance. The findings of Miyagi et al. ( 2011 ) were consistent with this hypothesis.
M.-E. P. Papadimitropoulos and M. I. Klapa