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CHAPTER
6
F
U N C T I O N A L
G
E N O M I C S
O
VERVIEW
Cellular processes are controlled at various levels. The basic information is
encoded by the genome, which essentially is identical in every cell of the
organism, irrespective of the stage of development or environment. Control
of the resultant bioactivity stemming from this invariant information can
occur at a number of points, as shown in Figure 6.1. 
The information contained in the DNA, the genome, can be transcribed
into RNA, but only a small part of the information in the DNA is ever tran-
scribed. The sum of all of the regions of genome that are transcribed is col-
lectively known as the transcriptome and comprises all of the sequences that
make up the complete RNA component of the organism. Because not all of
the DNA is transcribed, the transcriptome is less complex than the genome.
The products of the translation of the transcriptome generate the proteome.
However, because some of the RNA molecules are never translated into pro-
teins, the complexity of the proteome is less than that of the transcriptome.
However, this complexity can be increased through posttranslational modi-
fications of the proteins, giving the potential for more than one important
product to be derived from a given message. These proteins then function
in the synthesis of primary and secondary metabolites, the total of these
making up the metabolome. The combination of the RNAs, proteins, and
metabolites, functionally integrated together, results in the biological activ-
ity of a cell or tissue, and information on all of these processes is necessary
for a complete understanding of plant form, function, and development. 
DNA sequence information has been, and is continuing to be, gathered
both from genomic DNA and cDNA studies. However, all of this sequence
information is just a first step in understanding the coordinated control of
Plant Genomics and Proteomics, by Christopher A. Cullis
ISBN 0-471-37314-1 Copyright © 2004 John Wiley & Sons, Inc.
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gene expression, as well as understanding which of these potential genes are
actually expressed in a functional fashion. As mentioned in Chapter 2, the
annotation of the genomic sequence refers to the processes (both manual and
computer based) by which various regions of the genome are classified
(genic regions, nontranscribed regions, transposable elements, conserved
control regions). However, this analysis cannot address the spatial and tem-
poral patterns of expression of those genes, or even whether those sequences
are ever expressed. The data from ESTs and full-length cDNA clones directly
identify the genomic sequences transcribed into RNA. However, even these
data do not unambiguously identify those RNAs that ultimately influence
the phenotype of the organism. Three possible fates for an RNA molecule
are:
∑ It is translated into a protein.
∑ It functions as an RNA without any subsequent modification.
∑ It is degraded without ever actually performing a specific known
function. 
Therefore, to understand the functioning of the cell, additional information
concerning transcription and translation (if appropriate) of any of the puta-
tive genes and the subsequent activity of any protein products must be
obtained. 
The three levels of expression, RNA, proteins, and products are covered
in this chapter. Useful definitions are:
1. Expression profiling covers the methods used to acquire the infor-
mation related to the RNA components of the cell.
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6. F
U N C T I O N A L
G
E N O M I C S
Genome
Transcriptome
mRNA, ribosomal RNA, regulatory RNAs
Proteome
Post-translational modifications
Metabolome
primary metabolites
secondary metabolites
Possible control points
proteins
DNA
biological activity
FIGURE 6.1.
Levels of control for cellular processes (Adapted from Jacobs, D. I., 
R. van der Heijden, and R. Verpoorte (2000) Proteomics in plant biotechnology 
and secondary metabolism research. Phytochem. Anal. 11, 277–287).

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2. The whole complement of sequences that is ever transcribed is also
termed the transcriptome.
3. The identification and modification of proteins is now usually 
identified as proteomics, whereas the characterization of the final
products of protein activity is sometimes referred to as metabolomics. 
4. The term “proteome” refers to the complete cell protein complement,
including unmodified and posttranslationally modified proteins.
5. “Metabolomics” refers to the methods used to characterize the metab-
olism of the cell.
6. “Metabolome” refers to the suite of possible metabolites within a
plant.