Chapter 2
Escherichia coli
has about 5000 genes. Fungi normally have several thousand genes, e.g., baker’s
Saccharomyces cerevisiae
has about 6000 genes and filamentous fungi typically more than
8000 genes. Higher eukaiyotes such as plants, animals and humans clearly have a much larger
number of genes. In these organisms many functions may also be derived from the individual genes
through alternative splicing of the mRNA, i.e., the specific mRNA formed by gene transcription
can be modified and hereby encode the formation of several different proteins.
The collection of genes (normally referred to as the genome) represents the genotype of a given
organism, and through genomic sequencing programs all the genes of many different organisms
have become known (see e.g. www.genome.ad.jp for a list of sequenced organisms). The genome
represents all the possible functions a cell can express - often referred to as the
actual functions expressed by the cell do, however, depend on which genes are expressed and
further translated into active proteins, which are the key factors for determining the cellular
function. The term
is often used to express the actual functions expressed by a given cell,
and clearly the functions may depend on the environmental conditions experienced by the cells. A
given cell may therefore express several different phenotypes.
The phenotype of a given cell is controlled at many different levels (see Fig. 2.2):
transcriptional control
b) control of mRNA degradation
translational control
d) protein activation/inactivation
allosteric regulation of enzymes.
There is a certain degree of hierarchy in the overall control of cell function. The genes have an
overall control since they define all possible phenotypes, and the proteins have a control of the
actual phenotype. Signal transduction pathways that convey signals from the environment to
specific proteins controlling e.g. gene transcription are placed relatively high in the hierarchy. There
are, however, many feed-back loops in the hierarchical control structure, and it is therefore difficult
to predict the exact function of the individual genes and to assign function to genes identified via
sequencing of whole genomes (this is referred to as functional genomics). In this textbook we are
not going to consider in further detail the functional relationship between the genotype of the cell
and the phenotype. In most cases we shall take a given phenotype for granted and then analyze it at
the quantitative level to see what the consequences of this phenotype are for industrial exploitation
of the cell factory.
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