Page 135 - Academic Press Encyclopedia of Physical Science and Technology 3rd BioChemistry

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Encyclopedia of Physical Science and Technology en010k-502 July 16, 2001 16:56

Nucleic Acid Synthesis 873

Termination of eukaryotic transcription is coupled with signaling cascade is initiated in response to the first sig-
processing. The mature rRNA is obtained by cleavage of nal. The external ligand first binds to its receptor on the
a larger primary transcript synthesized by Pol I. Termina- cell surface, followed by internalization of the receptor
tion of Pol II transcription occurs at a repeat sequence of ligand complex. A series of reversible chemical modifica-
U, as in the case of E. coli RNA polymerase, but with- tion (mostly phosphorylation of the regulatory proteins)
out the presence of a hairpin structure. More importantly, finally activates the ultimate transcription factors, which

the 3 termini of mRNAs are generated by cleavage of then trigger transcription of target genes.
primary precursor transcripts followed by addition of a The unique difference between the eukaryotes and
tail of poly(A), a homopolymer of up to several hundred prokaryotes is in the utilization of transcription factors.
AMP residues synthesized by poly(A) polymerase in a In bacteria, one factor is usually specific for one gene or
template-independent reaction. one regulatory unit. In eukaryotes, on the other hand, a
single factor activates multiple target genes.
Prokaryotic regulatory processes have been elucidated
E. Regulation of Transcription in Eukaryotes
in remarkable detail by utilizing the power of molecular
While both prokaryotic and eukaryotic genes are regulated genetics, including “reverse genetics” by which the chro-
by activators and repressors, enhancer elements are unique mosomal genes in the organism could be mutated at spe-
to eukaryotic genes and can profoundly increase the rate cific sites and the mutant gene products purified and char-
of transcription. These elements are located at a variable acterized. Furthermore, these genes can be expressed in
distance from the basic promoter itself, can be present the episomal state by introducing them into autonomously
both upstream or downstream to the promoter, and, in fact, replicating recombinant plasmids.
can even be within the transcription unit. One unexpected Commensurate with the significantly higher complex-
feature is that they can function in either orientation and ity and size of the genome and differentiation and devel-
can activate any promoter located in the vicinity. opmental stages in metazoans, gene regulation in these
Upstream activating sequences (UAS) have been iden- organisms is very complex and occurs at many levels.
tified in yeast and are analogous to enhancers in the Sets of genes are activated at distinct stages of differ-
mammalian genes. Based on the known properties of en- entiation and development of multicellular organisms in
hancers, it appears that the presence of these sequences order to encode proteins which are required for special-
affects chromatin structure and/or the helical structure of ized functions of the cells in these stages. In contrast,
the DNA template itself. Further studies are needed to test certain “housekeeping” proteins, including enzymes for
other possibilities as well, e.g., whether the enhancer pro- metabolism and synthesis of all cellular components (i.e.,
vides an entry point for the transcription complex or is RNA, DNA, structural proteins, and lipids), as well as
needed to place the template at the nuclear matrix where enzymes for biosynthetic and degradative pathways, are
transcription takes place. needed in all cell types and developmental stages. Most
Positive and negative regulation of prokaryotic genes is somatic cells in adult mammals are nondividing and there-
achieved by binding of activators and repressors, respec- fore do not require DNA synthesis machinery. However,
tively, to their cognate binding sites in the genes. Down- all cells require transcription for generating proteins for
regulation is more common, at least in E. coli, than posi- other cellular functions. Unraveling the molecular mech-
tive regulation. In fact, the same protein can provide dual anisms of regulation is the major focus of current research
functions in a few cases, depending on the location of the in molecular biology. The regulatory process is affected
sequence motif. by multiple parameters.
In contrast, because of the complexity of chromatin Many genes are activated due to external stimuli, e.g.,
structure and genomic organization development, differ- exposure to hormones and growth factors. In these cases
entiation, and cell cycle-specific synthesis of proteins, reg- the extracellular signal often acts as a ligand to bind to cell
ulation of eukaryotic genes is extremely complex. This is surface receptors which activate the trans-acting factor(s)
evident from the large number of families of regulatory via multiple steps of signal transduction.
trans-acting factors which recognize similar if not identi-
cal sequence motifs in different genes. Sometimes, these
1. Regulation of Transcription via Chromatin
factors have a distinct modular structure—one module for
Structure Modulation in Eukaryotes
binding to target DNA sequence and another for interac-
tion with components of the transcription apparatus. The eukaryotic genome is organized at multiple levels,
On top of these complexities, the signal for initiation starting with the nucleosome core as described earlier. The
of transcription may be extracellular, e.g., a growth fac- nucleosomes are organized in a higher order chromatin
tor which induces cell proliferation. A highly complex structure due to increasing compaction of DNA: from