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Nucleic Acid Synthesis 871

genome is linearly integrated in the host chromosome. act as positioning factors for correct localization of Pol III
Here again, both positive and negative regulatory mecha- initiation.
nisms are in play to fine tune the expression of genes from Pol II is the most versatile and widely utilized RNA
a low maintenance level during lysogeny to large-scale polymerase in vivo and absolutely needs auxiliary, tran-
expression of the viral genome when the lysogenic virus scription factors (TFII) whose requirement is dependent
enters the lytic phase of growth and exploits the host cell on the nature of promoters.
synthetic machinery for replication of its own viral DNA, 3. The nature of eukaryotic promoters is quite different
RNA, and proteins. from the prokaryotic promoters. In addition to the bipartite
promoter of Pol I, both Pol II and Pol III have a “TATA
box” located about 25 bp upstream of the start site in Pol II
C. Eukaryotic Transcription
responsive genes. The 8-bp sequence consists of only A•T
The fundamental process is identical in prokaryotes and base pairs and is surrounded by G•C pair-rich sequences.
eukaryotes, in that an RNA polymerase complex binds to Interestingly, the TATA box is quite similar to the −10
the promoter and initiates transcription at a start site down- sequence in E. coli promoters.
stream to the promoter. De novo initiation of an RNA chain There is a second element called a CAAT box, usually

occurs with a purine nucleotide and creation of a tran- about −15 bp 5 of the TATA box. Alternatively a G•C
scription bubble with the open complex. The transcription rich sequence is present in some promoters, often at posi-
complex can slide back along the nascent chain and en- tion −90. The consensus GC box sequence is GGGCGG,
donucleolytically cleave off the 3 segment, then moves of which multiple copies are often present and occur in

forward along the DNA template chain; termination oc- both orientations. These elements are not all present in
curs at specific regions in the genes. all promoters; it appears that they work in a “mix and
In spite of this similarity, however, the details are match” fashion. These boxes, and also a octamer box,
very different in eukaryotic cells and are summarized as bind to specific trans-acting factors and are engaged in
follows. multiple protein interactions among themselves as well as
with components of the RNA Pol II holoenzyme.
1. Eukaryotic RNA polymerases contain many more There is no significant homology among transcription
subunits, located in the different regions of the nucleus. start sites of various genes, except for the tendency for the
Pol I, specific for synthesizing rRNA, is located in the nu- first base in the transcript to be an A flanked on either side
cleolus, a specialized structure within the nucleus, while by pyrimidines. This region is defined as the initiator.
Pol II and Pol III are in the nucleoplasm. These enzymes The first step in transcriptional initiation of a TATA-
have 8–14 subunits with a total molecular mass >500 kD. containing promoter is the binding of the factor TFIID to
The large subunits have some sequence similarity with the the region upstream of the TATA site. The TATA-binding
bacterial RNA polymerases. RNA polymerases of mito- protein, TBP, which specifically binds to the TATA box,
chondria and chloroplasts are phylogenetically closer to is a component of the TFIID complex, along with other
bacterial RNA polymerase, commensurate with the fact proteins collectively called TAFs (TBP-associated fac-
that the target genes of these enzymes are fewer and tors). TAFs can be variable in the TFIID complex, both
much smaller in organelles, which are thought to have in species and amounts, and provide the promoter speci-
arisen by symbiotic acquisition of bacteria by primitive ficity for initiation. Some TAFs are tissue specific. TFIID
eucaryotes. has a molecular mass of 800 kD, containing 1 TBP and
2. The promoter composition and organization of eu- 11 TAFs. TBP acts as a positioning factor and is able to
karyotic polymerases are quite specific for each poly- interact with a wide variety of proteins, including Pol II
merase. The promoters of rRNA genes contain a core and and Pol III. It binds to the minor groove of the DNA
an upstream control element which is needed for high pro- double helix and makes contact with other factors which
moter activity. Two ancillary factors, UBFl and SLl, bind mostly bind to the major groove and can make multiple
to these sequences. Although SLl binds only after UBFl in contacts. By bending the DNA at the binding site, it ap-
a cooperative fashion, SL1 is a σ-factor with four proteins pears to bring the factors and RNA polymerase into closer
among which TBP is also required for initiation by the proximity.
other polymerases. Pol I is akin to Pol III in that it utilizes Although TBP is utilized by both Pol II and Pol III,
both upstream and downstream promoters. There are two TFIID is the specific complex for Pol II recognition of a
types of internal promoters with distinct sequence boxes. promoter. Other transcription factors (e.g., TFIIA) bind
One transcription factor (TFIII B) is required for initia- to the TFIID promoter complex and cover increasing
tion of RNA synthesis by Pol III. Other factors (TFIII A segments of DNA. In addition to TFIIA, these include
and TFIII C) help TFIII B bind to the right location and TFIIE, TFIIF, TFIIH, and TFIIJ. Most of the TFII factors