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

870 Nucleic Acid Synthesis

one strand by RNA polymerase requires localized strand that are common constituents of promoters in prokary-
separation which is induced by the polymerase itself, re- otic genomes and are nominally referred to as −35 and
sulting in a transcription bubble. During chain elonga- −10 sequences signify that the midpoint of these se-

tion, this bubble moves along the DNA duplex. Initiation quences are located 35 and 10 bp 5 of the start site of
of RNA synthesis is enhanced in an in vitro reaction with transcription. However, the exact distance is somewhat
supercoiled duplex circular DNA template in which base variable for different genes. The consensus −35 sequence
pairs are destabilized due to torsional stress. Unwinding is TTGACA, and the consensus of −10 is TATAAT. How-
of the helix at the transcription site causes overwinding ever, both of the sequences are also somewhat variable.
(positive supercoiling) of the template DNA ahead of the The strength of a promoter, i.e., how efficiently it is rec-
transcription bubble and underwinding (negative super- ognized for transcriptional initiation, depends on the ex-
coiling) behind the bubble. act sequence of the −35 and −10 sequences and possibly
the intervening “spacer” sequences as well. The promoter
strength can vary widely among genes, and mutations in
A. Recognition of Prokaryotic Promoters
the −35 or −10 sequence in a particular gene can dramat-
and Role of σ-Factors
ically affect its promoter strength.
In prokaryotic RNA polymerases, the σ-factor is required
for promoter recognition and binding. It is loosely bound
B. Regulation of Transcription in Bacteria
to the core complex and released after the nascent RNA
chain becomes 8–9 nucleotides long. The core polymerase Unlike replication of the complete genome, which is es-
with σ-factor has a high affinity for nonspecificDNA.The sential for cellular propagation, not all genes need to be
σ-factor alters the conformation of the holoenzyme so that transcribed in a particular cell for its survival. Synthesis
its affinity for nonspecific DNA is reduced and the specific of mRNA is required for generation of proteins. Because
binding affinity for the promoter is significantly enhanced. not all proteins are required at all times for cellular sur-
More than one type of σ-factor is present in E. coli, and vival and metabolism, both in prokaryotes and eukary-
more such factors are present in other bacteria. These dif- otes, and many proteins are expressed only in specific
ferent factors may have specialized functions in altered stages of development and differentiation in higher eu-
growth conditions, cause a global change in transcrip- karyotes, a gene’s transcription is often highly regulated.
tionalinitiationduetotheirrecognitionofdistinct−35and Furthermore, the stability of mRNAs and the proteins they
−10 sequence elements, and have a preference for differ- encode vary over a wide range. Thus, different mRNAs
ent promoters. are not made at the same rate. Additionally, the bulk of
RNA chain termination in bacteria occurs by two mech- RNA, and in fact a large fraction of the cell mass, consists
anisms, one with assistance of a protein factor rho (ρ) and of ribosomal and transfer RNAs needed for carrying out
the other without need of a protein. In both cases, termina- protein synthesis. Both ribosomal and transfer RNAs are
tion occurs at a specific terminator sequence in the gene, extremely stable.
at which the RNA polymerase stops adding nucleotides to Regulation of transcription, first investigated in bac-
the growing RNA chain, which is then released from the terial viruses, primarily in E. coli, an intestinal microbe
template. The terminator sequence often has a “hairpin” and its bacteriophage λ, is the foundation of molecular
structure which results from intramolecular base pairing in genetics. The ease of generating and manipulating mu-
a palindromic sequence. It is likely that such hairpins at the tants of various genes in E. coli and λ led to the dis-
end of RNA promote its dissociation from DNA. Termina- covery of repressors, which are proteins that bind to
tion can be prevented by an anti-terminator protein, which operator sequences of genes and turn off transcription.
allows the polymerase to ignore the terminator signal. The genes that were originally studied encode enzymes for
A unique distinction between prokaryotic and eukary- sugar (lactose and galactose) metabolism. Inactivation of
oticRNAsynthesisisthetemporalrelationshipbetweenits these genes and their expression could be studied because
synthesis and utilization in information transfer. Prokary- the proteins are not essential for bacterial survival. An
otic transcription of mRNA is linked to its reading on activator needed for expression of lactose-metabolizing
the ribosome for protein synthesis. Thus, even before β-galactosidase was identified; it is downregulated in the
transcription is terminated, the 5 terminal region of the presence of glucose (“glucose effect”) and upregulated by

nascentmRNAis complexed with aribosome for initiation binding to 3 -5 cyclic AMP.

andpropagationofproteinsynthesis.Inthecaseofeukary- Significant advances in elucidating the mechanism of
otes, transcription occurs in the nucleus, from which the transcriptional regulation came from the life cycle studies
RNA has to be transported to the endoplasmic reticulum of the lysogenic λ virus, whose virus-specific proteins are
with ribosomes in the cytoplasm. Two sequence motifs not expressed in the lysogenic state, when its duplex DNA