This document provides information about transcription in prokaryotes. It defines transcription as the synthesis of RNA using single-stranded DNA as a template. It describes the basic requirements for transcription including the template, enzyme, regulatory proteins, ribonucleoside triphosphates, and energy. It then explains the three main steps of transcription - initiation, elongation, and termination - and provides details about each step. The document also discusses transcription regulation and inhibitors like rifampicin and actinomycin D.

1. Transcription
M.PRASAD NAIDU
MSc MEDICAL BIOCHEMISTY,
Ph.D.RESEARCH SCHOLAR

2. Definition
Synthesis of RNA using ssDNA as a template by DNA
dependent RNA polymerase
• Similar to replication in terms of chemical mechanism,
polarity, and use of template but differ in
-does not require primers
-only a short segment of DNA is transcribed

3. • All 3 types of cellular RNA’s are copied during transcription
• Messenger RNAs (mRNAs) encode the amino acid sequence
of one or more polypeptides specified by a gene or set of
genes.
• Transfer RNAs (tRNAs) read the information encoded in the
mRNA and transfer the appropriate amino acid to a growing
polypeptide chain during protein synthesis.
• Ribosomal RNAs (rRNAs) are constituents of ribosomes, the
intricate cellular machines that synthesize proteins.

4. Basic Requirements of Transcription--
prokaryotic
 Template ------ssDNA
 Enzyme-----RNA polymerase
 Regulatory proteins
 Ribonucleoside triphosphates ( A, G,C,U )
 Energy –uses the energy released from the cleavage of
pyrophosphates to two phosphates by pyrophosphotase

5. Steps involved in Transcription
 Initiation
-recognition of specific DNA sequence ( promoter region )
-beginning of bond formation process
Elongation
Termination & release

6. Initiation
Starts with the recognition of promoter sequence on the DNA
coding ( anti-template ) strand by RNA polymerase
Promoter sequence
• Present on the DNA
 Two common sequences are present on the upstream ( 5’ ) side
of the start site
 Start site is denoted by +1

7. Contd--
 -10 sequence & -35 sequence
 5’------TTGACA--------TATAAT--------start site --------terminator 3’
(-35 ) ( -10) +1
 Sequences are 6 bp long
 Distance b/n these two promoters is conserved & is a
separation of 17-19 nucleotides in normal
 -10 sequence is called Pribnow box ( TATA box )

9. Contd—
 Genes with strong promoters cause frequent initiation of
transcription as often as every two seconds ( E coli ) (strong
promoters have sequence that correspond closely to the
consensus sequence )
 Genes with weak promoters are transcribed about once in 10
minute ( weak promotes tend to have multiple substitution at
that site )

11. RNA Polymerase ( E.Coli )
• Multisubunit enzyme
• DNA dependent RNA polymerase
• Very large molecule ( 500 kd ) and complex enzyme consisting of
four kinds of subunits
• Prokaryotes have single RNA pol that transcribes all the three
RNA’s ( mRNA, t RNA, r RNA )
• α2 β β’ Ω σ ------holoenzyme
• RNA polymerase with out σ subunit is called core enzyme
• Core enzyme contains the catalytic activity.

13. Subunit Gene Number Mass
( kd )
Role
α rpo A 2 37 Binds regulatory proteins
β rpo B 1 151 Forms phosphodieter bond
β’ rpo C 1 155 Binds DNA template
σ rpo D 1 70 Recognizes promoter & initiates
synthesis

14. Contd--
• RNA polymerases lack a separate proofreading 3’ to 5’
exonuclease active site (such as that of many DNA
polymerases)
• The error rate for transcription is higher than that for
chromosomal DNA replication approximately one error for
every 10 4 to 10 5 ribonucleotides incorporated into RNA.

15. Contd--
 After recognizing & binding to the promoter region RNA pol
synthesizes complimentary RNA sequence to the DNA template
strand ( U instead T is paired with A )
 RNA synthezised from 5’ to 3’ ( template read from 3’ to 5’ )
 5’ end of new RNA chain is highly distinctive : a molecule starts
with either pppG or pppA ( DNA synthesis – Primers )
 Template strand is determined by the location of the promoter
region for that gene

16. Contd--
 RNA pol interacts with activator & repressor proteins that
modulate the rate of transcription
 In bacteria one species of RNA pol can synthezise all the RNA
molecules ( mRNA, tRNA, rRNA ) except short RNA primers
needed for DNA replication ( primase )

17. Elongation
• RNA polymerase elongates an RNA strand by adding
ribonucleotide units to the 3-hydroxyl end
• The 3-hydroxyl group acts as nucleophile, attacking the
phosphate of the incoming ribonucleoside triphosphate and
releasing pyrophosphate.
• By the time 10 nucleotides are added ,the σ factor dissociates &
the core enzyme continues the elongation of the transcript

18. Contd—
• The template DNA strand is copied in the 3’ to 5’ direction
(antiparallel to the new RNA strand), just as in DNA
replication.
• Each nucleotide in the newly formed RNA is selected by
Watson-Crick base-pairing interaction
RNA pol
(NMP)n + NTP (NMP)n+1 + PPi
RNA Lengthened RNA

20. Termination
E. coli has at least two classes of termination signals:
• one class relies on a protein factor called ρ (rho)
• the other is ρ independent.
 Most –ρ independent terminators have two distinguishing
features.
• The first is a region that produces an RNA transcript with self
complementary sequences, permitting the formation of a
hairpin structure centered 15 to 20 nucleotides before the
projected end of the RNA strand.

22. Contd--
• The second feature is a highly conserved string of A residues
in the template strand that are transcribed into U residues
near the 3 end of the hairpin.
• When a polymerase arrives at a termination site with this
structure, it pauses
• Formation of the hairpin structure in the RNA disrupts
several AUU base pairs in the RNA-DNA hybrid segment and
may disrupt important interactions

24. Contd—
 Rho (ρ ) dependent termination
• Rho factor is an ATP dependent RNA-DNA helicases
• Recognizes and bind to the termination signals and disrupts
the nascent RNA/DNA complex

26. Transcription Is Regulated at Several Levels
• Requirements for any gene product vary with cellular
conditions or developmental stage, and transcription of each
gene is carefully regulated to form gene products only in the
proportions needed.
• Regulation can occur at any step in transcription, including
initiation ,elongation and termination.
• Much of the regulation is directed at the polymerase binding
and transcription initiation

27. • The binding of proteins to sequences both near to and distant
from the promoter can also affect levels of gene expression.
• Protein binding can activate transcription by facilitating either
RNA polymerase binding or steps further along in the
initiation process, or it can repress transcription by blocking
the activity of the polymerase.
• In E. coli, one protein that activates transcription is the cAMP
receptor protein (CRP), which increases the transcription of
genes coding for enzymes that metabolize sugars other than
glucose when cells are grown in the absence of glucose.

28. Contd--
• Repressors are proteins that block the synthesis of RNA at
specific genes.
• In the case of the Lac repressor , transcription of the genes
for the enzymes of lactose metabolism is blocked when
lactose is unavailable

31. Inhibitors
• Rifampicin ( antitubercular
drug)
-semisynthetic derivative
( sterptomyces)
-specifically inhibit initiation not by
blocking the binding of RNA pol
but rather by interfering with
the formation of the first
phosphodiester bond
-Site of action is on β subunit of
RNA pol
-some mutants having an altered β
subunit are resistant to
rifampacin

32. Actinomycin D
-polypeptide derived from streptomyces
-binds tightly & specifically to double stranded DNA & prevents
it from being an effective template for RNA synthesis
-at low concentration inhibits transcription without appreciably
affecting replication & protein synthesis
-inhibitor of both prokaryotic & eukaryotic cell
-effective therapeutic agent in the treatment of some cancers