Gene Expression

Reference Books
and
Regulation 1. Principles of Genetics
D.P. Snustad and M.J. Simmson
John Willy & Sons, Inc, publishers, New York
Course GTB 204/3
2. Molecular Cell Biology
H. Lodish, A. Berk,S.L. Zipursky, P.Matsudaria, D. Baltimore
and J.Darnel. W.H. Freeman & Company publishers, New York

Dr. Mohammed Shahjahan 3. Principles of Genetics

Robert H. Tamarin, Mc Graw Hill publishers, Boston, USA

Syllabus outline Overview

of DNA and
Know the Gene expression & Regulation gene
Overview of gene expression
structure

Exons

Introns An eukaryotic gene

structure. In
mRNA-splicing prokaryotes
there is no intron.
Transcription terminator (Ref. DNA Technology, I.E.
Alcamco,chap-3)

Central dogma Comparison of gene expression in

prokaryotes and eukaryotes

Prokaryotes Eukaryotes

Simple Complex

Genes grouped in Operons Genes have Introns and Exons

Polycistronic- Multiple genes Monocistronic-Single gene

(Ref. Principle of Genetics, mRNA 5’-cap and 3’-polyA
Snustad & Simmons, chap-12)

No Post-translational Post-translational modifications

modifications e.g. glycosylation

1
 Gene organization in prokaryotes Prokaryotic polycistronic mRNA
and eukaryotes

(Ref. Princ. of Genetics, R.T.

Insert picture Tamarin, chap-11)

(Ref. Mol. Cell Biology

Lodish & Darnel, chap-9)

A typical prokaryotic promoter Promoters in prokaryotes and

eukaryotes

Eukaryotic promoter

(Ref. Principle of Genetics, (Ref. Principle of Genetics,

Snustad & Simmons, chap-12) Snustad & Simmons, chap-12)

Comparison of prokaryotic & Eukaryotic promoters
Prokaryotes
1.At -10 position a conserved
sequence TATAAT called
Pribnow or TATA box is
present
2. At -35 position a conserved
sequence TTGTCA is present
3. Both -10 & -35 conserved
sequences are recognised by
sigma factor of RNA ploymerase
4. Another conserved sequence
centered at -50 called upstream
element is found in ribosomal
RNA
Binding of RNA ploymerase II with eukaryotic
promoter
Eukaryotes
1. All the three eukaryotic RNA
ploymerases recognizes the conserved
sequence TATAAA (TATA box
at about -30 on the promoter DNA.
2 A second conserved sequence is
called CAAT box usually occurs at -80
(Ref. Prin. of Genetics,
and the consensus seq is GCCAATCT
3 Two other conserved seq the GC box, R.H. Tamarin, chap-10)
GGGCGG and the octamer box,
consensus ATTTGCAT are often
present in RNA pol II promoter
3. RNA pol II interact with several
proteins called transcriptional factors
(TF) in order to attack the promoter.
4. Activators (Enhancers) are also bind
to DNA seq often 100-1000bp
upstream of promoter.

2
 RNA
synthesis Gene
Expression
overview

(Ref. Principle of Genetics,

Snustad & Simmons, chap-12)

Initial steps in gene

expression

Gene expression and

regulation
in prokaryotes

What is an operon Inducible and Repressible operon

We can define an operon as a sequence of adjacent genes all under

The transcriptional control of the same promoter and operator.
Promoter
The region on DNA with which RNA polymerase binds immediately
before beginning transcription is known as a promoter. Promoter
have the information for transcription initiation and the major sites in
which gene expression is controlled.
Operator
Operator or Operator site is a control element (receptor site)
sequence of DNA that is recognized by the end product of regulator
gene, repressor. Binding of repressor protein at operator exert its
influence over transcription.
Inducible operon
The inducible operons are activated when the substrate that
is to be catabolized enters the cell. E.g. lac operon.
Repressible operon (Anabolic operon)
Repressible operons are are turned off (repressed) when
their end product accumulates in excess of the needs of the
cell. E.g. trp operon

3
 (Ref. Prin. Of Genetics by R. Tamarin Chap-10

lac operon

P/O

P; promoter, O; operator lac operon with control region

(inducible system)
(Ref. Mol. Cell Biology, Lodish & Darnell, chap-10)

lac operator sequence Jacob &

Monod model
of
transcriptional
regulation

(Ref. Mol. Cell

Biology, Lodish &
Darnell, chap-10)

(Ref. Mol. Cell Biology, Lodish & Darnell, chap-10)

lac operator lacl+ gene is trans-acting

(Oc)
mutantsare
cis-acting
Cis-acting; regulatory
seq in DNA (promoter)
that can control a gene
only on the same
chromosome
Trans-acting: DNAseq encoding
diffusible proteins that control genes
on the same or different
chromosomes

(Ref. Mol. Cell Biology, Lodish &

Darnell, chap-10) (Ref. Mol. Cell Biology, Lodish & Darnell, chap-10)

4
 lac operon inducer IPTG
Induction of
lac operon
E.coli growing on glucose

Induction with IPTG

Addition of 3H-uridine

Cell lysis & RNA isolation

Hybridization with lac

DNA

(Ref. Mol. Cell Biology, Lodish & Darnell, chap-10) (Ref. Mol. Cell Biology, Lodish & Darnell, chap-10)

Catabolite repression of lac operon Positive & negative transcriptional

An interesting property of the lac operon and other operons that
control of lac operon
code for enzymes that catabolize sugars ( e.g. arabinose and
galactose operons) is that they are all repressed by the presence
of glucose. That is glucose is cataboilized in preference to other
sugars this is called catabolic repression.

Catabolic repression involves cyclic AMP. cAMP work in

conjunction with another regulatory protein, the catabolic
repressor protein (CAP) to control the transcription of certain
operons

ATP Adenylcyclase Cyclic AMP CAP protein Catabolite repression

( inhibited by glucose) control of
transcription (Ref. Mol. Cell Biology, Lodish &
Darnell, chap-10)

Trp operon Repression in trp operon

(repressible
system)

(Ref. Prin. Of Genetics by R.

Tamarin Chap-13)

(Ref. Prin. Of Genetics by R. Tamarin Chap-13)

5
 Gene expression in Bacteria
Conc ept s

* Pr oka ryot es exhib it e ff ic ient gen etic m echan ism s to respond to

env ir onmen tal condi tion s
* L acto se me tabol ism i n E . co li is regu lat ed by an inducib le
Gene
sys tem
* Th e Ca tabol ite A ctiv ating Pr ote in (C A P) exe rt s po sit ive
con tr ol ov er
th e lac ope ron
Expression and
* C rysta l struc ture analy si s of rep re ssor comp lexe s h as
con fir med the
ope ron mode l
Regulation
* Th e tryp tophan ope ron in E. co li is a rep ress ibl e gen e syste m
* A tt enuat ion is a cr it ica l p roc ess du ring the r egula tion o f th e trp
ope ron
* Th e ara ope ron is cont rol led by a regul ato r p rotein tha t exe rts
in Eukaryotes
both
po sit ive and negat ive cont rol

GENE EXPRESSION IN EUKARYOTES

G ene tic regul a tion in euk ar yote s c an o c cu r at se ve ra l l e vel s , Stages of
but tran s c ri ption a l cont rol is the p rim ar y m e chan ism con tr oll ing
gen e exp re ss ion . Tr an s c rip tion is modu lat e d by the int er ac tion o f
regu lato ry
eukaryotic
mo lecu le s w ith s ho rt DN A s equenc e s mo s t o ften lo c ated up s tre a m
fr om a ff e c ted gene
gen e s. P o s tt ra ns cr ipt ional me c hani s m s involve th e s el e ct ion o f
a lte rn a tiv e expression
p roduc ts fr om a s ing le t ran s c rip t a nd th e con tr ol o f mR NA
s tab ili ty.

Conc e pt s

* Euk ar yoti c gen e regu lat ion is ve ry di ff e ren t fr o m p roc ar yoti c

gen e (Ref. Prin. Of Genetics by
regu lat ion Snustad & Simmons,
* Th e p romo te r is th e s ite o f a s se mbly o f the ba s al tran s c ri ption chap-24)
co m plex
* Enh a nce rs c ont rol ch rom a tin s truc tur e a nd th e ra te o f
tra ns cr ipt ion
* Th e ye a st g a l g e ne s a re po s itive -indu c ibl e a nd c a tabo lit e-
rep re ss ib le
* D N A m e thyl a tion can a ff e c t gene regul a tion
* P os t- tran s c ri ption a l re gula tion includ e s a lte rna te sp lic ing and
m e ss ag e
s tab ili ty

m-RNA Splicing Post-

transcriptional
In eukaryotes the exons ( protein coding regions) are interrupted by
introns (non-coding region).
processing in
eukaryotes
The primary transcripts or pre-mRNAs in eukaryotes often must be
processed by the excision of introns and the addition of 5’-methyl
guanosine caps (MG) and 3’-poly (A) tails. The post-transcriptional
regulation includes alternate splicing and message stability.

The processed mRNA is then transported to cytoplasm for protein

syntheis (translation). (Ref. Principle of Genetics,
Snustad & Simmons, chap-12)

6
 Self-splicing of
RNA Tetrahymena thermophilia
splicing rRNA precursor

(Ref. Principle of Genetics,

(Ref. Principle of Genetics, Snustad & Simmons, chap-12)
Snustad & Simmons, chap-12)

Alternate splicing Heat shock induction of Drosophila

hsp70 gene

(Ref. Principle of Genetics,

Snustad & Simmons, chap-24)

(Ref. Prin. Of Genetics by Snustad & Simmons, chap-24)

Regulation of gene expression by Regulation of gene expression by

steroid hormone peptide hormone

(Ref. Principle of Genetics,

Snustad & Simmons, chap-24)

(Ref. Principle of Genetics,

Snustad & Simmons, chap-24)

7
 Upstream activating sequences in
Structural Gal1 and Gal10 genes in yeast
motifs within
transcriptional
factors

(Ref. Principle of Genetics,

Snustad & Simmons, chap-24)

(Ref. Principle of Genetics,

Snustad & Simmons, chap-24)

Transcription terminator Terminator regions in DNA

There are 2 -types of terminators, rho-dependent and rho-independent.

Difference lies in their dependency on a protein called rho protein. Rho
(ρ) is a hexamer protein (six identical copies).
1. Rho-independent terminators
Rho-independent termination cause termination of transcription (Ref. Princ. of
even if rho is not present. Genetics, R.T.
Tamarin, chap-10)
2. Rho-dependent terminators
Rho-dependent terminators require the rho-protein;without it RNA
polymerase continues to transcribe, pass the terminator, called
read through.
(Ref. Princ. of Genetics, R.T. Tamarin, chap-10)

rho-dependent & rho-independent

Transcriptional terminator (rho-
termination
independent)

(Ref. Principle of Genetics,

Snustad & Simmons, chap-12)
(Ref. Principle of
Genetics, R.T.
Tamarin, chap-10)