1. Regulation of Gene Expression
Defects in gene regulation can alter
the development of an organism

2. Seven processes that affect the steady-state
concentration of a protein in a cell

3. Regulation of Gene Expression
Principles of gene regulation
Regulation of gene expression in prokaryotes
Regulation of gene expression in eukaryotes

4. Principles of Gene Regulation
constitutive vs. regulated gene expression
housekeeping genes, gene products that are required
at all times at a more or less constant level.
e.g., in citric acid cycle

5. Principles of Gene Regulation
1) RNA polymerase binds to DNA at promoters

6. Principles of Gene Regulation (cont’d)
2) Transcription initiation is regulated by proteins
that bind to or near promoters.
Repression of a repressible gene:(i.e., negative regulation)
repressors (vs. activators) bind to operators of DNA.
Repressor is regulated by an effector, usually a small molecule
or a protein, that binds and causes a conformational change.
Activator binds to DNA sites called enhancer to enhance
the RNA polymerase activity. (i.e., positive regulation)
Induction of an inducible gene, e.g., heat-shock genes.
Heat-shock promoters

8. Principles of Gene Regulation (cont’d)
3) Most prokaryotic genes are regulated in units
called operons.
Francois Jacob & Jacques Monod, 1960

9. Lactose metabolism in E. coli

10. 4) The lac operon is subject to negative regulation: repressor
tetrameric
repressor
IPTG induced
uninduced

12. 5) Regulatory proteins have discrete DNA-binding domains
Functional groups (pink) in DNA
available for protein binding

13. 5) Regulatory proteins have discrete DNA-binding domains
e.g., specific amino acid-base pair interactions
in DNA-protein interaction

14. e.g., a DNA-binding domain (3) interacts
directly with DNA at major groove

15. The DNA binding sites for regulatory proteins are often
inverted repeats of a short DNA sequence (a palindrome)
at which multiple subunits (usually two) of a
regulatory protein bind cooperatively.
inverted repeats
e.g., Lac repressor vs. operator
AATTGT…ACAATT
TTAACA…TGTTAA

16. Examples of DNA-binding motifs/domains:
helix-turn-helix: e.g., Lac repressor
zinc finger: e.g., Zif 268
homeodomain: e.g., Ultrabithorax (Ubx)

17. Helix-turn-helix Lac repressor, DNA-binding domains a tetramer
allolactose-binding
domains
hydrogen-bonding (red)
hydrophobic interactions (yellow)

18. zinc finger:
In many eukaryotic (few prokaryotic) DNA-binding proteins
e.g., Zif 268
~30 a.a.
Zn2+
(2 Cys, 2 His)

19. homeodomain: homeobox: DNA sequence encoding homeodomain
e.g., Ultrabithorax (Ubx)
a a helix (red) protruding
into the major groove

20. Leucine zippers 6) Regulatory proteins also have protein-protein
interaction domains
Leucine zippers
basic helix-loop-helix
interacting
Leu (red)
Leucine zippers

21. basic helix-loop-helix
e.g., transcription factor Max (dimeric)
A pair of
interacting Leu
helix-loop-helix
(red & purple)
DNA-binding
segment (pink)

22. Regulation of Gene Expression
Principles of gene regulation
Regulation of gene expression in prokaryotes
Regulation of gene expression in eukaryotes

23. The Lac Operon

24. The lac Operon Is Subject to Positive Regulation:
Activation by CRP (cAMP receptor protein)

25. CRP homodimer DNA is bended Region interacting with
RNA polymerase (yellow)
cAMP (pink)

26. The effect of glucose on CRP is mediated by cAMP.
Transcription occurs only at low glucose and high lactose.
cAMP & CRP are involved in the coordinated regulation of
many operons. A net of operons with a common regulator
is called regulon.

27. The ara operon undergoes both positive & negative regulation
by a single regulatory protein AraC.
Th end product of the arabinose metabolic pathway,
D-xylulose 5-phosphate, is an intermediate in the
pentose phosphate pathway.

28. When the AraC repressor is depleted,
The araC gene is transcribed from its own promoter.

29. At high glucose and low arabinose, AraC binds and
brings araO2 and araI sites together to form a
DNA loop, repressing araBAD.

30. At low glucose, but arabinose is present, AraC repressor binds
arabinose and changes conformation to become an activator.
DNA loop is opened, and AraC binds to each half-site of
araI and araO1. The proteins interact with each other, and act
in concert with CRP-cAMP to facilitate transcription of
the araBAD genes.

31. Many Genes for Amino Acid Biosynthesis Are Regulated
by Transcription Attenuation
e.g., the trp operon
At high tryptophen, 1) the repressor binds its operator,
2) transcription of trp mRNA is attenuated.

32. Trp repressor
dimeric,
helix-turn-helix
bound tryptophen (red)

33. Transcription attenuation in the trp operon
The trp mRNA leader (trpL):
Sequence 1 encodes a small peptide, leader peptide,
containing two Trp residues.

34. Transcription attenuation in the trp operon
attenuator
At high trp
At low trp

35. The Trp Operon

37. Induction of the SOS Response in E. coli Requires
Destruction of Repressor Protein LexA:
Operon-like regulation
Coprotease RecA is activated by DNA damage
(single stranded DNA)
LexA is cleaved and inactivated by RecA

38. Synthesis of Ribosomal Proteins Is Coordinated with rRNA Synthesis
mRNAs of some ribosomal proteins (r-protein):
r-protein acts as a
translational repressor
yellow: RNA pol subunits
blue: EFs

39. Synthesis of Ribosomal Proteins Is Coordinated with rRNA Synthesis
e.g., stringent response in E. coli, response to amino acid starvation
uncharged tRNA binding > stingent factor (RelA) binding >
catalysing ppGpp synthesis > binding to b-subunit of pol >
rRNA synthesis reduced

40. Some Genes Are Regulated by Genetic Recombination
e.g., regulation of flagellin
genes in Salmonella:
phase variation allows
evasion of host immune
response.
repressor

42. Regulation of Gene Expression
Principles of gene regulation
Regulation of gene expression in prokaryotes
Regulation of gene expression in eukaryotes

43. Extraordinary complexity of gene regulation in eukaryotes
Transcriptional Active Chromatin is Structurally Different from
Inactive Chromatin:
hypersensitive sites (100 ~ 200 bp), DNaseI sensitive sequences whithin
the 1000 bp flanking the 5’ end of transcribed genes.
Modifications Increase the Accessibility of DNA:
e.g., 5’-methylation of cytosine of CpG sequences is common in
eukaryotic DNA, active genes tend to be undermethylated. ……

44. Extraordinary complexity of gene regulation in eukaryotes
Chromatin Is Remodeled by Acetylation
and Nucleosome Displacements
chromatin remodeling: the detailed mechanisms for
transcription-associated structure changes in chromatin.

45. Extraordinary complexity of gene regulation in eukaryotes
Many Eukaryotic Promoters Are Positively Regulated
DNA-Binding Transactivators and Coactivators Facilitate
Assembly of the General Transcription Factors
enhancer in higher eukaryotes,
upstream activator sequences (UASs) in yeast.

46. Three Classes of Proteins Are Involved in Transcriptional Activation
basal transcription factors, DNA-binding transactivators, and coactivators.

47. A wide variety of repressors function by a range of mechanisms

48. The Genes Required for Galactose Metabolism in Yeast Are
Subject to Both Positive and Negative Regulation
Binding of galactose to Gal3p and its interaction with Gal80p produce
a conformation change in Gal80p that allows Gal4p to function in transcription activation.
regulated 6 genes (table 28-3)
regulatory proteins:
Gal4p, Gal80p & Gal3p

49. Unlike bacteria, there is no operons in yeast.
Each of the GAL genes is transcribed separately.

50. The GAL system is shown to illustrate the transcription activation
of a group of related eukaryotic genes.
The initiation complexes
assemble stepwise:
DNA-binding transactivators
Basal transcription factors/pol II
Additional protein complexes
needed to remodel the chromatin
e.g., SWI/SNF: histone remodeling
SAGA: histone acetylation

51. Typical DNA-binding transactivators
have a DNA-binding domain and an activation domain.
e.g., Gal4p, acidic activation domain function in activation
CTF1(CCAAT-binding transcription factor 1), proline-rich activation domain
Sp1, glutamine-rich activation domain

52. “Domain-swapping” experiment: A chimeric protein
containing the DNA-binding domain of Sp1 and the
activation domain of CTF1 activates transcription
if a GC box is present.

53. Eukaryotic Gene Expression Can Be Regulated by
Intercellular and Intracellular Signals
e.g., steroid hormone (estrogen) receptors

55. Regulation Can Occur through Phosphorylation of
Nuclear Transcription Factors
e.g., The catalytic subunit of protein kinase A, released when
cAMP levels rise, enters the nucleus and phosphorylates
a nuclear protein, the CRE-binding protein (CREB),
>> binding to CREs near certain genes and acting as a
transcription factor.

56. Many Eukaryotic mRNAs Are Subject to Translational Repression
e.g., translational repressors (RNA-binding proteins) interact with
initiation factors or with the ribosome to prevent or
slow translation

57. Development Is Controlled by Cascades of Regulatory Proteins

58. Maternal Genes Christiane Nusslein-Volhard (p.1112)
bicoid (bcd) gene product gradient
Two posteriors

61. Segmentation genes e.g., ftz gene product (Ftz) Early embryo
Late embryo

62. Homeotic genes:
Antennapaedia (~ mouse HOX 1.1)

63. The discovry of structural determinants
with identifiable molecular functions
is the first step in understanding the
molecular events underlying development.
bithorax mutation