Chapter 11:

Regulation of Gene Expression

1. Differential gene expression
2. *The operon
3. Global gene regulation
4. Post-initiation control of gene expression
5. *Quorum sensing
6. Two-component regulatory systems
7. Chemotaxis
The operon:
Operon (Table 11.1, Fig. 11.3)
• What is operon?
• E.g. lac operon

Fig. 11.3
 The operon:
lac operon (Fig. 11.4)
• has genes for use of
lactose
• Expression is inducible
– produced only when
needed
• Use both positive and
negative control

Fig. 11.4
 Inducible Negative Control
The operon: Repressor is produced by this
gene, _______
• Negative control of transcription Where does repressor bind to?
(A) Promoter
– Use repressor (LacI) to block RNAP  no transcription (B) Operator
– How inducer works? (Fig. 11.5) (C) RNA polymerase

Show Video/Demo
 The operon:
• Positive control of transcription
– Use activator, CRP-cAMP, to help RNAP-promoter
– How it works? (Fig. 11.7) What is the co-activator?
(A) Lactose cAMP-CRP
– What is the signal for low glucose? (B) Inducer (cAMP receptor protein)
(C) cAMP binding to DNA
 The operon:
• How positive and negative control coordinate? Why controls? (Fig. 11.8)
Positive Negative
control control

cAMP is a signal of
“low glucose”

lac operon is only expressed under

____ glucose AND ____ lactose
 Biphasic growth when both
glucose and lactose are present
What is the preferred sugar for cells? Why?

C How lac operon controls the sugar

preference?
Answer these questions for points A, B, and C.
B

• lac Inducer YES or NO

• cAMP YES or NO
• lac operon ON or OFF

Fig. 11.9
 Quorum sensing: Click to see
video

• How bacteria communicate with each other?

• Quorum sensing: cell density
 control gene expression based on quorum (votes!)
• E.g., bioluminescence of Vibrio fischeri
– in light organ of squid

Fig. 11.19 Symbiosis

https://youtu.be/6zAcenHFwvY
 Quorum sensing:
• What is the signaling chemical?
– Autoinducer
– Gram negative bacteria use
AHL (N-acyl-homoserine lactone) (Fig. 11.20)
– Gram positive bacteria use small peptides
– Species-specific

TED Talk: Bonnie Bassler: The secret, social lives of bacteria:

https://www.youtube.com/watch?v=TVfmUfr8VPA
Animation: https://www.youtube.com/watch?v=LfDM95gsEQA (2 minutes)
 Quorum sensing:
• How lux operon works? (Fig. 11.21)
– consists of genes for AHL synthase (LuxI), luciferase, etc. for
light production
– What is the activator?

Fig. 11.21A
WileyPlus video

No activation; basal level of expression

 Quorum sensing:
Quorum: high cell density  AHL reaches critical conc.
Sensing: AHL-LuxR = activator (specificity: key and lock)
Activation: Activator binds to lux box activate transcription  more
AHL, luciferase  light

The lux operon can also be

considered as a _______
control?
A) Positive
B) Negative

Activation Fig. 11.21B

 Quorum sensing:
• QS also used in
– Motility
– Conjugation
– Biofilm formation
– Pathogenesis
 Chapter 11 Textbook Study Guide
• This chapter introduces how genes are regulated. We will focus on
sections 11.2 and 11.5. Gene regulation is a busy field of research. The
authors did a great job summarizing the current updates. If you are
interested, you may want to read it over, especially the new stuff on
regulatory RNA.
• Textbook reading will be required for Sections 11.2 and 11.5 (see below
for specific parts).
• Sec 11.2: most is covered, except the trp operon (Fig. 11.6) and lac
mutants (Fig. 11.10 and 11.11)
• Sec 11.5: everything is covered.
 Chapter 9:
Bacterial Genetic Analysis
1. Bacteria as subjects of genetic research
2. Mutations, mutants, and strains
3. *Restriction enzymes, vectors, and cloning
4. Recombination and *DNA transfer
 Restriction enzymes, vectors, and cloning:
• What is Restriction enzymes (REs)
– Cut DNA at a specific site, i.e. restriction site (usually Restriction enzyme is a
type of endonuclease
palindromic)
– Bacteria use it to cut foreign DNA
– REs make recombinant DNA possible
– Example of palindromic sequences (Table 9.3)

http://study.com/academy/lesson/restriction-
enzymes-function-and-definition.html (1:00 -3:00)
 How Restriction enzyme
helps cloning in vitro (Fig. 9.11)

• What chemical bond does REs

cleave?
• Which enzymes are used in
Generate sticky this experiment?
(cohesive) end
sequences 1. DNA polymerase
2. Restriction enzyme
3. Gyrase
4. DNA ligase
 Cloning Vectors (Fig. 9.13)

• Plasmid cloning vectors need:

– Origin of replication
– Selectable marker gene
– Multiple cloning site
– Small size
– High copy number

Fig. 9.13
How to clone a gene (Fig. 9.14)

Select for proper

phenotypes

https://www.youtube.com/watch?v=MIfDx417SD
s&list=PLb0WW0k29aHpIR44YLwrQol_cgisaDw-B
(0:45 – 3:30)
Polymerase chain reaction (PCR) made genomic
sequencing possible (Toolbox 1.1)
• In vitro amplification of
DNA
• What molecules are
needed in PCR?
• What are the order of the
three PCR steps? (not in
order)
A. Annealing
B. Denaturing
C. Extension

Toolbox 1.1
https://www.youtube.com/wat
ch?v=2KoLnIwoZKU
 Recombination and DNA transfer:
• Horizontal gene transfer (HGT): a key event in evolution and speciation
• What are the three major mechanisms of HGT?

More than 50% of human

genome belongs to mobile
elements
https://www.youtube.com/watch?v=Fq0YSTyJlpk
 Recombination and DNA transfer:
• Transformation (Fig. 9.22)
– Taken naked DNA into a competent bacterial cell
– Naturally competent, e.g. Streptococcus
– Artificially competent by chemicals or electroporation

Fig. 9.22 – do not need to

know the details of the
receptor and translocation
protein complex
Conjugation (Fig. 9.23)
– Transfer of DNA from cell to
cell via sex pilus
– e.g. F plasmid

Fig. 9.23

http://highered.mheducation.com/sites/0072556781/student
_view0/chapter13/animation_quiz_3.html (all)
https://www.youtube.com/watch?v=EtxkcSGU698
 Recombination and DNA
transfer:

• Transduction (Fig. 9.33)

– By bacteriophages
– Due to packaging mistake

http://highered.mheducation.com/sites/0072
556781/student_view0/chapter13/animation_
quiz_2.html (all)
 Recombination and DNA transfer:
• Transposition “jumping gene” (Fig. 9.31-32)
– Movement of DNA via mobile genetic elements
• Insertion sequence (IS) or Transposon (Tn)
• Key components: transposase and IR (inverted repeat)
• Still need to use some mechanisms to travel cell-to-cell

IS

Tn

http://highered.mheducation.com/sites/0072556
781/student_view0/chapter13/animation_quiz_5.
html (all)
 Chapter 9 Textbook Study Guide
• Only covers 9.3 and 9.4 on selected topics
• Sec 9.3: study restriction enzyme and cloning vectors (only the
plasmid cloning vector)
– Restriction enzyme: know how it involves in recombinant DNA (Fig. 9.11); no
need to remember the sequences in Table 9.3, but need to know what the
restriction sites look like.
– Plasmid cloning vector: know the features of a basic cloning vector (Fig.9.13,
p. 283’s five bullet points); know how cloning works (Fig. 9.14);
– Focus your reading on understanding the figures mentioned above. No need
to know the specific plasmid vectors and how they work.
• Sec 9.4: Focus on transformation (Fig. 9.22 part 1),
conjugation mechanism (Fig. 9.24), transposition (Fig. 9.31
and 9.32), and transduction (Fig. 9.33).
– You may skip the headings started with “uses of ….” and
“Recombination”
– Study the listed figures and their corresponding textbook contents will be
sufficient.
 Chapter 10:
Microbial Genomics

1. Genome sequencing
2. *Genomic analysis of gene expression
3. *Comparative genomics
4. *Metagenomics
All in selected topics; see the study guide; focus
on terminology and applications
 Introduction:
• What is Genomics -omes vs -omics

– studying the entire genome of an organism

• When is the first genome sequences known?
– 1995 Haemophilus influenzae (bacterium)
– 2003 Human genome
– Now, over thousands of genomes in GenBank
• http://www.ncbi.nlm.nih.gov/genome (browse by organisms)
 Genomic analysis of gene expression:
• What is Transcriptomes?
– Collection of mRNA in a cell
– Why?
• Know what are expressed
– How to analyze? (not in test)
• Microarray
• Sequencing
 Genomic analysis of gene expression:
• What is Proteomes
– Collection of proteins in a cell (Fig. 10.12)
• Why?
– Study all proteins that are produced
• How to analyze? (not in test)
– 2D-PAGE
– Mass spectrometry
– X-ray crystallography
– Nuclear magnetic resonance (NMR)
 Comparative genomics:
• What is Comparative Genomics
– Study of evolutionary processes using genomic tools
• What can it reveal?
– Genetic variability during evolution
– Horizontal gene transfer (HGT)
• Evidence of gene transfers, e.g. genomic islands (Fig. 10.17)

Fig. 10.17
Evidence of
Genomic Island
 Metagenomics:
• What is Metagenomics?
– Study of DNA extracted directly from microbial communities (=
Microbiomes)
• Less than 1% of microbes can be cultured in lab
– What can you learn in metagenomics analysis?
• species diversity & abundance
• Discover new genes/microbes
– new applications
Metagenomics:
• How it works? (Fig. 10.18)
 Summary of Chapter 10
• You have learned these new terms:
– Genomes (or genomics for the study)
Pure
culture(s)
– Transcriptomes Examples:
– Proteomes A. Study gene expression pattern of a cancer cell in
responding to therapy
Mixed
– Comparative Genomics B. Study genes/DNAs in ocean water samples
cultures  – Metagenomes C. Compare the genomes of E. coli and Salmonella
D. Analyze all DNAs of Cyanobacterium
• All of above required computational analysis of a
large amount of sequence data (BIG DATA)
Bioinformatics or computational biology
A great field to get into…..