Download Regulation of Gene Expression

Regulation of Gene
Expression
What are some benefits of regulating
gene regulation?
What novel features of viruses and
bacteria are relevant to learning about
gene regulation and ultimately to
controlling or changing it ourselves?
Regulation of Gene Expression
Key Concepts
• Several Strategies Are Used to Regulate
Gene Expression
• Many Prokaryotic Genes Are Regulated in
Operons
• Eukaryotic Genes Are Regulated by
Transcription Factors and DNA Changes
• Eukaryotic Gene Expression Can Be
Regulated after Transcription
Regulation of Gene Expression
Negative regulation(Repressor genes)
Genes are turned off.
or
Positive regulation (Inducible genes)
Genes are turned on.
Figure 11.2 Positive and Negative Regulation (Part 1)
Figure 11.2 Positive and Negative Regulation (Part 2)
Regulation can occur:
Prior to transcription
During Transcription
After Transcription, before Translation
During Translation
After Translation
Figure 11.1 Potential Points for the Regulation of Gene Expression
Review the actions of viruses
Lytic cycle:
Lysogenic
cycle:
Figure 11.3 A Gene Regulation Strategy for Viral Reproduction
Gene Regulation by Viruses –
used to take over cellular
“machinery” to reproduce virus.
Bacteriophage – Lytic cycle 
Virus has a promoter that binds
to RNA polymerase causing the
transcription of some of its own
genes. Protein products shut
down host genes (degrade DNA or
interfere post- transcriptionally),
also stimulate production of viral
genome replication and
transcription. (will actually use
nucleotides from degraded host
DNA).
Figure 11.4 The Reproductive Cycle of HIV
HIV – Retrovirus – Reverse transcriptase is used to make DNA
from an RNA template. In turn, the viral DNA integrates into
the host DNA (provirus- lysogenic cycle).
Triggering event initiates the lytic cycle. TAT (transActivator of
transcription) keeps host cell from mounting a defense to stop
viral transcription. As virus leaves host cell it incorporates itself
in a phospholipid membrane from the cell (a further deterrent
to viral destruction)
Figure 11.5 Regulation of Transcription by HIV
Made in its entirety
Figure 11.5 Regulation of Transcription by HIV
mRNA transcription terminated
early
Figure 11.6 Two Ways to Regulate a Metabolic Pathway
Gene Regulation in Prokaryotes
We have already learned how enzyme activity can be
regulated through feedback systems. Regulation of enzyme
activity is another method cells may employ.
E. coli in the gut can undergo a rapid change in gene
production to exploit changing food source
ex. Glucose  lactose.
Three enzymes (β-galactoside permease,
β-galactosidase, β-galactoside transacetylase)
needed for lactose digestion are normally present in very
small amounts.
With the presence of lactose, these enzymes can be made
1000’s of times over within as little as 10 minutes.
Operons – units of transcriptional regulation consisting of
promoter & operator sequences, plus
structural genes.
Usually upstream from the operon are DNA sequences to
promote and transcribe a repressor protein.
lac operon- an inducible operon
Normally the repressor protein is present in the cell and
physically binds to the operator site, preventing
transcription.
Figure 11.8 The lac Operon: An Inducible System (Part 2)
The inducer (in this case allolactose –lactose isomer) binds to the
repressor, releasing it from the operator, allowing transcription of
the genes z,y,a for the production of the lactose digesting enzymes.
Figure 11.9 The trp Operon: A Repressible System (Part 1)
trp operon –
a repressible operon
Normally the structural
genes (which are used to
synthesize tryptophan) for
this operon, are operational.
These genes are repressed
when tryptophan is readily
available to the bacteria
from the environment. A
corepressor (tryptophan)
binds to the repressor,
altering its shape so that it
binds to the operator region
of the DNA sequence. This
then stops the transcription
of the structural genes and
tryptophan synthesis is
halted.
.
Figure 11.9 The trp Operon: A Repressible System (Part 2)
What type of feedback is demonstrated upon the structural genes
in each “operon” case?
lac operon demonstrates positive feedback
trp operon demonstrates negative feedback
Most inducible operons are like the lac operon. Therefore,
what type of pathway do inducible operons generally
control:
Anabolic or Catabolic?
May be inducible (generally control catabolic pathways)
repressible (usually control anabolic pathways)
Global gene regulation –
Sigma factors - Proteins that can bind to RNA
polymerase and direct it to specific promoters located in
various locations throughout the bacterial genome in
order to initiate transcription. This is useful when
conditions warrant more than one related function to be
carried out in a cell. Each set of genes rely on the same
promoter.
(Also found in eukaryote cells however, eukaryotic cells do
not necessarily have functionally related genes clustered
together, thus sigma factors may work between several
chromosomes)
DO NOW
Get a “do now” slip and
Briefly describe how lactose influences the lac operon.
Gene Regulation in Eukaryotes
Prior to transcription
Cell signaling – Extracellular  initiation of signal transduction pathway
from ligand binding to Receptor
Intracellular  cellular environment triggers gene production
ex. Cyclin
Chromatin remodeling – Nucleosome consists of negatively
charged DNA wrapped around 8 positively charged histone proteins
which prevents DNA unwinding.
Various enzymes (influenced by chemical environment) can change
the interactions, causing nucleosomes to unwind.
In-Text Art, Ch. 11, p. 219 (1)
Figure 11.15 Epigenetic Remodeling of Chromatin for Transcription
DNA methylation – cystosine modification w/methyl group
(heterochromatin vs. euchromatin)
Ex. Barr body formation (X inactivation)
Histone modification – methylation or phosphorylation
- similar to above
These can actually cause epigenomes of monozygotic
twins to differ over time, causing different gene
expression.
Ex. One twin gets cancer.
Figure 11.13 DNA Methylation: An Epigenetic Change (Part 1)
Figure 11.13 DNA Methylation: An Epigenetic Change (Part 2)
CpG islands (DNA regions rich
In C and G doublets are areas
Often heavily methylated.
Upon replication, the new
strands are unmethylated.
New strands are then
methylated, preventing
transcription.
Demethylation occurs when
transcription is required.
Figure 11.14 X Chromosome Inactivation
Barr Body
During Transcription
Transcription factors  promoter binds to specific
DNA sequence (enhancer) to begin ex. TATA
 repressor binds to specific DNA
sequence (silencer) to stop
Sigma factors - coordinate the expression of several
related genes, even on different chromosomes.
For instance – drought response in plants requires
conservation of water, protection from excessive salt in
soil.
All genes are activated to initiate a stress response.
Figure 11.10 The Initiation of Transcription in Eukaryotes (Part 1)
First transcription factor
binds to the promoter….
…another joins it.
Figure 11.10 The Initiation of Transcription in Eukaryotes (Part 2)
Other factors and RNA
polymerase bind to DNA
Transcription is ready to
begin.
In-Text Art, Ch. 11, p. 216
Figure 11.11 A Transcription Factor Protein Binds to DNA
DNA is then bound to
transcription factor.
Transcription factor
recognizes DNA sequence
adjacent to promoter.
Figure 11.12 Coordinating Gene Expression
Transcription factors
activated by change in
cellular environment….
….bind to DNA…..
…proteins
produced to
deal with stress.
After Transcription, before Translation
RNA processing  unmodified GTP cap – oocyte –
modified after fertilization thus transcription held until
fertilization occurs.
Figure 11.16 Alternative Splicing Results in Different Mature mRNAs and Proteins
Alternative splicing  same gene, different RNA due to
different intron excision, resulting in different proteins
Original estimation of genes was 80-100,00 now scaled
back to @ 25,000….can you explain why?
microRNA – approx. 25 base nucleotides made from what
was formally thought to be noncoding or junk DNA
siRNA – Short interfering RNA -  Both target and
degrade RNA ex. Transitional stage of larva
Translational repressor proteins –RNAses
During Translation
Length of Poly A tail determines mRNA stability preventing
degradation, therefore translation continues.
Location/chemical environment – influences embryo
development –cell differentiation
Figure 11.19 A Proteasome Breaks Down Proteins
After Translation
Binding to ubiquitin recognized by proteasome complex
resulting in hydrolyzed protein
Protein not modified to finished product –
proteolysis (proteases cleave protein), glycoylation
and phosphorylation do NOT take place.
Suggest detailed reasons why a protein may not be
modified to its finished product.