Download The On’s and Off’s of Gene Expression

The On’s and Off’s of Gene
Expression
Gene expression is regulated
• The fact:
– Virtually every cell in an organism contains the
same DNA and the same genes.
• The big questions:
– Why are liver cells liver and not brain?
– Why are leaf cells leaf and not root?
• The answer:
– Not all genes are expressed in all cells.
Why regulate gene expression?
• To conserve energy
• To respond to intracelluar signals
• To respond to environmental conditions
Pierce, B. 2005. Genetics, a conceptal approach. 2nd Ed. WH Freeman.
How does gene regulation occur?
Genes can be regulated
anywhere in the process of
information transfer.
DNA
mRNA
protein
protein function
• Promoter: site for RNA polymerase binding
• RNA coding region
• Transcription termination signals
Pierce, B. 2005. Genetics, a conceptal approach. 2nd Ed. WH Freeman.
Organization of a transcription unit
In prokaryotes, DNA sequences--located about 10 and
about 35 bases upstream of the transcription start site-serve as binding sites for RNA polymerase.
Pierce, B. 2005. Genetics, a conceptal approach. 2nd Ed. WH Freeman.
What makes a promoter?
In prokaryotes, regulation is pretty simple
• Prokaryotic transcription is controlled by
binding of RNA polymerase to the promoter.
• Two options
– If RNA polymerase is bound, gene is transcribed.
• The gene is “on”.
• The gene is “expressed”.
– If RNA polymerase does not bind, gene is not
transcribed.
• The gene is “off”.
• The gene is “not expressed”,
How is RNA polymerase binding
controlled?
• Negative regulation
– Interferes with RNA polymerase binding
– Binding of repressor proteins
• Positive regulation
– Promotes RNA polymerase binding
– Binding of activator proteins.
Negative regulation example: lac genes
• In Escherichia coli, the lac genes are
needed to use the sugar lactose as a carbon
source.
• Expression of the lac genes is regulated.
– The genes are expressed only if lactose is in
the growth medium.
– The genes are not expressed if glucose is
present instead.
• When glucose is present, the lac genes are
turned off by a repressor protein.
The lac repressor binds DNA
• lac repressor binds to a DNA sequence called the
operator.
• The operator sequence overlaps the promoter.
• When repressor binds to the operator, it interferes
with RNA polymerase binding to the promoter.
Pierce, B. 2005. Genetics, a conceptal approach. 2nd Ed. WH Freeman.
Eukaryotic gene regulation is complex
• Three types of RNA polymerase.
– RNA polymerase I transcribes the large
ribosomal RNAs.
– RNA polymerase II transcribes mRNAs.
– RNA polymerase III transcribes tRNAs and
small ribosomal RNAs.
• Each polymerase recognizes its own
promoter.
• Core of the promoter contains binding sites
for basal transcription machinery
• Regulatory part of the promoter contains
binding sites for regulatory proteins
Pierce, B. 2005. Genetics, a conceptal approach. 2nd Ed. WH Freeman.
RNA polymerase II promoters
Transcription Factors
• Positive activators of transcription
• Basal transcription factors bind to core
promoter or to each other to facilitate
binding RNA polymerase II. This positions
RNA polymerase II for transcription.
• Regulatory transcription factors bind to
regulatory promoter elements. Their binding
permits transcription by RNA polymerase II.
Pierce, B. 2005. Genetics, a conceptal approach. 2nd Ed. WH Freeman.
Assembly of basal transcription
machinery
Pierce, B. 2005. Genetics, a conceptal approach. 2nd Ed. WH Freeman.
Initiation of transcription
Different sequence motifs can be “mixed
and matched” to recruit binding by various
transcription factors.
Pierce, B. 2005. Genetics, a conceptal approach. 2nd Ed. WH Freeman.
Modular nature of regulatory promoters
Expression of transcription factors
• Constitutive
– Expressed all the time, in many cell types
– Examples include factors for: glucose
metabolism; RNA and protein synthesis; ATP
synthesis
• Regulated
– Expressed at specific times, in specific places
– Examples include factors that respond to
various signals (internal or external)
• Synthesis of purple
anthocyanin pigments in
corn can occur in the kernel
or in the plant.
• The tissue-specificity is due
to expression of different
regulatory transcription
factors.
Karen Cone
Anthocyanin pigment synthesis in corn
Tissue-specificity of anthocyanin
synthesis
• Kernel-specific
– Genes in the pigment pathway are turned on by
the colored kernel (C1) transcription factor.
– C1 is only expressed in the kernel, not in the
plant.
• Plant-specific
– Genes in the pigment pathway are turned on by
the purple plant (PL1) transcription factor.
– PL1 is expressed only in plant organs, not in the
kernel.
Environmental regulation of anthocyanin
synthesis
MaizeGDB.org
Light-dependent (“sun-red”) pigmentation
What causes the “sun-red” pigmentation?
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Light
turns on expression
Light-dependent Transcription Factor
pl1 gene
LRE*
promoter
* Light-responsive element
TATA
Transcription
• Water
– Too much (flooding):
wilting, yellowing,
death
– Too little (drought):
wilting, yellowing,
death
– Wilt in motion
http://plantsinmotion.bio.indiana.edu/pla
ntmotion/vegetative/veg.html
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Coffee plant under drought stress
http://www2.hawaii.edu/~coffee/drought2.jpg
Other environmental cues and effects
Other environmental cues and effects
• Nitrogen deficiency
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Coffee plants: Normal on left, nitrogen-deprived on right
http://www2.hawaii.edu/~coffee/y-nitrogen1.jpg
Other environmental effects on gene
expression
Light effects on development of bean plants
http://facstaff.bloomu.edu/chamuris/concepts2/pics/bean_etiol1.jpg
Pathogen-induced changes in gene
expression
http://www.apsnet.org/education/LessonsPlantPath/BacterialSpot
Susceptible pepper plant
infected with bacterial pathogen
Disease resistant pepper plant
inoculated with bacterial pathogen
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Disease spreads
through leaf.
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Expression of plant
resistance gene
limits spread of
bacteria.
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Examples of intracellular modulators of
gene expression
• Hormones
– Auxin in plants regulates phototropism
(growth towards light)
– Sex hormones in animals control sexual
development
• Growth factors
• Small molecules
– cyclic AMP
– Ca++
– Lipids
Summary
• All cells of an organism contain the same
DNA and thus the same genes
• Not all of the genes are expressed in every
cell.
• Some genes (housekeeping) are expressed
in many cell types.
• Expression of most genes is regulated in
response to environmental or cellular
signals.