The On

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The Ons and Offs of Gene Expression
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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.

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Why regulate gene expression?

• To conserve energy
• To respond to intracelluar signals
• To respond to environmental conditions

4
How does gene regulation occur?

• Genes can be regulated anywhere in the process
  of information transfer.
• DNA
• mRNA
• protein
• protein function

Pierce, B. 2005. Genetics, a conceptal approach.
2nd Ed. WH Freeman.
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Organization of a transcription unit
Pierce, B. 2005. Genetics, a conceptal approach.
2nd Ed. WH Freeman.

• Promoter site for RNA polymerase binding
• RNA coding region
• Transcription termination signals

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What makes a promoter?

• 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.
7
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,

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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.

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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.

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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.
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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.

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RNA polymerase II promoters

• 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.
13
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.

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Assembly of basal transcription machinery
Pierce, B. 2005. Genetics, a conceptal approach.
2nd Ed. WH Freeman.
15
Initiation of transcription
Pierce, B. 2005. Genetics, a conceptal approach.
2nd Ed. WH Freeman.
16
Modular nature of regulatory promoters

• 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.
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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)

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Anthocyanin pigment synthesis in corn

• 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
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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.

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Environmental regulation of anthocyanin synthesis

• Light-dependent (sun-red) pigmentation

MaizeGDB.org
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What causes the sun-red pigmentation?
turns on expression
Light
Light-dependent Transcription Factor
pl1 gene
LRE
TATA
Transcription
promoter
Light-responsive element
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Other environmental cues and effects

• Water
• Too much (flooding) wilting, yellowing, death
• Too little (drought) wilting, yellowing, death
• Wilt in motion http//plantsinmotion.bio.indiana.e
  du/plantmotion/vegetative/veg.html

http//www2.hawaii.edu/coffee/drought2.jpg
Coffee plant under drought stress
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Other environmental cues and effects

• Nitrogen deficiency

Coffee plants Normal on left, nitrogen-deprived
on right
http//www2.hawaii.edu/coffee/y-nitrogen1.jpg
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Other environmental effects on gene expression

• Light effects on development of bean plants

http//facstaff.bloomu.edu/chamuris/concepts2/pics
/bean_etiol1.jpg
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Pathogen-induced changes in gene expression
Susceptible pepper plant infected with bacterial
pathogen
Disease resistant pepper plant inoculated with
bacterial pathogen
Disease spreads through leaf.
Expression of plant resistance gene limits
spread of bacteria.
http//www.apsnet.org/education/LessonsPlantPath/B
acterialSpot
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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

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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.