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REGULATION OF GENE EXPRESSION

NOTE:

Genome – the entire complement of genetic material carried

by an individual

Transcriptome – the entire set of transcribed sequences

from a genome

Proteome – the entire set of proteins encoded by the

genome

Genomes, genome size, gene #

Organism/Particle Genome size Gene number

Plasmid 3 kb A few
Bacteriophage 50 kb Dozens
E.coli 5 Mb ~4000
S. cerevisiae 15 Mb ~6000
C. elegans 97 Mb ~19,000
D. melanogaster 150 Mb ~13,000
H. sapiens 3000 Mb ~30,000

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NOTE:

Gene – a sequence of genomic DNA or RNA that is

essential for a specific function

– used to be defined as giving rise to an enzyme

(one-gene-one enzyme)

– based on Beadle & Tatum’s experiment on

Neurospora mutants

Beadle and Tatum’s One Gene-One Enzyme Hypothesis

•Synthesis of amino acid arginine in Neurospora

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Beadle and Tatum’s One Gene-One Enzyme Hypothesis

•Synthesis of amino acid arginine in Neurospora

arg 1 (A) arg 2 (B) arg 3 (C)

PRECURSOR ORNITHINE CITRULINE ARGININE

HOWEVER, not all genes code for enzymes

Types of Genes

1. protein-coding genes – TRANSLATED

2. RNA-specifying genes – TRANSCRIBED ONLY

3. untranscribed genes

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NOTE:

Monocistronic mRNA – contains 1 gene only

– common in eukaryotes
Polycistronic mRNA – contains several genes in tandem
array
– common in prokaryotes

REGULATION OF GENE EXPRESSION

•Not all genes within a cell are active at the same time.

•Gene activity is regulated at various stages:

•Transcription
•Post-transcription

•Translation

•Post-translation

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I. Transcriptional Regulation

•Constitutive genes – genes that are transcribed

continuously
– not affected by the environment

•Non-constitutive genes – governed by regulatory

proteins

I. Transcriptional Regulation

•Types of regulatory proteins:

1. Repressor – protein that prevents transcription

– binds to an operator sequence
upstream of the gene
– negative control

2. Activator – protein that promotes transcription

– binds to promoter or enhancer sites
– positive control

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I. Transcriptional Regulation

Promoters
•Sequences found at the 5’ flanking region of a gene

•Signals that regulate initiation of transcription

I. Transcriptional Regulation

Promoter sequences in EUKARYOTES

1. TATA Box – (TATAAA), Hogness-Goldberg box

– 19-27 bp upstream of start of transcription

2. CAAT Box – (CAAT), upstream of TATA Box, either

orientation

3. GC Box – (GGGCGG), either orientation

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Promoter sequences in eukaryotes

Transcribed to mRNA

5’ 3’

CAAT Box Initiation Exon Stop

TATA Box codon codon Transcription
GC Box
termination
5’ UTR Intron 3’ UTR

NOTE:
Exon – sequence that is translated
Intron – intervening sequence, eventually spliced off
UTR – untranslated region

Construction of transcription complex in eukaryotes

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I. Transcriptional Regulation

Promoter sequences in PROKARYOTES (eubacteria)

1. TATAAT – Pribnow Box, 10-bp (-10) upstream of

start of transcription

2. TTGACA – 35-bp (-35) upstream of start of

transcription

I. Transcriptional Regulation

Operon – unit of bacterial gene expression & regulation

– polycistronic

– contains regulator elements

– e.g. lac operon

– e.g. trp operon

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I. Transcriptional Regulation

•The lac operon

1. Promoter – site to which RNA polymerase binds

2. Operator – site to which repressor protein binds

3. Structural genes
•Lac Z – codes for beta-galactosidase
•Lac Y – codes for permease
•Lac A – codes for transacetylase

4. Repressor – codes for repressor protein

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Parts of a lac operon

Absence of lactose

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Presence of lactose

•The lac operon is therefore under NEGATIVE INDUCIBLE

CONTROL

– the presence of lactose induces the transcription of

the structural genes

– negative control because of presence of repressor

protein that prevents transcription

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I. Transcriptional Regulation

•The trp operon

1. Promoter – site to which RNA polymerase binds

2. Operator – site to which repressor protein binds

3. Structural genes
•Trp E •Trp B
•Trp D •Trp A
•Trp C

4. Repressor – codes for repressor protein

5. Attenuator – regulates mRNA transcription

•Parts of the trp operon

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Absence of tryptophan

Presence of tryptophan

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•The trp operon is therefore under NEGATIVE REPRESSIBLE

CONTROL

– the presence of tryptophan represses the transcription

of the structural genes

– negative control because of presence of repressor

protein that prevents transcription

I. Transcriptional Regulation

•Eukaryotic genes are not arranged under the control of one

promoter.

•Genes are also regulated by enhancers

•Enhancer – several hundreds or thousands of bp
upstream or downstream of gene it
regulates

•Note: promoters + enhancers = cis-acting elements

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I. Transcriptional Regulation

•Eukaryotic genes are also regulated by transcription factors

•Transcription factors – proteins encoded by separate

genes

– bind to specific DNA sequences

– also known as trans-acting

factors

I. Transcriptional Regulation

•Transcription factors have 3 types of DNA binding sites:

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I. Transcriptional Regulation
•Examples of transcription factors – steroid hormones (e.g.
estrogen)
•Bind to hormone responsive elements (HRE)

I. Transcriptional Regulation

T3 = Triiodothyronine
T4 = Thyroxine

 Hormones responsible
for regulation of
metabolism in
vertebrates

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II. Post-transcriptional Regulation (RNA editing)

pre-mRNA – (precursor mRNA), immediate product of

transcription

hnRNA – (heterologous nuclear RNA) pre-mRNAs found in

nucleus of eukaryotes

•Pre-mRNAs are edited before they are used or translated

II. Post-transcriptional Regulation (RNA editing)

•Takes place in eukaryotes

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II. Post-transcriptional Regulation (RNA editing)

1. 5’ capping – lends protection and stability to 5’ end

7-methylguanosine cap
(7mGppp cap)

NOTE: unique to eukaryotes

II. Post-transcriptional Regulation (RNA editing)

2. 3’ polyadenylation – addition of poly-A tail

– protects the 3’ end from
exonucleases

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II. Post-transcriptional Regulation (RNA editing)

3. Splicing – removal of introns

•Methods of splicing:
•splicosomes
•ribozymes
•ribonucleases and ligases

NOTE:

Alternative splicing – alternative ways of splicing introns

– produces different mRNAs
(transcript variants/ isoforms)

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Example of alternative splicing

•Production of tachykinins (sensory neurotransmitters)

•Transcription of preprotachykinin mRNA (PPT mRNA)

•Types of tachykinins synthesized:

•P – nervous system

•K – nervous system, intestine, thyroid

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