Regulation of gene expression
GENE REGULATION
• Virtually every cell in your body contains a complete set of genes
• But they are not all turned on in every tissue
• Each cell in your body expresses only a small subset of genes at any time
• During development different cells express different sets of genes in a precisely
regulated fashion
GENE REGULATION
• Gene regulation occurs at the level of transcription or production of mRNA
• A given cell transcribes only a specific set of genes and not others
• Ex. Insulin is made by pancreatic cells
• Gene regulation has been well studied in E.
coli
• When a bacterial cell encounters a potential food source it will manufacture the enzymes necessary to metabolize that food
What is gene expression?
• Biological processes, such as transcription, and in case of proteins, also translation, that yield a gene product.
• A gene is expressed when its biological product is present and active.
• Gene expression is regulated at multiple levels.
Regulation of gene expression
Plasmid
Gene (red) with an intron (green) Promoter
2. Transcription
Primary transcript 1. DNA replication
3. Posttranscriptional processing
4. Translation
mRNA degradation
Mature mRNA
5. Posttranslational processing
Protein degradation inactive
protein
active protein
single copy vs. multicopy plasmids
Gene regulation (1)
Chr. I
Chr. II Chr. III
Condition 1
“turned on”
“turned off”
Condition 2
“turned off”
“turned on”
1 2 3 4 5 6 7 8 9
10 11 12 13 14 15 16 17 18
19 20 21 22 23 24 25 26
constitutively expressed gene
induced gene
repressed gene
inducible/ repressible genes
Gene regulation (2)
constitutively expressed gene
1 2 3 4 5 6 7 8 9
10 11 12 13 14 15 16 17 18
19 20 21 22 23 24 25 26
Condition 3
Condition 4 upregulated
gene expression
down regulated gene expression
Definitions
• Constitutively expressed genes:
– Genes that are actively transcribed (and
translated) under all experimental conditions, at essentially all developmental stages, or in virtually all cells.
• Inducible genes:
– Genes that are transcribed and translated at higher levels in response to an inducing factor
• Repressible genes:
– Genes whose transcription and translation decreases in response to a repressing signal
Definitions
• Housekeeping genes:
– genes for enzymes of central metabolic pathways (e.g. TCA cycle)
– these genes are constitutively expressed – the level of gene expression may vary
Modulators of transcription
• Modulators:
(1) specificity factors, (2) repressors, (3) activators
1. Specificity factors:
Alter the specificity of RNA polymerase Examples: s-factors (s70, s32 ), TBPs
s70 s32
Heat shock gene Housekeeping gene Heat shock
promoter Standard
promoter
Modulators of transcription
2. Repressors:
mediate negative gene regulation
may impede access of RNA polymerase to the promoter
actively block transcription
bind to specific “operator” sequences (repressor binding sites)
Repressor binding is modulated by specific effectors
Coding sequence Repressor
Operator Promoter Effector
(e.g. endproduct)
Negative regulation (1)
Source: Lehninger pg. 1076 Repressor
Effector Example:
lac operon RESULT:
Transcription occurs when the gene is derepressed
Negative regulation (2)
Source: Lehninger pg. 1076 Repressor
Effector (= co-repressor) Example:
pur-repressor in E. coli;
regulates transcription of genes involved in
nucleotide metabolism
Modulators of transcription
3. Activators:
mediate positive gene regulation
bind to specific regulatory DNA sequences (e.g.
enhancers)
enhance the RNA polymerase -promoter interaction and actively stimulate transcription
common in eukaryotes
Coding sequence Activator
promoter
RNA pol.
Positive regulation (1)
Source: Lehninger pg. 1076 RNA polymerase Activator
Positive regulation (2)
Source: Lehninger pg. 1076 RNA polymerase Activator Effector
Operons
– a promoter plus a set of adjacent genes whose gene products function together.
– usually contain 2 –6 genes, (up to 20 genes)
– these genes are transcribed as a polycistronic transcript.
– relatively common in prokaryotes – rare in eukaryotes
Gene Regulation
• In addition to sugars like glucose and lactose E. coli cells also require
amino acids
• One essential aa is tryptophan.
• When E. coli is swimming in
tryptophan (milk & poultry) it will absorb the amino acids from the media
• When tryptophan is not present in the media then the cell must manufacture its’ own amino acids
Trp Operon
• E. coli uses several proteins encoded by a cluster of 5 genes to manufacture the amino acid tryptophan
• All 5 genes are transcribed together as a unit called an operon, which produces a single long piece of mRNA for all the genes
• RNA polymerase binds to a promoter located at the beginning of the first gene and proceeds
down the DNA transcribing the genes in sequence
Fig. 16.6
GENE REGULATION
• In addition to amino acids, E. coli cells also metabolize sugars in
their environment
• In 1959 Jacques Monod and
Fracois Jacob looked at the ability
of E. coli cells to digest the sugar
lactose
GENE REGULATION
• In the presence of the sugar lactose, E. coli makes an enzyme called beta galactosidase
• Beta galactosidase breaks down the sugar lactose so the E. coli can digest it for food
• It is the LAC Z gene in E coli that codes for the enzyme beta galactosidase
Lac Z Gene
• The tryptophane gene is turned on when there is no tryptophan in the media
• That is when the cell wants to make its’
own tryptophan
• E. coli cells can not make the sugar lactose
• They can only have lactose when it is present in their environment
• Then they turn on genes to beak down lactose
GENE REGULATION
• The E. coli bacteria only needs beta galactosidase if there is lactose in the environment to digest
• There is no point in making the enzyme if there is no lactose sugar to break down
• It is the combination of the promoter and the DNA that regulate when a gene will be transcribed
GENE REGULATION
• This combination of a promoter and a gene is called an OPERON
• Operon is a cluster of genes
encoding related enzymes that are
regulated together
GENE REGULATION
• Operon consists of
– A promoter site where RNA polyerase binds and begins transcribing the message
– A region that makes a repressor
• Repressor sits on the DNA at a spot between the promoter and the gene to be transcribed
• This site is called the operator
LAC Z GENE
• E. coli regulate the production of Beta Galactocidase by using a regulatory protein called a repressor
• The repressor binds to the lac Z gene at a site between the promotor and the start of the coding sequence
• The site the repressor binds to is called the operator
LAC Z GENE
• Normally the repressor sits on the operator repressing transcription of the lac Z gene
• In the presence of lactose the
repressor binds to the sugar and this
allows the polymerase to move down
the lac Z gene
LAC Z GENE
• This results in the production of beta galactosidase which breaks down
the sugar
• When there is no sugar left the
repressor will return to its spot on the chromosome and stop the
transcription of the lac Z gene
GENE REGULATION
• In eukaryotic organisms like ourselves there are several methods of regulating protein production
• Most regulatory sequences are found upstream from the promoter
• Genes are controlled by regulatory
elements in the promoter region that act like on/off switches or dimmer switches
GENE REGULATION
• Specific transcription factors bind to
these regulatory elements and regulate transcription
• Regulatory elements may be tissue
specific and will activate their gene only in one kind of tissue
• Sometimes the expression of a gene requires the function of two or more different regulatory elements
INTRONS AND EXONS
• Eukaryotic DNA differs from prokaryotic DNA it that the coding sequences along the gene are interspersed with noncoding sequences
• The coding sequences are called
– EXONS
• The non coding sequences are called
– INTRONS
RNA Splicing
• Provides a point where the expression of a gene can be controlled
• Exons can be spliced together in different ways
• This allows a variety of different
polypeptides to be assembled from the same gene
• Alternate splicing is common in insects and vertebrates, where 2 or 3 different proteins are produced from one gene
