Transcript Document

Gene Expression and
Signal Transduction
Shane Burgess CVM
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Why Gene Expression and
Signal Transduction ?
Fundamental to all biology
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A. Biological basics and paradigms
B. Gene Expression
C. Signaling
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A. BIOLOGICAL BASICS AND
PARADIGMS
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Most cell biology is poorly understood.
Cells are complex systems in themselves but
……then add environment and a very complex web
of inter-actions is created.
All human cells have identical (we hope) genetic
material yet, there are >200 types of cells/ human.
These cells are different shapes, sizes and and carry
out different functions.
And ALL of these cells were developed from a
single cell (from two halves of two cells if you are
human).
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Evolution
“Nothing in Biology Makes Sense - Except in
the Light of Evolution”
Theodosius Dobzhansky (1900-1975)
•Genetic variation leading to difference in phenotype (trait)
•Pressures in environment select these and increase the frequency of
the selected gene (allele) in the population
•Polymorphic genes suggest high selection pressures
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Key gene terms:
Polymorphism: “many shapes” i.e.
different versions of genes coding for the
same protein in a population.
The versions are called ALLELES
Note on trait: Pronounced tr[=a], as in French, and still so pronounced by english speakers.
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The “Molecular Arms Race” and
the “Red Queen’s Hypothesis”
“For an evolutionary system,
continuing development is needed just
in order to maintain its fitness relative
to the systems it is co-evolving with (
L. van Valen, 1973).”
Based on the observation, to Alice, by the Red Queen in Lewis
Carroll's Through the Looking Glass that “....in this place it takes all
the running you can do, to keep in the same place."
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Disease
Sensitive dependence on initial conditions
B
A
Health
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What are we (A) ?
Proteins (amino acids) : N, H, C, O
Fats: C, H, O
Sugars: C, H, O
Matter cannot be created or destroyed; the
molecules in us could well once have been
in dinosaurs or mushrooms - in fact any
life form you would like to name.
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What are we (B)?
“Gene machines”; structures designed to
pass genetic information through time.
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Genotype defines phenotype
…well almost……
“Central Dogma” (Francis Crick):
1 gene gives 1 mRNA gives 1 protein
(predicted hundreds of thousands of genes in humans)
Today
1 gene gives >1 mRNA gives >1
functional protein/mRNA species
(Now estimate there are only 35 –40 K genes in human
genome, but still hundreds of thousands of proteins)
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Differentiation:
All cells have the same genome
(compliment of genes)
So why do they look, and function
differently ?
(CLONES)
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Ecosystems
Communities of many interacting species (including
pathogens)
ENVIRONMENT
Interacting groups of the same species
Individuals (± sexual reproduction)
Organs
Cells
Proteins and lipids (ENZYMES)
mRNA
DNA (Chromosomes , Alleles)
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Death is the Default.
Activation (induce cell proliferation) of
any cell and it will die unless told
(signaled) to do otherwise (programmed
cell death).
Cancer is hyper-proliferation without
compensatory cell death.
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Genetics and Epigenetics
Genetics : the study of the heritable code
of life . Only 4 letters: A, T, C, G;
Which, as triplets, code for only 20 amino
acids eg ATG = methionine.
Epigenetics: heritable phenotypes that are
not derived from the code
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Structure defines function
These “structures” function in interacting
networks
i.e. we are (structured) bags of interacting
proteins that “stick” together (and come
apart again) with different affinities.
But the functions of these structures is not
fixed, it is context dependant.
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GENE EXPRESSION
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The genome (the gene compliment – fixed)
The transcriptome (the mRNA compliment
– context dependant)
The proteome (the protein compliment –
context dependant)
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The Code
Genes:
TAG CGA AGG ACG TCG GAC TCT GAC
ATG GCT TCC TGC AGC CTG AGA CTG
mRNA:
AUG GCU UCC UGC AGC CUG AGA CUG
Protein:
M
A
S
C
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S
L
R
L
Genes
appliedbiosystems
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Gene structure
Exon
Intron
Regulation
1
2
3
ORF
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4
Transcription
DNA to messenger (m)RNA
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Regulation
1
Exon
2
Intron
3
Polymerase
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4
Regulating Transcription
Regulation
1
Exon
2
Intron
3
4
TF
±
TF = transcription factor
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Access (cell differentiation, structural change to DNA
[epigenetic])
Regulation
Exon
1
H
C
TF
H
2
H
Intron
3
4
No Transcription;
gene permanently
silenced. The opposite
can also happen e.g.
carinogens
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Transcription
Regulation
1
Exon
2
Intron
3
4
TF
±
1
2
3
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4
mRNA Splicing and export from nucleus
The first main source of complexity.
Differential splicing in different cells or in
different conditions.
1
1
2
or
2
3
3
4
or
1
2
4
1
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4
2
etc
3
The Transcriptome
Two conditions: healthy (h) vs. poisoned (p)
P>H
H>P
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H=P
The amount of mRNA that gets to the
ribosome (where translation occurs) depends
not only on the amount of transcription but
also on longevity.
mRNA longevity can be context dependent
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Translation (making protein)
Exons usually encode protein domains
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Functional implications of alternate splicing
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Post-translational modification
SH
S
S
SH
O
O
P
O
O
O
O
P
O
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O
Functional implications of post-translational
modification
SH
SH
S
S
SH
SH
O
O
O
O
P
P
O
O
O
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O
Still not done…….
Protein transport to appropriate site
Protein stability
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The proteome
•Dr Michael J Dunn Reader in Biochemistry National Heart and Lung Institute Imperial College
School of Medicine Heart Science Centre Harefield Hospital Harefield Middlesex UB9 6JH
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To re-emphasize, there is no linear
relationship between the transcriptome and
the proteome
The two more often than not, do not
correlate at all.
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signals
Michael W. KING, Ph.D
Terre Haute Center for Medical Education
Indiana State University
Protein: signaling, structure, enzyme
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Go to excell
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C. Signal transduction (communication)
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•Environment to cells (light, sound, temperature,
chemicals [toxins])
•Cells from one organism to cells of another
another organism (pheromones, pollens, colors
[light] and scents)
• Cells from one organ to cells of another organ
within an organism (endocrine)
• Cells from one organ to other cells in the same
organ (paracrine)
• Cells to themselves (autocrine)
• One organelle to another organelle within cells
(trafficking)
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Intracellular: Cancer signaling networks
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Wingender, E., Chen, X., Hehl, R., Karas, H., Liebich, I., Matys, V.,
Meinhardt, T., Prüß, M., Reuter, I. and Schacherer, F.:
TRANSFAC: an integrated system for gene expression regulation
Nucleic Acids Res. 28, 316-319 (2000).
Steroid - direct
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Wingender, E., Chen, X., Hehl,
R., Karas, H., Liebich, I.,
Matys, V.,
Meinhardt, T., Prüß, M.,
Reuter, I. and Schacherer, F.:
TRANSFAC: an integrated
system for gene expression
regulation
Nucleic Acids Res. 28, 316-319
(2000).
Wingender, E., Chen, X., Hehl,
R., Karas, H., Liebich, I.,
Matys, V.,
Meinhardt, T., Prüß, M.,
Reuter, I. and Schacherer, F.:
TRANSFAC: an integrated
system for gene expression
regulation
Nucleic Acids Res. 28, 316-319
(2000).
burgess sept 2002 compubiol
Wingender, E., Chen, X., Hehl,
R., Karas, H., Liebich, I.,
Matys, V.,
Meinhardt, T., Prüß, M.,
Reuter, I. and Schacherer, F.:
TRANSFAC: an integrated
system for gene expression
regulation
Nucleic Acids Res. 28, 316-319
(2000).
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ORI
ORF
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Go to word
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The apex of biological cascades
1.APC migration to site
2.Antigen uptake
3.Inflammation
recognition
4. Decision
CpG
IFNa/b
CXC
IL-18
1L-1b
GMCSF
LPS-BP1
ES622
MBP
TOLL
AnnexinV (P-S)
HSP
C’r
FcR
APC
IL-12 ICAM-1 MHC class I,II
LFA-3
IL-6
5. Antigen presentation
6. Co-stimulation
7. Soluble enhancement burgess sept 2002 compubiol
CD40
CD80/86
OX40L
4-1BBL
LIGHT
The apex of biological cascades
HVEM
IL-12
LIGHT
CD28
CD80/86
CTLA-4
T
ICOS
“HELPER”
TCR
CD4
ICOS-L
CD80/86
APC
MHC I
TCR
CD8
4-1BBL
4-1BB
MHC II
CD154
CD40
OX40
OX40L
B7-H1L B7-H1
IL-2
CD28
CTLA-4
IL-2
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T
“KILLER”
On/OFF switches:
Antigen recognition with out co-stimulation causes anergy
(tolerance, “ignorance)
T
APC
CD4/ 8
CD40
CD154
CD80
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CD28
Gene Expression and Signaling (or life):
a summary.
A finite set of relatively simple self
replicating error prone instructions, which
create a finite (but much greater and more
complicated) set of structures, which
interact in context-dependant networks to
create an infinitely variable diversity of
forms based on a standard design, which
is affected by, and can in turn affect, its
environment.
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