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Gene Expression and Signal Transduction. Shane Burgess CVM. Why Gene Expression and Signal Transduction ?. Fundamental to all biology. A. Biological basics and paradigms B. Gene Expression C. Signaling. A. BIOLOGICAL BASICS AND PARADIGMS. Most cell biology is poorly understood. - PowerPoint PPT Presentation
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burgess sept 2002 compubiol
Gene Expression and Signal Transduction
Shane Burgess CVM
burgess sept 2002 compubiol
Why Gene Expression and Signal Transduction ?
Fundamental to all biology
burgess sept 2002 compubiol
A. Biological basics and paradigms
B. Gene Expression
C. Signaling
burgess sept 2002 compubiol
A. BIOLOGICAL BASICS AND PARADIGMS
burgess sept 2002 compubiol
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).
burgess sept 2002 compubiol
“Nothing in Biology Makes Sense - Except in the Light of Evolution”
•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
Evolution
Theodosius Dobzhansky (1900-1975)
burgess sept 2002 compubiol
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.
burgess sept 2002 compubiol
The “Molecular Arms Race” and the “Red Queen’s Hypothesis”
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."
“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).”
burgess sept 2002 compubiol
Sensitive dependence on initial conditions
Dis
ease
Health
A
B
burgess sept 2002 compubiol
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.
burgess sept 2002 compubiol
What are we (B)?
“Gene machines”; structures designed to pass genetic information through time.
burgess sept 2002 compubiol
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)
burgess sept 2002 compubiol
Differentiation:
All cells have the same genome (compliment of genes)
So why do they look, and function differently ?
(CLONES)
burgess sept 2002 compubiol
Ecosystems
Communities of many interacting species (including pathogens)
Interacting groups of the same species
Individuals (± sexual reproduction)
Organs
Cells
Proteins and lipids (ENZYMES)
mRNA
DNA (Chromosomes , Alleles)
ENVIRONMENT
burgess sept 2002 compubiol
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.
burgess sept 2002 compubiol
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
burgess sept 2002 compubiol
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.
burgess sept 2002 compubiol
GENE EXPRESSION
burgess sept 2002 compubiol
The genome (the gene compliment – fixed)
The transcriptome (the mRNA compliment – context dependant)
The proteome (the protein compliment – context dependant)
burgess sept 2002 compubiol
The Code
Genes: TAG CGA AGG ACG TCG GAC TCT GAC ATG GCT TCC TGC AGC CTG AGA CTG
Protein: M A S C S L R L
mRNA: AUG GCU UCC UGC AGC CUG AGA CUG
burgess sept 2002 compubiol
appliedbiosystems
Genes
burgess sept 2002 compubiol
1 2 3 4
Regulation
ORF
Exon IntronGene structure
burgess sept 2002 compubiol
Transcription
DNA to messenger (m)RNA
burgess sept 2002 compubiol
1 2 3 4
Regulation Exon Intron
Polymerase
burgess sept 2002 compubiol
1 2 3 4
Regulation Exon Intron
TF
±
Regulating Transcription
TF = transcription factor
burgess sept 2002 compubiol
Access (cell differentiation, structural change to DNA [epigenetic])
1 2 3 4
Regulation Exon Intron
TF
C HH
H
No Transcription; gene permanently silenced. The opposite can also happen e.g. carinogens
burgess sept 2002 compubiol
1 2 3 4
Regulation Exon Intron
TF
±
Transcription
1 2 3 4
burgess sept 2002 compubiol
mRNA Splicing and export from nucleus
The first main source of complexity.Differential splicing in different cells or indifferent conditions.
1 2 3 4
1 2 3 4 or 1 2 3
or1 2 4 etc
burgess sept 2002 compubiol
The TranscriptomeTwo conditions: healthy (h) vs. poisoned (p)
P > H H > P H = P
burgess sept 2002 compubiol
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
burgess sept 2002 compubiol
Translation (making protein)1
23
4
12
3
Exons usually encode protein domains
burgess sept 2002 compubiol
Functional implications of alternate splicing
burgess sept 2002 compubiol
Post-translational modification
O
O
O
P O
SH
SH
O
O
O
P O
SS
burgess sept 2002 compubiol
Functional implications of post-translational modification
SH
SH
O
O
O
P O
SS
O
O
O
P O
SH
SH
burgess sept 2002 compubiol
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
burgess sept 2002 compubiol
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.
burgess sept 2002 compubiol
Michael W. KING, Ph.DTerre Haute Center for Medical EducationIndiana State University
signals
Protein: signaling, structure, enzyme
burgess sept 2002 compubiol
Go to excell
burgess sept 2002 compubiol
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)
burgess sept 2002 compubiol
burgess sept 2002 compubiol
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 regulationNucleic Acids Res. 28, 316-319 (2000).
Steroid - direct
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 regulationNucleic 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 regulationNucleic 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 regulationNucleic Acids Res. 28, 316-319 (2000).
burgess sept 2002 compubiol
ORF
ORI
burgess sept 2002 compubiol
Go to word
burgess sept 2002 compubiol
APC
1.APC migration to site 2.Antigen uptake 3.Inflammation recognition
5. Antigen presentation 6. Co-stimulation7. Soluble enhancement
4. Decision
AnnexinV (P-S)HSPC’rFcR
LPS-BP1
ES622
MBPTOLL
IFN/CXCIL-181L-1GMCSF
CpG
MHC class I,II CD40CD80/86OX40L4-1BBLLIGHT
IL-12IL-6
ICAM-1LFA-3
The apex of biological cascades
burgess sept 2002 compubiol
T“HELPER”
HVEM
CD28 CTLA-4
ICOS
TCRCD4
CD154
OX40
B7-H1L
APC
LIGHT
CD80/86
ICOS-L
MHC II
CD40
OX40L
B7-H1
T“KILLER”
IL-2IL-2
CD80/86
MHC I
4-1BBL
CD28CTLA-4
TCRCD8
4-1BB
IL-12
The apex of biological cascades
burgess sept 2002 compubiol
TAPC
CD28
CD40 CD154
CD80
CD4/ 8
On/OFF switches:Antigen recognition with out co-stimulation causes anergy (tolerance, “ignorance)
burgess sept 2002 compubiol
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.