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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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“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)

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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”

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).”

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Sensitive dependence on initial conditions

Dis

ease

Health

A

B

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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)

Interacting groups of the same species

Individuals (± sexual reproduction)

Organs

Cells

Proteins and lipids (ENZYMES)

mRNA

DNA (Chromosomes , Alleles)

ENVIRONMENT

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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

Protein: M A S C S L R L

mRNA: AUG GCU UCC UGC AGC CUG AGA CUG

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appliedbiosystems

Genes

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1 2 3 4

Regulation

ORF

Exon IntronGene structure

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Transcription

DNA to messenger (m)RNA

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1 2 3 4

Regulation Exon Intron

Polymerase

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1 2 3 4

Regulation Exon Intron

TF

±

Regulating Transcription

TF = transcription factor

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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

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1 2 3 4

Regulation Exon Intron

TF

±

Transcription

1 2 3 4

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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

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The TranscriptomeTwo conditions: healthy (h) vs. poisoned (p)

P > H H > P H = P

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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)1

23

4

12

3

Exons usually encode protein domains

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Functional implications of alternate splicing

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Post-translational modification

O

O

O

P O

SH

SH

O

O

O

P O

SS

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Functional implications of post-translational modification

SH

SH

O

O

O

P O

SS

O

O

O

P O

SH

SH

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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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Michael W. KING, Ph.DTerre Haute Center for Medical EducationIndiana State University

signals

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 regulationNucleic 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 regulationNucleic Acids Res. 28, 316-319 (2000).

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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).

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).

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ORF

ORI

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Go to word

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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

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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

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TAPC

CD28

CD40 CD154

CD80

CD4/ 8

On/OFF switches:Antigen recognition with out co-stimulation causes anergy (tolerance, “ignorance)

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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.