Chp 3Genomics, Proteomics, and

Related Approaches to Physiology

Genomics• Genomics: study of the

genome of organisms

• Helps elucidate the evolution of genes and genomes

• Helps elucidate the current functioning of genes and genomes

The case of the Ice FishEcological and metabolic points of view

• Found in Antarctica• No hemoglobin in the

blood

• From the point of view of metabolism and survival: How is it possible for these fishes to thrive with a lack of hemoglobin?

The case of the Ice FishGenetic point of view

• There are about 16 species of Ice Fishes, all in Antarctica

• So, the following questions:– Did they evolve from a

single ancestor or did the gene evolved separately?

– What kind(s) of mutation inactivated the gene?

– Is the gene non functional?

– Or is the gene functional but not activated?

The case of the Ice FishEvolutionary point of view

• Phylogenetic reconstruction:

• Based on mitochondrial DNA

• Why is the phylogenetic reconstruction not based on the hemoglobin gene?

• The loss of hemoglobin is deleterious compared to the ability to synthesize Hb

• This trait appeared once and was kept.

• What could be the underlying mechanism?– Founder effect?– Selection?

The case of the Ice FishMyoglobin

• Six of the Ice fish species lack myoglobin white myocardium

• Trait appeared several times.

• The mutations are different

The Ice FishThe antifreeze protein

• The body fluids of bony fishes are more dilute than sea-water these body fluids will freeze at higher temperature than sea-water (at 33ppt freezing point (-1.9oC)

• All ice fishes and all red blood fishes in Antarctica have the same antifreeze protein

• So, when did this trait appear? Prior to or after the appearance of ice fishes?

Genomics: Summary

• The systematic sequencing of animal genome allows for a survey for the presence of genes based on previous knowledge

• The presence of gens infers a potential function• Evolutionary history of the genes can be inferred

• Top-down order of study: from animal function to tissue function and biochemistry and genes

• Bottom-up order of study: study from gene to gene expression, then to tissue and to animal function

Transcriptomics• Study of mRNA expression - Use of microarrays- Manipulation of gene

expression

Gene manipulation

• Gene deletion = gene knockout

• RNA interference

Proteomics and Metabolomics• Proteomics: Study of

all the proteins present in a cell at a particular time

• Metabolomics: Study of all organic compounds in a cell

• Helps to clarify metabolic pathways

• Helps quantify responses to environmental changes