Vermont Genetics Network Outreach Proteomics Module Proteomics Overview

“What is Proteomics ?” or Proteome - “ics” ? or Protein - “omics” ? CREDIT: JOE SUTLIFF, Science 291: 1221. 2001

First let’s ask, “What is Genomics?” or Genome - “ics” ? or Gene - “omics” ?

The Human Genome and the “Birth” of Genomics You have likely heard, that not long ago (2001) the human genome was sequenced. What does this mean? Genomics is the study of an organism’s (sometimes a cell’s or a tissue’s) DNA (includes all genes) in its totality.

“ OMICS ” The term “omics” is of recent origin but Is now used by biologists to refer to the study of a type of molecule or compound in its totality (or at least on a large scale) Some examples of “omic” disciplines are: genomics, lipidomics, metabolomics and proteomics.

So, now, what is Proteomics? Proteomics is the study of an organism’s (or a cell’s or a tissue’s or an organelle’s) Proteins in their totality (or at least on a large scale). So, a large-scale study of proteins is proteomics.

What can we learn from seeing things in their totality that we can’t learn from seeing them individually? What things can we learn from seeing things individually that we can’t see from seeing them in their totality?

“I can’t see the forest for the trees.” “I can’t see the trees for the forest.” Guard Cell Chloroplast But I can see the trees! But I can see the forest!

Technological Advances Help Us See Both the Forest and the Trees

Remembering the “Central Dogma” of biology and how Inherited information is (most usually) interpreted by a cell. DNA Transcription ( Splicing ) Translation mRNA Protein Smith et al. 2000 Ann. Rev. of Biochem.

Remembering what a protein is: Proteins are Polymers of amino acids, whose unique sequence Gives them unique structures and thereby unique functions.

Remembering what an amino acid is:

The Scope of Proteomics In Humans there are ~20,000-25,000 genes (almost all genes encode proteins). So humans have ~ 20,000-25,000 basic protein “ types ”.

The Scope of Proteomics However !!! There can be great variability in proteins due to: ● Alternative Splicing ● Post Translational Modifications: ● phosphorylation ● methylation ● glycosylation ● ubiquitylation ● acetylation ● Proteolysis ● Polymorphisms (Single Nucleotide Polymorphisms)

Phosphorylation is a Common Protein Modification Humans Devote 653 (roughly 3% of their genes) to proteins that directly add phosphate (Kinases) or remove phosphate (Phosphatases).

The Complexity of Protein Phosphorylation About 22,000 proteins encoded in the human genome About 10,000 proteins made in a given cell type Rough estimates are 1/3 of proteins are phosphorylated at a given time. If phosphorylated a protein may average 3 phosphorylation sites There may be then ~10,000 Phosphorylation Sites / Cell ! Upper limit for humans? Estimates are between 66,000 – 500,000 ?

Is Protein Modification Important? ab/ab ab/ab = 2 tyrosine to phenylalanine mutations, or loss of only 2 hydroxyl groups!

Is Protein Modification Important? Red Ys MSTETELQVAVKTSAKKDSRKKGQDRSEATLIKRFKGEGVRYKAKLIGIDEVSAARGDKLCQDSMMKLKGVVAGARSKGEHKQKIFLTISFGGIKIFDEKTGALQHHHAVHEISYIAKDITDHRAFGYVCGKEGNHRFVAIKTAQAAEPVILDLRDLFQLIYELKQREELEKKAQKDKQCEQAVYQTILEEDVEDPVYQYIVFEAGHEPIRDPETEENIYQVPTSQKKEGVYDVPKSQPVSAVTQLELFGDMSTPPDITSPPTPATPGDAFLPSSSQTLPGSADVFGSMSFGTAAVPSGYVAMGAVLPSFWGQQPLVQQQIAMGAQPPVAQVIPGAQPIAWGQPGLFPATQQAWPTVAGQFPPAAFMPTQTVMPLAAAMFQGPLTPLATVPGTNDSARSSPQSDKPRQKMGKESFKDFQMVQPPPVPSRKPDQPSLTCTSEAFSSYFNKVGVAQDTDDCDDFDISQLNLTPVTSTTPSTNSPPTPAPRQSSPSKSSASHVSDPTADDIFEEGFESPSKSEEQEAPDGSQASSTSDPFGEPSGEPSGDNISPQDGS Feng and Cooper. MCB 2009 Red Ys

Examples of Proteomics Studies—What Proteins Are Differentially Produced to Govern Behavior?

Phosphoproteomics—What Proteins are Phosphorylated Following Various Treatments or In Different Cell Types or States?

Identification of Proteins in Embryonic Cerebral Spinal Fluid— What Proteins are in What Tissues? Zappaterra et al, Journal of Proteome Research, 2007

Cellular Fractionation—What Proteins are in What Organelles?

Protein-Protein Interactions in Drosophila (“ Interactomes ”) Proteomic Scientists often seek to understand and monitor how proteins behave collectively inside a cell—Protein Networks. Protein-Protein Interactions in Drosophila (“ Interactomes ”) 2346/~ total 5000 proteins Science 302:1727 - 1736

Two Essential Partner Tools in Proteomics Mass Spectrometry Gel Electrophoresis