Transcript Proteomics_Overview_BB_10_09

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.”
But I can see the trees!
Guard Cell
Chloroplast
“I can’t see the trees for the forest.”
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:
Protein
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?
MSTETELQVAVKTSAKKDSRKKGQDRSE
ATLIKRFKGEGVRYKAKLIGIDEVSAAR
GDKLCQDSMMKLKGVVAGARSKGEHKQK
IFLTISFGGIKIFDEKTGALQHHHAVHE
ISYIAKDITDHRAFGYVCGKEGNHRFVA
IKTAQAAEPVILDLRDLFQLIYELKQRE
ELEKKAQKDKQCEQAVYQTILEEDVEDP
VYQYIVFEAGHEPIRDPETEENIYQVPT
SQKKEGVYDVPKSQPVSAVTQLELFGDM
STPPDITSPPTPATPGDAFLPSSSQTLP
GSADVFGSMSFGTAAVPSGYVAMGAVLP
SFWGQQPLVQQQIAMGAQPPVAQVIPGA
QPIAWGQPGLFPATQQAWPTVAGQFPPA
AFMPTQTVMPLAAAMFQGPLTPLATVPG
TNDSARSSPQSDKPRQKMGKESFKDFQM
VQPPPVPSRKPDQPSLTCTSEAFSSYFN
KVGVAQDTDDCDDFDISQLNLTPVTSTT
PSTNSPPTPAPRQSSPSKSSASHVSDPT
ADDIFEEGFESPSKSEEQEAPDGSQASS
TSDPFGEPSGEPSGDNISPQDGS
Red Ys
Red Ys
Feng and Cooper.
MCB 2009
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?
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
Gel Electrophoresis
Mass Spectrometry