Unseen proteome: mining below the tip of the iceberg to find low abundance and membrane proteins.
Abundant and hydrophilic nonmembrane proteins with isoelectric points below pH 8 are the predominant proteins identified in most proteomics projects. In yeast, however, low-abundance proteins make up 80% of the predicted proteome, approximately 50% have pl's above pH 8 and 30% of the yeast ORFs are predicted to encode membrane proteins with at least 1 trans-membrane span. By applying highly solubilizing reagents and isoelectric fractionation to a membrane fraction of yeast we have a purified and identified 780 protein isoforms, representing 323 gene products, including 28% low abundance proteins and 49% membrane or membrane associated proteins. More importantly, considering the frequency and importance of co- and post-translational modifications, the separation of protein isoforms is essential and two-dimensional electrophoresis remains the only technique which offers sufficient resolution to address this at a proteomic level.
Pedersen
Susanne K
SK
Proteome Systems, 35 Waterloo Rd, North Ryde, Sydney, NSW 2113, Australia.
Harry
Jenny L
JL
Sebastian
Lucille
L
Baker
Jasmine
J
Traini
Mathew D
MD
McCarthy
John T
JT
Manoharan
Abi
A
Wilkins
Marc R
MR
Gooley
Andrew A
AA
Righetti
Pier Giorgio
PG
Packer
Nicolle H
NH
Williams
Keith L
KL
Herbert
Ben R
BR
D000595:Amino Acid Sequence; D042966:Cytochrome-B(5) Reductase / Q000235:genetics; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods; D057927:Hydrophobic and Hydrophilic Interactions; D008565:Membrane Proteins / Q000235:genetics* / Q000502:physiology; D008969:Molecular Sequence Data; D040901:Proteomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000502:physiology
D008565:Membrane Proteins; D042966:Cytochrome-B(5) Reductase