What is a Proteome ?
The proteome is defined as the entire set or complement of proteins that is or can be expressed by a cell, tissue, or organism. The term originates from a word play blending the words protein and genome to create a newer term now called “The Proteome”. Since the set of expressed proteins in a cell, tissue or organelle is dynamic the actual proteome reflects a particular set of biochemical conditions viewed as a snapshot-in-time of the biochemical system studied. In addition, the number of proteins, for example, in the human proteome, can be as large as 2 million. Marc Wilkins is reported to have coined the term proteome in 1994 in a symposium on "2D Electrophoresis: from protein maps to genomes" held in Siena, Italy and part of his PhD thesis appeared in print in 1996. The publication showed that proteins can be separated and identified by two-dimensional (2-D) electrophoresis allowing for protein-based gene expression analysis. Identification of unknown proteins was achieved by matching their amino acid composition, estimated pI and molecular weight against all E. coli entries in the SWISS-PROT database. This approach allowed large-scale screening of the protein complement of simple organisms, or tissues in normal and disease states. In the following years proteomics became a popular approach for the study and identification of whole protein assemblies leading to a new biochemistry branch called “proteomics” that is concerned with the analysis of the structure and functions of proteins occurring in living organisms. A PubMed search for the term proteome revealed that since 1995 over 30,000 papers have been published in this field. The term proteome was used by Mark to describe the entire complement of proteins expressed by a genome, cell, tissue or an organism. Since its appearance, it has been applied to several different types of biological systems. For example, a cellular proteome describes the whole collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation or different drugs. However the term “complete proteome” may be used to describe the complete set of proteins from all of the various cellular proteomes which could be very used to roughly describe the whole protein equivalent of the genome. Furthermore the term "proteome" has also been used to refer to the collection of proteins in certain sub-cellular biological systems. For example, all of the proteins in a virus can be called a viral proteome. In conclusion, proteomes are now routinely investigated using a combined approach of amino acid analysis and peptide-mass fingerprinting allowing gene products to be linked to homologous genes in a variety of organisms.
Selected References
Patterson SD, Aebersold RH; Proteomics: the first decade and beyond. Nat Genet. 2003 Mar; 33 Suppl: 311-23.
Marc R. Wilkins, Christian Pasquali, Ron D. Appel, Keli Ou, Olivier Golaz, Jean-Charles Sanchez, Jun X. Yan, Andrew. A. Gooley, Graham Hughes, Ian Humphery-Smith, Keith L. Williams & Denis F. Hochstrasser (1996). "From Proteins to Proteomes: Large Scale Protein Identification by Two-Dimensional Electrophoresis and Arnino Acid Analysis". Nature Biotechnology 14 (1): 61–65.
Wasinger VC, Cordwell SJ, Cerpa-Poljak A, Yan JX, Gooley AA, Wilkins MR, Duncan MW, Harris R, Williams KL, Humphery-Smith I. (1995). "Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium". Electrophoresis 7 (7): 1090–94.
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03/24/2014