CHAPTER 3 - NUCLEIC ACIDS 

D:  BIOINFORMATICS - GENOMES AND OTHER OMES (NOT GNOMES)

BIOCHEMISTRY - DR. JAKUBOWSKI

08/26/2010

The human genome project was a cinch compared to the complexity of understanding the extent and type of gene expression in a given cell, the proteins produced, and how these proteins interact to create biological function.   Since the human genome sequence has been solved, attention is being turned to other "omes" 

Proteome:  Here are some recent definitions

Proteome (Pasteur Insititute) is the protein complement expressed by a genome. While the genome is static, the proteome continually changes in response to external and internal events.

Proteomics (Pasteur Institute):  Proteomics aims at quantifying the expression levels of the complete protein complement (the proteome) in a cell at any given time. While proteomics research was initially focused on two-dimensional gel electrophoresis for protein separation and identification, proteomics now refers to any procedure that characterizes the function of large sets of proteins. It is thus often used as a synonym for functional genomics

Proteomics:   the qualitative and quantitative comparison of proteomes (PROTEin complement to a genOME) under different conditions to further unravel biological processes ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics

The emerging field of proteomics, which will study these types of questions, will revolutionize our understanding of normal and disease processes in cells.  Richard Burgess, UW Madison, includes the following activities in proteomics: (C&E New, July 31, 2000, pg 31)

Glycome -

From Wikipedia, the free encyclopedia

"The glycome is the collective identity of the entirety of carbohydrates in an organism. The glycome may in fact be one of the most complex entities in nature. The glycome is studied by glycobiology sometimes referred to as glycomics.

The genome is one of the most complex structures in an organism (although not necessarily as complex as, for example, the brains of higher organisms). The genome is responsible for the proteome, which is more complex than the genome by virtue of the fact that it combines the complexity of the genome with the complexity of the proteins which the genome specifies, proteins whose characteristics are at least partially determined by the phenomenon of molecular folding, which is one of the most complex phenomena known to science.

The glycome exceeds the complexity of the proteome as a result of the even greater diversity of the glycome's constituent carbohydrates and is further complicated by the sheer multiplicity of their possibilities of combination and interaction of the carbohydrates with each other and with proteins.

An alternative definition is the collective identity of the entirety of carbohydrates in a cell. In those definitions, the word sugar, the word glycan and the word polysaccharide can be meaningfully substituted for carbohydrate.

Ajit Varki, professor of medicine and cell and molecular biology, and director of the Glycobiology Research and Training Center at the University of California, San Diego has illustrated the scale of the glycome challenge by claiming that the glycome is:

"...probably thousands of times as complicated as the genome, in magnitude of complexity and level of diversity". (Perkel 2002)

There is a pivotal body in this field, called the Consortium for Functional Glycomics (CFG) funded by the (US) National Institute of General Medical Sciences. This body (which operates in a field called glycosciences) includes participants in 'glycome projects' within its remit. The US Federal grant which can be said to have 'put the glycome on the political map' was described as a 'glue grant' of $34M (for the formation of the CFG, see above"

 

Kinome  -  the entire repertoire of protein kinases in the genome 

Lipome -

Phosphoproteome - A description of all post-translational phosphorylations of proteins.

Reactome -  a curated knowledgebase of biological pathways

"The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology. The information in this database is authored by biological researchers with expertise in their fields, maintained by the Reactome editorial staff, and cross-referenced with PubMed, GO, and the sequence databases at NCBI, Ensembl and UniProt. In addition to curated human events, inferred orthologous events in 21 non-human species including mouse, rat, chicken, fugu fish, worms, fly, yeast and E.coli are also available."

Receptome - "Multi-cellular organisms rely upon intercellular signaling molecules to coordinate the functions of different cells by interacting with plasma membrane receptors to activate downstream signaling pathways in target cells. The Human Plasma Membrane Receptome (HPMR) is dedicated to studies on plasma membrane receptors in the human genome, combining text-based and sequence-based search tools. The web site categorizes major groups of human plasma membrane receptors based on protein sequences, evolutionary relationships, and published literature.
There are more than 1200 individual human plasma membrane receptors in more than 20 families. Individual receptor gene pages can be searched by key words and sequences as well as by their family relationships. Each page provides summary and links to major literature, sequence, and expression databases. The evolutionary relationships among receptors are documented by family trees and subfamily sequence comparisons, allowing ortholog tracing in model organisms." (from link below)

Web Links:

Recent References

  1. MacBeath and Schreiber.  Printing Proteins as Microarrays for High-throughput function determination.  Science. 289. pg 1760 (2000)  

 

Navigation