Proteome
Encyclopedia
The proteome is the entire set of protein
s expressed by a genome, cell, tissue or organism. More specifically, it is the set of expressed proteins in a given type of cells or an organism at a given time under defined conditions. The term is a portmanteau of proteins and genome
.
The term has been applied to several different types of biological systems. A cellular proteome is the collection of proteins found in a particular cell
type under a particular set of environmental conditions such as exposure to hormone stimulation
. It can also be useful to consider an organism's complete proteome, which can be conceptualized as the complete set of proteins from all of the various cellular proteomes. This is very roughly the protein equivalent of the genome
. 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.
The proteome is larger than the genome
, especially in eukaryotes, in the sense that there are more protein
s than gene
s. This is due to alternative splicing
of genes and post-translational modifications like glycosylation
or phosphorylation
.
Moreover the proteome has at least two levels of complexity lacking in the genome. While the genome is defined by the sequence of nucleotide
s, the proteome cannot be limited to the sum of the sequences of the proteins present. Knowledge of the proteome requires knowledge of (1) the structure
of the proteins in the proteome and (2) the functional interaction between the proteins.
Proteomics
, the study of the proteome, has largely been practiced through the separation of proteins by two dimensional gel electrophoresis
. In the first dimension, the proteins are separated by isoelectric focusing
, which resolves proteins on the basis of charge. In the second dimension, proteins are separated by molecular weight
using SDS-PAGE
. The gel is dyed with Coomassie Brilliant Blue or silver
to visualize the proteins. Spots on the gel are proteins that have migrated to specific locations.
The mass spectrometer
has augmented proteomics. Peptide mass fingerprinting
identifies a protein by cleaving it into short peptides and then deduces the protein's identity by matching the observed peptide masses against a sequence database
. Tandem mass spectrometry, on the other hand, can get sequence information from individual peptides by isolating them, colliding them with a non-reactive gas, and then cataloguing the fragment ions produced.
coined the term proteome in 1994 in a symposium on "2D Electrophoresis: from protein maps to genomes" held in Siena in Italy. It appeared in print in 1995, with the publication of part of Wilkins's PhD thesis. Wilkins used the term to describe the entire complement of protein
s expressed by a genome, cell, tissue or organism.
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s expressed by a genome, cell, tissue or organism. More specifically, it is the set of expressed proteins in a given type of cells or an organism at a given time under defined conditions. The term is a portmanteau of proteins and genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
.
The term has been applied to several different types of biological systems. A cellular proteome is the collection of proteins found in a particular cell
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....
type under a particular set of environmental conditions such as exposure to hormone stimulation
Hormone
A hormone is a chemical released by a cell or a gland in one part of the body that sends out messages that affect cells in other parts of the organism. Only a small amount of hormone is required to alter cell metabolism. In essence, it is a chemical messenger that transports a signal from one...
. It can also be useful to consider an organism's complete proteome, which can be conceptualized as the complete set of proteins from all of the various cellular proteomes. This is very roughly the protein equivalent of the genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
. 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.
The proteome is larger than the genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
, especially in eukaryotes, in the sense that there are more protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s than gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
s. This is due to alternative splicing
Alternative splicing
Alternative splicing is a process by which the exons of the RNA produced by transcription of a gene are reconnected in multiple ways during RNA splicing...
of genes and post-translational modifications like glycosylation
Glycosylation
Glycosylation is the reaction in which a carbohydrate, i.e. a glycosyl donor, is attached to a hydroxyl or other functional group of another molecule . In biology glycosylation refers to the enzymatic process that attaches glycans to proteins, lipids, or other organic molecules...
or phosphorylation
Phosphorylation
Phosphorylation is the addition of a phosphate group to a protein or other organic molecule. Phosphorylation activates or deactivates many protein enzymes....
.
Moreover the proteome has at least two levels of complexity lacking in the genome. While the genome is defined by the sequence of nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
s, the proteome cannot be limited to the sum of the sequences of the proteins present. Knowledge of the proteome requires knowledge of (1) the structure
Protein structure
Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...
of the proteins in the proteome and (2) the functional interaction between the proteins.
Proteomics
Proteomics
Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
, the study of the proteome, has largely been practiced through the separation of proteins by two dimensional gel electrophoresis
Gel electrophoresis
Gel electrophoresis is a method used in clinical chemistry to separate proteins by charge and or size and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge...
. In the first dimension, the proteins are separated by isoelectric focusing
Isoelectric focusing
Isoelectric focusing , also known as electrofocusing, is a technique for separating different molecules by their electric charge differences...
, which resolves proteins on the basis of charge. In the second dimension, proteins are separated by molecular weight
Molecular mass
The molecular mass of a substance is the mass of one molecule of that substance, in unified atomic mass unit u...
using SDS-PAGE
SDS-PAGE
SDS-PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis, describes a collection of related techniques widely used in biochemistry, forensics, genetics and molecular biology to separate proteins according to their electrophoretic mobility...
. The gel is dyed with Coomassie Brilliant Blue or silver
Silver
Silver is a metallic chemical element with the chemical symbol Ag and atomic number 47. A soft, white, lustrous transition metal, it has the highest electrical conductivity of any element and the highest thermal conductivity of any metal...
to visualize the proteins. Spots on the gel are proteins that have migrated to specific locations.
The mass spectrometer
Mass spectrometry
Mass spectrometry is an analytical technique that measures the mass-to-charge ratio of charged particles.It is used for determining masses of particles, for determining the elemental composition of a sample or molecule, and for elucidating the chemical structures of molecules, such as peptides and...
has augmented proteomics. Peptide mass fingerprinting
Peptide mass fingerprinting
Peptide mass fingerprinting is an analytical technique for protein identification that was developed in 1993 by several groups independently. In this method, the unknown protein of interest is first cleaved into smaller peptides, whose absolute masses can be accurately measured with a mass...
identifies a protein by cleaving it into short peptides and then deduces the protein's identity by matching the observed peptide masses against a sequence database
Sequence database
In the field of bioinformatics, a sequence database is a large collection of computerized nucleic acid sequences, protein sequences, or other sequences stored on a computer...
. Tandem mass spectrometry, on the other hand, can get sequence information from individual peptides by isolating them, colliding them with a non-reactive gas, and then cataloguing the fragment ions produced.
History
Marc WilkinsMarc Wilkins (geneticist)
Marc R. Wilkins is an Australian scientist who is credited with the concept of the proteome, and is a Professor in the School of Biotechnology and Biomolecular Sciences at the University of New South Wales, Sydney, Australia....
coined the term proteome in 1994 in a symposium on "2D Electrophoresis: from protein maps to genomes" held in Siena in Italy. It appeared in print in 1995, with the publication of part of Wilkins's PhD thesis. Wilkins used the term to describe the entire complement of protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s expressed by a genome, cell, tissue or organism.
See also
- ProteomicsProteomicsProteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
- MetabolomeMetabolomeMetabolome refers to the complete set of small-molecule metabolites to be found within a biological sample, such as a single organism...
- CytomeCytomeCytomes are the cellular systems, subsystems, and functional components of thebody. The cytome is the collection of the complex and dynamic cellular processes underlying physiological processes. It describes the structural and functional heterogeneity of the cellular diversity of an organism...
- BioinformaticsBioinformaticsBioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
- List of omics topics in biology
- Plant Proteome Database
- TranscriptomeTranscriptomeThe transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells.-Scope:...
External links
- Bioinformatics Journal
- Grid Computing of the Human Proteome Dead link
- Databases: PIR | Swissprot | Pfam