Gene nomenclature


Gene nomenclature is the scientific naming of genes, the units of heredity in living organisms. It is also closely associated with protein nomenclature, as genes and the proteins they code for usually have similar nomenclature. An international committee published recommendations for genetic symbols and nomenclature in 1957. The need to develop formal guidelines for human gene names and symbols was recognized in the 1960s and full guidelines were issued in 1979. Several other genus-specific research communities have adopted nomenclature standards as well, and have published them on the relevant model organism websites and in scientific journals, including the Trends in Genetics Genetic Nomenclature Guide. Scientists familiar with a particular gene family may work together to revise the nomenclature for the entire set of genes when new information becomes available. For many genes and their corresponding proteins, an assortment of alternate names is in use across the scientific literature and public biological databases, posing a challenge to effective organization and exchange of biological information. Standardization of nomenclature thus tries to achieve the benefits of vocabulary control and bibliographic control, although adherence is voluntary. The advent of the information age has brought gene ontology, which in some ways is a next step of gene nomenclature, because it aims to unify the representation of gene and gene product attributes across all species.

Relationship with protein nomenclature

Gene nomenclature and protein nomenclature are not separate endeavors; they are aspects of the same whole. Any name or symbol used for a protein can potentially also be used for the gene that encodes it, and vice versa. But owing to the nature of how science has developed, proteins and their corresponding genes have not always been discovered simultaneously, which is the largest reason why protein and gene names do not always match, or why scientists tend to favor one symbol or name for the protein and another for the gene. Another reason is that many of the mechanisms of life are the same or very similar across species, genera, orders, and phyla, so that a given protein may be produced in many kinds of organisms; and thus scientists naturally often use the same symbol and name for a given protein in one species as in another species. Regarding the first duality, the context usually makes the sense clear to scientific readers, and the nomenclatural systems also provide for some specificity by using italic for a symbol when the gene is meant and plain for when the protein is meant. Regarding the second duality, the nomenclatural systems also provide for at least human-versus-nonhuman specificity by using different capitalization, although scientists often ignore this distinction, given that it is often biologically irrelevant.
Also owing to the nature of how scientific knowledge has unfolded, proteins and their corresponding genes often have several names and symbols that are synonymous. Some of the earlier ones may be deprecated in favor of newer ones, although such deprecation is voluntary. Some older names and symbols live on simply because they have been widely used in the scientific literature and are well established among users. For example, mentions of HER2 and ERBB2 are synonymous.
Lastly, the correlation between genes and proteins is not always one-to-one ; in some cases it is several-to-one or one-to-several, and the names and symbols may then be gene-specific or protein-specific to some degree, or overlapping in usage:
  • Some proteins and protein complexes are built from the products of several genes, which means that the protein or complex will not have the same name or symbol as any one gene. For example, a particular protein called "example" may have 2 chains, which are encoded by 2 genes named "example alpha chain" and "example beta chain".
  • Some genes encode multiple proteins, because post-translational modification and alternative splicing provide several paths for expression. For example, glucagon and similar polypeptides all come from proglucagon, which comes from preproglucagon, which is the polypeptide that the GCG gene encodes. When one speaks of the various polypeptide products, the names and symbols refer to different things, but when one speaks of the gene, all of those names and symbols are aliases for the same gene. Another example is that the various μ-opioid receptor proteins are all splice variants encoded by one gene, OPRM1; this is how one can speak of MORs in the plural even though there is only one MOR gene, which may be called OPRM1, MOR1, or MOR—all of those aliases validly refer to it, although one of them is preferred nomenclature.

    Species-specific guidelines

The HUGO Gene Nomenclature Committee is responsible for providing human gene naming guidelines and approving new, unique human gene names and symbols. For some nonhuman species, model organism databases serve as central repositories of guidelines and help resources, including advice from curators and nomenclature committees. In addition to species-specific databases, approved gene names and symbols for many species can be located in the National Center for Biotechnology Information's "Entrez Gene" database.

Bacterial genetic nomenclature

There are generally accepted rules and conventions used for naming genes in bacteria. Standards were proposed in 1966 by Demerec et al.

General rules

Each bacterial gene is denoted by a mnemonic of three lower case letters which indicate the pathway or process in which the gene-product is involved, followed by a capital letter signifying the actual gene. In some cases, the gene letter may be followed by an allele number. All letters and numbers are underlined or italicised. For example, leuA is one of the genes of the leucine biosynthetic pathway, and leuA273 is a particular allele of this gene.
Where the actual protein coded by the gene is known then it may become part of the basis of the mnemonic, thus:
  • rpoA encodes the α-subunit of RNA polymerase
  • rpoB encodes the β-subunit of RNA polymerase
  • polA encodes DNA polymerase I
  • polC encodes DNA polymerase III
  • rpsL encodes ribosomal protein, small S12
Some gene designations refer to a known general function:
In a 1998 analysis of the E. coli genome, a large number of genes with unknown function were designated names beginning with the letter y, followed by sequentially generated letters without a mnemonic meaning. Since being designated, some y-genes have been confirmed to have a function, and assigned a synonym name in recognition of this. However, as y-genes are not always re-named after being further characterised, this designation is not a reliable indicator of a gene's significance.

Common mnemonics

Biosynthetic genes

Loss of gene activity leads to a nutritional requirement not exhibited by the wildtype.
Amino acids:
  • ala = alanine
  • arg = arginine
  • asn = asparagine
Some pathways produce metabolites that are precursors of more than one pathway. Hence, loss of one of these enzymes will lead to a requirement for more than one amino acid. For example:
  • ilv: isoleucine and valine
Nucleotides:
  • gua = guanine
  • pur = purines
  • pyr = pyrimidine
  • thy = thymine
Vitamins:
  • bio = biotin
  • nad = NAD
  • pan = pantothenic acid

    Catabolic genes

Loss of gene activity leads to loss of the ability to catabolise the compound.
  • ara = arabinose
  • gal = galactose
  • lac = lactose
  • mal = maltose
  • man = mannose
  • mel = melibiose
  • rha = rhamnose
  • xyl = xylose

    Drug and bacteriophage resistance genes

  • amp = ampicillin resistance
  • azi = azide resistance
  • bla = beta-lactam resistance
  • cat = chloramphenicol resistance
  • kan = kanamycin resistance
  • rif = rifampicin resistance
  • tonA = phage T1 resistance

    Nonsense suppressor mutations

  • sup = suppressor

    Mutant nomenclature

If the gene in question is the wildtype a superscript '+' sign is used:
  • leuA+
If a gene is mutant, it is signified by a superscript '-':
  • leuA−
By convention, if neither is used, it is considered to be mutant.
There are additional superscripts and subscripts which provide more information about the mutation:
Other modifiers:
  • Δ = deletion
  • - = fusion
  • : = fusion
  • :: = insertion
  • Ω = a genetic construct introduced by a two-point crossover
  • interrupted gene::interrupting gene = a gene that has been interrupted by another gene inserted into it, resulting in its inactivation.
  • Δdeleted gene::replacing gene = deletion with replacement

    Phenotype nomenclature

When referring to the genotype the mnemonic is italicized and not capitalised. When referring to the gene product or phenotype, the mnemonic is first-letter capitalised and not italicized.

Bacterial protein name nomenclature

Protein names are generally the same as the gene names, but the protein names are not italicized, and the first letter is upper-case. E.g. the name of RNA polymerase is RpoB, and this protein is encoded by rpoB gene.