Bacterial Genetic Nomenclature
Encyclopedia
Bacterial genetic nomenclature is a set of generally accepted rules and conventions used for naming bacteria
l gene
s. Standards for were proposed in 1966 by Demerec et al..
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:
Some gene designations refer to a known general function:
) not exhibited by the wildtype (prototrophy).
Amino acids:
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:
Nucleosides:
Vitamins:
If a gene is mutant, it is signified by a superscript '-':
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:
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
l 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. Standards for were proposed in 1966 by Demerec et al..
General rules
Each bacterial gene is denoted by a mnemonicMnemonic
A mnemonic , or mnemonic device, is any learning technique that aids memory. To improve long term memory, mnemonic systems are used to make memorization easier. Commonly encountered mnemonics are often verbal, such as a very short poem or a special word used to help a person remember something,...
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
Allele
An allele is one of two or more forms of a gene or a genetic locus . "Allel" is an abbreviation of allelomorph. Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation...
number. All letters and numbers are underlined or italicised. For example, leuA is one of the genes of the leucine
Leucine
Leucine is a branched-chain α-amino acid with the chemical formula HO2CCHCH2CH2. Leucine is classified as a hydrophobic amino acid due to its aliphatic isobutyl side chain. It is encoded by six codons and is a major component of the subunits in ferritin, astacin and other 'buffer' proteins...
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:
- dna is involved in DNA replication
Biosynthetic genes
Loss of gene activity leads to a nutritional requirement (auxotrophyAuxotrophy
Auxotrophy is most commonly defined as the inability of an organism to synthesize a particular organic compound required for its growth . An auxotroph is an organism that displays this characteristic; auxotrophic is the corresponding adjective...
) not exhibited by the wildtype (prototrophy).
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
Nucleosides:
- 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 (use) the compound.- ara: arabinose
- gal: galactose
- lac: lactose
- mal: maltose
- man: mannose
- mel: melibiose
- rha: rhamnose
- xyl: xylose
Drug and bacteriophage resistance genes
- 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 (for instance, supF suppresses amber mutations)
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:
- ts: temperature sensitive (leuAts)
- cs: cold sensitive (leuAcs)
- am: amber mutation (leuAam)
- um: umber (opal) mutation (leuAum)
- oc: ochre mutation (leuAoc)
- R: resistant (rifR)
Other modifiers:
- Δ: deletion (Δ leuA)
- :: : insertion (pyrC103::Tn10)
- Δgene name::drug resistance marker: deletion/replacement (ΔrpoS::npt indicates that the rpoS gene has been deleted and replaced with the gene for neomycin phosphotransferase, which confers resistance to kanamycin)
Phenotype nomenclature
When referring to the genotype (the gene) the mnemonic is italicized and not capitalised. When referring to the gene product or phenotype, the mnemonic is first-letter capitalised and not italicized (e.g. DnaA – the protein produced by the dnaA gene, or LeuA- – the phenotype of a leuA mutant).External links
- Coli Genetic Stock Center is responsible for bacterial genetic nomenclature pertaining to Escherichia coli.
- Escherichia coli genes nomenclature (gene name aliases). See Stan Maloy's page at San Diego State
- Escherichia coli genetic nomenclature (rules for gene naming and meaning of other symbols used in Molecular Biology) on EcoliWiki, the community annotation system of EcoliHub.