- Bacterial Genetic Nomenclature
Bacterial genetic nomenclature is a set of generally accepted rules and conventions used for naming
bacterial genes. Standards for were proposed in 1966 by Demerec et al. [Demerec M et al. (1966) A proposal for a uniform nomenclature in bacterial genetics. Genetics 54:61-76] .
Each bacterial gene is denoted by a
mnemonicof 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 allelenumber. All letters and numbers are underlined or italicised. For example, "leuA" is one of the genes of the leucinebiosynthetic 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
Loss of gene activity leads to a nutritional requirement (
auxotrophy) not exhibited by the wildtype( prototrophy).
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
*"pan": pantothenic acid
Loss of gene activity leads to loss of the ability to catabolise (use) the compound.
Drug and Bacteriophage Resistance Genes
*"azi": azide resistance
*"bla": beta-lactam resistance
*"cat": chloramphinicol resistance
*"kan": kanamyacin resistance
*"rif": rifampicin resistance
*"tonA": phage T1 resistance
Nonsense Suppressor Mutations
*"sup": suppressor (for instance, "supF" suppresses amber mutations)
If the gene in question is the wildtype a superscript '+' sign is used:
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:
*ts: temperature sensitive ("leuAts")
*cs: cold sensitive ("leuAcs")
*am: amber mutation ("leuAam")
*um: umber (opal) mutation ("leuAum")
*oc: ochre mutation ("leuAoc")
*R: resistant ("rifR")
* Δ: deletion (Δ "leuA")
* :: : insertion ("pyrC103::Tn10")
When referring to the genotype (the gene) the mnemonic is italicized and not capitalised. When referring to the phenotype (the gene product), the mnemonic is first-letter capitalised and not italicized (e.g. DnaA - the protein produced by the "dnaA" gene).
* [http://ecoliwiki.org/colipedia/index.php/Help:Genetic_nomenclature Genetic nomenclature on EcoliWiki] , the community annotation system of [http://ecolicommunity.org EcoliHub]
* [http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/mutations/nomenclature-v3.pdf Stan Maloy's page at San Diego State]
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