Bacterial Genetic Nomenclature


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] .

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:
*"dna" is involved in DNA replication

Common Mnemonics

Biosynthetic Genes

Loss of gene activity leads to a nutritional requirement (auxotrophy) 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": chloramphinicol resistance
*"kan": kanamyacin 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")

Phenotype Nomenclature

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).

References

External links

* [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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