Bacterial genetic nomenclature - Wikipedia, the free encyclopedia

http://en.wikipedia.org/wiki/Bacterial_Genetic_Nomenclature

Bacterial genetic nomenclature

From Wikipedia, the free encyclopedia

(Redirected from 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.[1]

Contents
1 General rules 2 Common mnemonics 2.1 Biosynthetic genes 2.2 Catabolic Genes 2.3 Drug and bacteriophage resistance genes 2.4 Nonsense suppressor mutations 3 Mutant nomenclature 4 Phenotype nomenclature 5 References 6 External links

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 -subunit of RNA polymerase rpoB encodes the -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
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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

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

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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 '-': leuABy 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) = amber mutation (leuAam) am

um oc R

= umber (opal) mutation (leuAum)

= ochre mutation (leuAoc) = resistant (rifR)

Other modifiers: = deletion (leuA) - = fusion (leuA-lacZ) : = fusion (leuA:lacZ) :: = insertion (leuA::Tn10) = a genetic construct introduced by a two-point crossover (leuA) gene name::drug resistance marker = deletion/replacement (leuA::npt indicates that the leuA 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).

References
1. ^ Demerec M et al. (1966) A proposal for a uniform nomenclature in bacterial genetics. Genetics 54:6176

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External links
Coli Genetic Stock Center (http://cgsc.biology.yale.edu/index.php) 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 (http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/mutations/nomenclature-v3.pdf) Escherichia coli genetic nomenclature (rules for gene naming and meaning of other symbols used in Molecular Biology) on EcoliWiki (http://ecoliwiki.org/colipedia/index.php/Help:Genetic_nomenclature), the community annotation system of EcoliHub (http://ecolicommunity.org). Retrieved from "http://en.wikipedia.org/w/index.php?title=Bacterial_genetic_nomenclature&oldid=542838839" Categories: Bacteriology Genetics This page was last modified on 8 March 2013 at 16:25. Text is available under the Creative Commons Attribution-ShareAlike License; additional terms may apply. By using this site, you agree to the Terms of Use and Privacy Policy. Wikipedia is a registered trademark of the Wikimedia Foundation, Inc., a non-profit organization.

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