Genetic Nomenclature, Bacteria
S Maloy, San Diego State University, San Diego, CA, USA
© 2013 Elsevier Inc. All rights reserved.
Glossary
Allele Alternative forms of a gene. For example, the
mutants putA601 and putA736 each have a different
mutation in the putA gene.
Genotype A specific description of the genetic constitution
of an organism. The genotype is defined by the allelic form
of each gene in an organism, but for simplicity usually only
differences from the wild type are described.
Nomenclature
Until the mid-1960s, there were no clear rules for naming genes
and mutants of bacteria. Many investigators assigned different
names to mutants with the same phenotype, which resulted in
different names being applied to the same gene and the same
name being applied to two different genes. To further confuse
the issues, different investigators would each assign allele num­
bers based upon the order of isolation in their own laboratory,
such that two very different alleles of the same gene might have
the exact same designation. To eliminate this confusion, a
group of bacterial geneticists led by Demerec proposed a uni­
form nomenclature for bacterial genes, mutants, and
phenotypes. This nomenclature was adopted by many journals
and soon became the standard genetic nomenclature for bac­
teria. As new genetic techniques have been developed, some
modifications have been incorporated into the standard genetic
nomenclature to describe mutations such as transposon inser­
tions and fusions. The basic rules of bacterial genetic
nomenclature are described below.
Genotypes
Each gene is assigned a three-letter designation, usually an
abbreviation for the pathway or the phenotype of mutants.
When the genotype is indicated, the three-letter designation is
written in lowercase and italicized. Different genes that affect
the same pathway are distinguished by a capital letter following
the three-letter designation. For example, mutations affecting
purine biosynthesis are designated pur. The purA gene encodes
the enzyme adenylosuccinate synthetase and the purB gene
encodes the enzyme adenylosuccinate lyase.
Each mutation in the pathway is consecutively assigned a
unique allele number. For example, purA56 refers to a particu­
lar pur mutation that affects the purA gene. In order to
distinguish different mutations that affect a related group of
genes, no other pur mutation, regardless of the gene affected,
will be assigned the allele number 56. A separate series of allele
numbers is used for each three-letter locus designation. The
entire genotype is italicized. (In the days before word proces­
sing on computers, the genotype was underlined instead of
italicized.)
Brenner’s Encyclopedia of Genetics, 2nd edition, Volume 3 doi:10.1016/B978-0-12-374984-0.01048-2
Phenotype The appearance or other observable
characteristics of an organism. The phenotype expressed
by an organism depends upon the particular forms of its
genes (e.g., its wild-type or mutant alleles) and the
environmental conditions.
Transposable element A transposon or insertion
sequence. An element that can insert in a variety of DNA
sequences.
When the precise DNA sequence change responsible for
the mutation is known, it can be substituted for the allele
number. For example, a change in position 257 of the putA
gene product from alanine to leucine may be indicated
putAA257L. However, even when the DNA sequence of a
mutation is known, a specific allele number is invaluable
for tracking the history of a strain when maintaining large
strain collections.
Phenotype
To distinguish the phenotype of a strain from its genotype, the
phenotype is usually indicated with the same three-letter des­
ignation as the genotype but phenotypes start with capital
letters and are not underlined. For example, strain TR251
[hisC527 cysA1349 supD] has a Cys+ His+ phenotype because
the supD mutation suppresses the amber mutations in both the
cysA and the hisC genes.
Transposon Insertions
Transposable elements can insert in known genes or in a site
on the chromosome where no gene is yet known. When an
insertion is in a known gene, the mutation is given a three-
letter designation, gene designation, and allele number as
described above, followed by a double colon, then the type
of insertion element. For example, putA1005::Tn10 designates
a particular insertion of the transposon Tn10 within the putA
gene.
When a transposon insertion has been mapped but is not
within a known gene, it is named according to the map posi­
tion of the insertion on the chromosome. Such insertions are
named with a three-letter symbol starting with z. The second
and third letters indicate the approximate map position in
minutes: the second letter corresponds to 10-min intervals of
the genetic map numbered clockwise from minute 0 (a = 0–9;
b = 10–19; c = 20–29, etc.); the third letter corresponds to min­
utes within any 10-min segment (a = 0; b = 1; c = 2; etc). For
example, a Tn10 insertion located near putA at 22 min on the
Salmonella enterica chromosome is designated zcc::Tn10. Allele
numbers are assigned sequentially to such insertions regardless
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of the letters appearing in the second and third positions;
therefore, if more refined mapping data suggest a new three-
letter symbol, the allele number of the insertion mutation is
retained. This nomenclature uses zaa (0 min) to zjj (99 min).
Insertion mutations on extrachromosomal elements are desig­
nated with zz, followed by a letter denoting the element used.
For example, zzf is used for insertion mutations on an
F′ plasmid.
Chromosome Rearrangements
Common types of chromosome rearrangements include dele­
tions (designated Del), duplications (designated Dup), and
inversions (designated Inv). Chromosome rearrangements are
indicated by the type of rearrangement followed by a paren­
thetic designation of the endpoints of the rearrangement. For
example, a deletion within the putA gene is simply indicated
Del(putA), and a duplication between the pyrD and pyrC genes
would be indicated Dup(pyrD-pyrC). When a chromosome
rearrangement is held by a selectable genetic element such as
a transposon, the position of the transposon is indicated. For
example, Dup (trp-248*MudP*hisD9953) describes a duplica­
tion between a particular site in trp and a particular site in the
hisD gene with a MudP insertion at the join point. Similar to
other types of mutations, chromosome rearrangements should
be designated with allele numbers.
Strain Collections
The ease of rapidly accumulating a large number of mutants
requires careful bookkeeping to avoid confusing one mutant
with another. Each mutant should be assigned a strain num­
ber. Strains in collections are usually named using a short
string of letters designating by the laboratory where the
mutant was isolated with a serial numbering of the strains
in the collection. For example, John Roth’s collection of
Salmonella enterica strains that carry transposon insertions is
designated TT.
See also: Allele Specificity; Genotype.
Further Reading
Demerec M, Adelberg EA, Clark AJ, and Hartman PE (1966) A proposal for a uniform
nomenclature in bacterial genetics. Genetics 54(1): 61–67.
Hughes K and Maloy S (2007) Strain collections, genetic nomenclature. Methods in
Enzymology 421: 3–10.