Nomenclature Guidelines

[Summary]

Dictyostelium discoideum has a genome of approximately 34 Mb, containing between 10,000 and 12,000 genes. Thousands of mutant strains have been obtained, many of which are available from the Dicty Stock Center. A uniform nomenclature is essential to compile all the available information and provide easy access for the research community. We therefore encourage researchers to conform to the following guidelines for naming Dictyostelium genes, proteins, strains, mutant alleles, phenotypes, genotypes, molecular genetic constructs, and plasmids.

See the Procedure for naming genes for more details.

Questions and comments should be addressed to dictyBase.

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Gene Nomenclature Guidelines

We strongly discourage using "D", "d", or "Dd" for Dictyostelium, and "g" and "p" for "gene" and "protein", as these abbreviations are not informative.

1. Established nomenclature for gene families has precedence over other names.
   Examples: abcA1, abcA2, abcB1, atg1, atg4.
   
   
2. New gene names should conform to the following conventions derived from Demerec et al. (1966). A locus description consisting of three lower-case, italicized letters, followed by a capital italicized letter to distinguish genes with the same descriptor that are related in a significant way.
   Examples: rdeA, rdeB and rdeC; or tagA, tagB and tagC.
   
   
3. Existing gene names remain unchanged.
   Examples: act6, act15, pyr5-6 and EB1.
   
   
4. Original naming authors can change any gene name by describing the name change in their next publication containing the gene and informing dictyBase.
   Example: “The spore coat protein gene cotB (formerly referred to as “SP70”) was introduced under the control of...” This change was made by Bill Loomis in 1990.
   
   
5. All names that are found in the literature will remain in dictyBase as synonyms.
   Example: pkaC has five synonyms: PKA, pkacat, DdPK3, DdPK2, PKA-C.

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Proteins

1. A protein may be named after the gene encoding it by capitalizing the first letter and without the use of italics.
   Examples: RegA (encoded by regA), RegA(D212A) (encoded by regA(D212A)).
   
   
2. A protein can also be referred to by its full name or a protein synonym.
   Examples: actin, ribonucleotide reductase small subunit, RNR, protein kinase C, PKC.
   
   
3. Proteins that have been identified by physical properties are sometimes named following this property; however this practice is discouraged because many different proteins can have the same attribute.
   Examples: p34, 34kDa protein, actin-binding protein, calcium-binding protein.

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Strains

Strains available for distribution must have an unambiguous name, consisting of 2 or 3 capitals plus a unique serial number (e.g. HM1 or HTY217). Labs or workers should always use the same capital prefixes or small group of prefixes. The prefixes are assigned by a clearinghouse upon request. See Appendix 1 for a current list of assigned strain prefixes. In the past all lab designations started with either H (for haploid) or D (for diploid) and many of these strains are still in use.

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Mutant Alleles

1. Allele names should be italicized and placed in parentheses following the gene name without a space.
   Examples: yakA(AK235) and yakA(AK800): different insertion mutations in the yakA gene.
   
   
2. Where the nature of the mutation is not known or only a single allele is relevant, a superscript minus sign can be used for brevity.
   Example: regA^-.
   
   
3. The use of superscripts to describe the general nature of an allele can be used but should be limited to two or three letters, e.g. ts (temperature sensitive), cs (cold sensitive), hc (high copy) or dn (dominant negative).
   Examples: regA(AK202^ts), regA^ts.
   
   
4. Amino acid substitutions should be given as the old residue in single-letter code with its codon location followed by the new (mutant) amino acid. The amino acid change is an interpretation of what the gene will produce and refers to a protein so it is not put in italics.
   Example: regA(D212A) has an alanine in place of the aspartate at position 212.
   
   
NOTE: AX4 is the reference strain for the “wild-type” amino acid sequence within proteins since it is the first strain to be sequenced.

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Phenotypes

No convention for describing phenotypes of Dictyostelium genes has been invoked, but when used they should not be italicized. Three letter abbreviations of phenotypes can be used to name genes once the relevant genes are cloned, characterized and found to have a novel structure (e.g. tagA for the “tip-less aggregate” phenotype). The following names should be used to indicate common drug resistance/sensitivity and nutrient auxotrophy/prototrophy. For clarity, relevant phenotypic markers should be included at the end of formal genotypes (no italics):

neo^r: indicates a neomycin phosphotransferase gene is functional.

neo^s: for clarity, or when G418 selection on a neo^r strain is relaxed and G418-sensitive strain is isolated.

thy^-: indicates thy1 is mutant and the strain requires thymidine.

thy⁺: used when a thy1 mutant has been complemented.

bs^r: indicates the blasticidin resistance gene bsr is present.

bs^s: for clarity, or when bsr has been introduced but is non-functional.

ura⁺: uracil independent. Note that this can be different from pyr5-6+.

ura^-: most often used to indicate pyr5-6-.

foa^r: most often this will be redundant with ura-.

hyg^r: hygromycin resistance.

ble^r: bleomycin resistance.

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Genotypes

Genotypes should describe the relevant genetic modifications present in a given strain. Genes listed in a genotype are considered to be mutant in some way. Every genetic element described in a genotype (gene, plasmid, DNA fragment) should be separated by a comma. To distinguish chromosomal loci from exogenous genes, every gene or construct contained on DNA that was introduced into cells by transformation should be listed within brackets regardless of whether that DNA is carried on a plasmid, integrated as a fragment or was amplified by replication once inside cells.

Constructs carried within cells should be described in the formal genotype of that strain and placed in brackets. Thus, a cotB promoter b-galactosidase reporter construct in a mutant strain might have a formal genotype of “regA(AK202^ts), p88d1[cotB/lacZ] neo^r”, but could be shortened to “regA^-[cotB/lacZ]” in the context of a sentence describing the strain’s properties in the results section of a paper.

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Molecular Genetic Constructs

Reporter genes and gene fusions should be named with the relevant components separated by slashes and dashes to indicate DNA fusion, as follows. Typically, the components will be a promoter, a coding sequence or ORF encoding a reporter protein. Promoters (± a few codons) should be separated from coding sequence by a slash (/) and coding sequences separated by dashes (-).
Examples: cotB/talA-gfp (talin-GFP fusion under the transcriptional control of the cotB promoter), talA/talA-gfp or talA-gfp (talin gene under the transcriptional control of the native promoter), talA-gfp(S65T).

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Plasmids

Naturally occurring plasmids are named by a prefix indicating the genus and species, as in Ddp1. Derivatives of the natural plasmids and other shuttle vectors should be indicated with a lowercase “p” prefix (pDXA-3C). For genes on a plasmid, and any other gene that is introduced into a strain by experiment (see below), use the same naming system as for chromosomal genes, but placed within square brackets.
Example: pDneo67[act6/regA] indicates that the regA coding sequence is fused to the promoter of the actin6 gene on plasmid pDneo67).

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Management

dictyBase acts as the centralized clearinghouse for gene and strain names. Scientific curators at dictyBase will verify proposed gene and strain names to encourage the application of these guidelines and to ensure that names are not duplicated. Questions or naming suggestions can be addressed to: dictybase@northwestern.edu.

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References

This document is based on the Nomenclature Proposal written in November 2000 by the Dictyostelium Community Organizing Committee: Adam Kuspa (Chairman), Robert R. Kay, Alan R. Kimmel, Hideko Urushihara, Richard Kessin (ex officio) Chairman.

General:

Demerec, M. et al., (1966). A proposal for a uniform nomenclature in bacterial genetics. Genetics 54:61-76.

Kay, Loomis, Devreotes (2001) TIG S.5-S.6

Gene Lists:

Kuspa, A., D. Maghakian, P. Bergesch, and W.F. Loomis. 1992. Physical mapping of genes to specific chromosomes in Dictyostelium discoideum. Genomics 13:49-61.

Loomis, W.F., D. Welker, J. Hughes, D. Maghakian, and A. Kuspa. 1995. Integrated maps of the chromosomes in Dictyostelium discoideum. Genetics 141:147-157.

Kuspa, A., and W.F. Loomis. 1996. Ordered yeast artificial chromosome clones representing the Dictyostelium discoideum genome. Proc. Natl. Acad. Sci. USA 93:5562-5566.

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Appendix 1. List of Known Strain Prefixes by Laboratory

Updated October 6, 2005

AD, HAD	Adrian Harwood
AK	Adam Kuspa
BS	Bubba Singleton
CT	Chris Thompson
CW	Tom Egelhoff
DG	Bill Loomis
DH	Dale Herald (except DH100-199: Rich Kessin)
GS	Gad Shaulsky
HAD	Adrian Harwood
HC, DCB	Barrie Coukell
HDK, DDK	David Knecht
HG, DG	Guenther Gerisch
HGR	Michel Sartre
HH, DH100-199	Rich Kessin
HK, DK	Gene Katz
HKT	Kei Inouye
HL, DL	Bill Loomis
HM, DM	Rob Kay
HP, HPX	Pasteur Institute
HPF, DPF	Paul Fisher
HPS, DPS	Reg Deering
HR	Herb Ennis and Rich Kessin (a few strains from Frank Rothman were labeled HR too)
HS, DS	Jim Spudich
HSB	Salvo Bozzaro
HT	Adrian Tsang
HTU	Taro Uyeda
HTY	Kaichiro Yanagisawa
HU, DUK	Keith Williams
HUD, DUD	Dennis Welker
IIB	Instituto de Investigaciones Biomedicas
IR, DIR, RI (old)	Rob Insall
JH	Jeff Hadwiger
KS	Karl Saxe
KY	Kaichiro Yanagisawa (or T. Yamada?)
NP, DP	Peter Newell
QS	Queller-Strassmann lab
RI	Rob Insall (old prefix)
SA, DSA	Steve Alexander
TL	Bill Loomis
V	Adam Kuspa
W	Adam Kuspa
X, XP	Peter Newell

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