At the conference on 'Higher Plant Mitochondrial DNA', held at Airlie House, Virginia, USA in October 1986, a discussion on the possibility of creating a standardized nomenclature for plant mitochondrial and nuclear genes encoding mitochondrial proteins and RNAs was held. This proposal details the consensus opinion of that meeting and of a number of interested individuals who responded to the circulars. An overriding aim was to retain, wherever possible, the current commonly used gene designations and the general principles of chloroplast gene nomenclature were followed (R.B. Hallick and W. Bottomley, Plant Mol. Biol. Rep. 1:38-43, 1983).
Mitochondrial proteins: The polypeptide products of both nuclear
and mitochondrial genes are to be designated by capital letters, e.g.:
ATPB-1: beta-subunit of the mitochondrial ATPase.
COXII: subunit 2 of cytochrome oxidase.
Mitochondrial genes: Genes on the mitochondrial chromosome or
associated with mitochondrial plasmids will take a three letter code in
lower case which will be either italicised or underlined, for example:
: Cox trn rrn orf urf
Any suffixed descriptors will also be italicised (underlined), for example:
Nuclear genes (specifying mitochondrial components): Nuclear
genes will be distinguished from mitochondrial genes by being in UPPER
CASE. Again a three letter italicised or underlined code will be used,
The accepted convention for nuclear genes is to use numbers to identify genes with a related function or different members of the same gene family. However, we feel that where multipolypeptide complexes exist and where these have several components with unknown numbers of constituent polypeptides, for example the F0 and F1 components of ATP synthase, both letters and numbers should be used to distinguish the components of the complex whether or not the individual polypeptides of the components are mitochondrial encoded. This will allow additional polypeptides to be assigned to a complex regardless of the compartment in which it is encoded.
Mutations: In some instances mitochondrial genes specifying a
gene product in one species or cytoplasm will be non-functional in another
species or in another cytoplasm of the same species. It is therefore necessary
to distinguish between functional and non-functional genes. The simplest
way of achieving this is to provide the non-functional gene with a prefix,
preferably a Greek symbol, e.g. phi (lower case).
|Functional Gene||Mutant Gene|
Gene copy number: In both the nuclear and organelle compartments
gene copy number may exceed one. In such instances genes will take a suffixed
arabic number, for example:
atpA-1 atpA-2 trnS1 trnS2
Where the physical map of the mitochondrial genome has been determined, repeated sequences, if present, will be numbered sequentially from the origin of the map, the genes within repeats will be given the same reiteration-number as the repeat.
Species and cytoplasm designation: Species can be designated
by the standard three letter code, for example:
Oenothera berteriana : Obe
Triticum aestiuum : Tae
Zea mays : Zma
Many higher plant species have more than one cytoplasm. If no nomenclature exists to distinguish these then they should be distinguished by an upper case letter. In many instances cytoplasms have been described as either fertile or sterile. In these instances S and F will suffice. In maize the accepted designations of N, T, S and C will be retained. These cytoplasm descriptors will follow the three letter species code, for example:
|Zma C||The C-cytoplasm of maize|
This type of abbreviation is most often used with restriction endonucleases.
Without exception these cytoplasm identifiers must precede the gene to
which they may be hyphenated, for example:
T-urf13 N-atpA-1 N-atpA-2 S-pcf
Such cytoplasm identifiers can be optional to reduce the size of the gene acronyms. Please note that the species acronym (if used) and the cytoplasm identifier are NOT to be italicised or underlined.
Genes of plasmids: Plasmids, both linear and circular, DNA or
RNA are associated with some cytoplasms but not all. There is a growing
body of evidence to suggest that specific plasmids are NOT associated with
a particular cytoplasm. In order to account for this, we propose that a
plasmid designation replaces the cytoplasm identifier. It will be necessary
for the research worker to specify the cytoplasm elsewhere. Where many
plasmids are associated with one cytoplasm it may be useful to identify
them by mp1 : mitoplasmid 1, mp2 etc. Alternatively, trivial and commonly
used designations may be retained, for example S1, S2, R2 etc. An mp prefix
will assume a circular topology. Linear plasmids, not having commonly known
designations, can be identified by their size in nucleotides or nucleotide
base pairs and an L descriptor. Singlestranded molecules can be noted using
the 'ss' abbreviation. Perhaps, fortunately, there are sufficiently few
linear nucleic acid entities associated with motochondria for them to retain
or be given trial designations.
Recommended nomenclature for known m itochondrial genes
The designation rDNA (e.g. 26S rDNA) includes the ribosomal gene as well as the transcriptional promoters and the transcribed flanking sequences.
Transfer RNA genes-Transfer RNA genes are designated 'trn' with
the addition of the single letter amino-acid code to identify the species;
isoaccepting species will be designated with the anticodon following the
amino acid code. Duplicated genes, for example those associated with repeated
sequences, will be identified with a reiteration-number corresponding to
the reiteration-number of the repeat. Unfortunately, it is impossible to
distinguish between tRNA gene duplications which have occurred due to promiscuous
DNA transfer between organelles. A few of the chloroplast tRNA genes in
the mitochondrial genome of maize, for example trnW-TGG, are transcribed,
but their ability to accept amino acids and transfer these to growing polypeptide
chains has never been demonstrated. Therefore, they could be considered
pseudogenes and be designated as such.
|trnM or trnM-ATG||tRNAMet||Elongator species|
|trnfM or trnfM-ATG||tRNAfMet||Formyl-methionine initiator species|
Where there are isoacceptors:
Where gene duplication has occurred:
|trnL1 or trnL1-CTA||tRNALeu1-UAG|
|trnL2 or trnL2-CTA||tRNALeu2 -UAG|
The mitochondrial genetic code has one possible anomaly: CGG specifies
tryptophan instead of arginine. It is therefore recommended that in this
instance it be fully abbreviated as follows:
Mitochondrial polypeptide genes: The gene designations in this section will make use of the commonly used or accepted gene designations where possible.
Ribosomal protein genes-The designations 'rps' for small subunit
proteins, 'rpl' for large subunit proteins, are recommended. Where homology
to an existing E. coli ribosomal protein exists the gene can be
designated with the same number. If no homology exists then the identifier
should be a letter. For example:
|rps13||RPS13||ribosomal protein S13|
Polypeptides of the electron transport chain
Complex I: NADH-ubiquinone oxidoreductase-The components of this complex will be designated 'nad'. Individual genes will be given numerical identifiers, these will indicate homology or functional equivalence to the mammalian subunits. Additional genes will accept the next number of the series.
|Gene*||Gene product||Mammalian gene|
*These gene designations presume a mitochondrial location. To date only sequences related to nad1 and nad5 have been identified.
ATP synthase-The two multicomponent subunits of this complex, F0 and F1, will be differentiated by suffixed letters (F1) and suffixed arabic numbers (F0).
Subunits of the F1 complex:
Subunits of the F0 complex:
Genes of other complexes, including complex III and complex IV
|coxI||COXI||subunit 1 of cytochrome oxidase|
|coxII||COXII||subunit 2 of cytochrome oxidase|
|coxIII||COXIII||subunit 3 of cytochrome oxidase|
Open reading frames and unidentified reading frames-Open reading
frame, orf, is a gene for which no specific gene product has been
identified. Unassigned reading frame, urf, is an open reading frame
which is transcribed and translated into a polypeptide whose function has
not been assigned. Individual orf's and urf's will be distinguished
by the number of amino acids which are coded for by the open reading frame.
An urf can also accept the size of the polypeptide in kilo daltons
as its descriptor, for example:
|T-urf115 or T-urf13||T-URF13||Gene coding for the 13 kDa polypeptide which is unique to the T-cytoplasm of maize.|
Gene library and central registrar: It is hoped that during 1988 a gene library will be established at the Institute of Plant Science Research in Cambridge. The clones deposited will be freely available on request. As an adjunct to this facility it would be recommended that people wishing to designate a new gene would first check to ensure that the nomenclature is consistent with this proposal. The contents of the library and the rules of gene nomenclature should be accessible via Bitnet using the following address: Lonsdale @ UK.AC.AFRC.CAMB.
D.M. Lonsdale and C.J. Leaver
[Ed. note: This proposed nomenclature, like that for chloroplasts, should be considered a working framework, just as are those for nuclear genomes; readers and users are urged to deliberate on these nomenclatures and to convey suggestions and criticisms to the authors. The editor would appreciate receiving copies of correspondence, toward internally consistent evolution of all nomenclatures]
Return to the MNL 62 On-Line Index
Return to the Maize Newsletter Index
Return to the Maize Genome Database Page