We were led to propose a standardized nomenclature for plant genes encoding sigma factors by two unrelated events: a request in June for a proposal by Carl Price on behalf of the CPGN and a note submitted by Pal Maliga in July to the Plant Molecular Biology Reporter in which he stressed the importance of establishing a common nomenclature for sigma factors.
The following proposal is a consensus among the workers with sigma factors listed below.
As a basis for the subdivision of plant sigma factors, we have prepared a phylogenetic tree using the amino acid sequence data registered in GenBank. We then proceeded on the following principles:
- Genes encoding sigma factors among different species should be named according to a shared system across the plant kingdom.
- Each gene family will share the common mnemonic "Sig".
- We recognize six gene families among eukaryotic plants; they will be numbered Sig1, Sig2, ... on the basis of priority or acceptance by the majority of researchers.
- For naming individual genes within a species we prefer the traditional format, e.g., for Sig1 genes in tobacco: NtSig1A, NtSig1B, ... (According to the CPGN format they would be NICta;Sig1;1, NICta;Sig1;2, ...)
The problem with numbered sigma factors in developing a common nomenclature among plant species has been pointed out by Bob Troxler and Lori Allison: it may be difficult for investigators to access the proposed phylogenetic tree before publishing newly discovered sigmas. We hope this problem will be resolved with a public announcement of the plan.
Kan Tanaka would have preferred having members of multigene families within a species identified alphatically, such as SigA, SigB, ... We preferred numbers for the following reasons: numbers are preferred by the CPGN, as well as science communities concerned with the gene nomenclature of individual species, such as those representing Chlamydomonas, maize, and Arabidopsis (see Trends in Genetics, Genetic Nomenclature Guide, 1995); in addition SigA in Arabidopsis and tobacco is not the counterpart of sigA in bacteria. The adoption of Sig1 in plants would avoid confusion.
Working Group
Curator's note: We hope this material will be useful. Please send your comments to hirokazu@smail.u-shizuoka-ken.ac.jp and copy to me at cpgn@mbcl.rutgers.edu. We shall post discussions on this Web site. Carl Price, 11/16/00
