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LETTER TO THE EDITOR

Nomenclature for Two-Component Signaling Elements of Rice

Department of Biological Sciences, Dartmouth College, Hanover, NH 03755

Kazuyuki Doi

Plant Breeding Laboratory, Kyushu University, Higashi-ku, Fukuoka 812–8581, Japan

Ildoo Hwang

Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790–784, Korea

Joseph J. Kieber

Department of Biology, University of North Carolina, Chapel Hill, NC 27599–3280

Jitendra P. Khurana

Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India

Nori Kurata

Plant Genetics Lab, Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka 411–8540, Japan

Takeshi Mizuno

Laboratory of Molecular Microbiology, School of Agriculture, Nagoya University, Chikusa-ku, Nagoya 464–8601, Japan

Ashwani Pareek

Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India

Shin-Han Shiu

Department of Plant Biology, Michigan State University, East Lansing, MI 48824

Ping Wu

Institute of Plant Sciences, College of Life Sciences, Zhejiang University, Hangzhou 310029, People's Republic of China

Wing Kin Yip

Department of Botany, University of Hong Kong, Hong Kong, People's Republic of China

Plants make use of two-component systems for signal transduction, and these are involved in vital cellular processes such as the responses to cytokinins, ethylene, red/far-red light, and osmosensing (Schaller et al., 2002). Two-component systems were originally identified in bacteria, and in their simplest form involve a His kinase and a response regulator that participate in a phosphorelay (Mizuno, 1997). Of particular relevance to plants is a permutation on the two-component system known as the multistep phosphorelay, which incorporates an additional protein called a His-containing phosphotransfer protein into the phosphorelay (Schaller et al., 2002).

In plants, two-component signaling has been studied most extensively in the dicot Arabidopsis (Arabidopsis thaliana; Schaller et al., 2002). But in the past several years, as the rice (Oryza sativa) genome has been sequenced (Feng et al., 2002; Goff et al., 2002; Sasaki et al., 2002; Yu et al., 2002; Rice Chromosome 10 Sequencing Consortium, 2003; International Rice Genome Sequencing Program, 2005), publications have begun to appear on the two-component signaling elements of rice (Murakami et al., 2003; Doi et al., 2004; Han et al., 2004; Yau et al., 2004; Murakami et al., 2005; Ito and Kurata, 2006; Jain et al., 2006; Pareek et al., 2006). Given the broad impact that the two-component signaling systems have on plant growth and development, the number of publications describing their action in rice is likely to increase rapidly in the coming years. It is thus necessary that a uniform nomenclature be adopted to facilitate scientific communication.

Unfortunately, because publications on two-component signaling elements of rice appeared from multiple laboratories within a short period of time, it was not possible to coordinate the terminology being used. This resulted in multiple designations being applied to the same gene, different criteria being used for classifying genes into families, and some redundancy with previously used gene symbols. Now with a high-quality rice genome sequence available and most if not all of the two-component signaling elements identified, it is timely to implement a standardized nomenclature for the rice two-component signaling elements.

In assigning gene symbols, we followed the rules for gene symbols in rice adapted from the 1986 report of the Committee on Gene Symbolization, Nomenclature, and Linkage (the November 7, 2005 draft document is available at http://www.gramene.org/documentation/nomenclature/). Thus all gene symbols are given in italics with the first letter capitalized. Although not shown in the tables , the protein symbol should be identical to the adopted gene symbol, the only difference being that it is written using all uppercase characters in italics followed by the numeric locus identifier. Precedence of publication was the primary determinant of the gene symbol and, whenever possible, we used the same gene symbol for all related genes. Additional symbols for the same gene were assigned as synonyms. A rice designation (e.g. Os) is not part of the gene symbol but may be added when needed to differentiate between similar genes of other species.

The His-containing phosphotransfer proteins are given the gene symbol Ahp (authentic His-containing phosphotransfer protein) if they contain the conserved His residue that is phosphorylated, and the gene symbol Php (pseudo His-containing phosphotransfer protein) if they lack the conserved His. These new symbols are in accordance with nomenclature for genes encoding response regulators (see below), and will simplify discussion of the His-containing phosphotransfer proteins because the symbols carry information related to function.

The rice response regulators are given the gene symbol Rr if they contain the conserved Asp that serves as the phosphorylation site (Jain et al., 2006), and the gene symbol Prr if they lack the conserved Asp (Murakami et al., 2003). The rice response regulators are numbered according to type (the gene symbols for type A starting from Rr1, type B starting from Rr21, and type C starting from Rr41), such that if additional response regulators of each type are found in annotation of the genome, they may still be numbered in sequence with their more closely related sequences. Note that we are using the same definition of the type A response regulators as that employed for Arabidopsis (short N- and C-terminal extensions in addition to the receiver domain, related at the sequence level based on phylogenetic analysis, and induced by cytokinin). The type B response regulators are transcriptional regulators with C-terminal extensions containing a Myb-like DNA-binding domain, although it should be pointed out that there is substantial sequence variation among the rice Myb-like motifs. We also introduce the term type C response regulator to refer to OsRr41 and 42 (along with AtARR22 and 24) which, although the proteins lack long C-terminal extensions, are not closely related to the type A response regulators based on phylogenetic analysis (Schaller et al., 2002).

	FOOTNOTES

 
www.plantphysiol.org/cgi/doi/10.1104/pp.106.093666

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