A new nomenclature for the cytoplasmic ribosomal proteins of Saccharomyces cerevisiae
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A new nomenclature for the cytoplasmic ribosomal proteins of Saccharomyces cerevisiae
A new nomenclature for the cytoplasmic ribosomal proteins of Saccharomyces cerevisiae
W. H. Mager, R. J. Planta*, J.-P. G. Ballesta1, J. C. Lee2, K. Mizuta3, K. Suzuki4, J. R. Warner5 and J. Woolford6
Department of Biochemistry and Molecular Biology, Vrije Universiteit, de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands, 1Centro de Biologia Molecular, Universidad Autonoma de Madrid, Canto Blanco, 28049 Madrid, Spain, 2University of Texas, Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78284-7760, USA, 3Faculty of Engineering, Hiroshima University, 4-1, Kagamiyama 1 chome, Higashi-Hiroshima 739, Japan, 4Department of Biochemistry and Biophysics, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734, Japan, 5Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA and 6Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
Received November 3, 1997; Accepted November 3, 1997
ABSTRACT
The availability of the complete sequence of the Saccharomyces cerevisiae genome has allowed a comprehensive analysis of the genes encoding cytoplasmic ribosomal proteins in this organism. On the basis of this complete inventory a new nomenclature for the yeast ribosomal proteins is presented.
In the past, cytoplasmic ribosomal proteins of the yeast Saccharomyces cerevisiae have been characterized using different two-dimensional electrophoretic separation methods. As a consequence, at least three different nomenclatures for yeast ribosomal proteins came into existence, viz. according to Kruiswijk and Planta (1 ), Warner and Gorenstein (2 ), and Otaka and Osawa (3 ), as indicated in Table 1 , second column, from left to right, respectively. Attempts to correlate these different nomenclatures have only partly been successful (4 ).
Table 1 . Nomenclature for cytoplasmic ribosomal proteins of S.cerevisiae
Screening of the complete sequence of the S.cerevisiae genome by a combination of in silicio and transcriptional analysis has made it possible to compile a comprehensive list of the genes encoding cytoplasmic ribosomal proteins in this organism (see ref. 5 for full details). The yeast genome appears to contain 137 genes encoding 78 different ribosomal proteins (59 genes are duplicated), 32 of the small subunit and 46 of the large subunit. All yeast ribosomal proteins have a mammalian counterpart. However, there is no yeast equivalent of rat ribosomal protein L28.
Therefore, we are now in a position to propose a new, unequivocal nomenclature, as presented in Table 1 . Reflecting the remarkable conservation of eukaryotic ribosomal proteins, this numbering system follows as closely as possible the nomenclature for mammalian ribosomal proteins (6 ); 64 of the yeast ribosomal proteins are proposed to be (re-)numbered according to their rat counterpart. Since many of the yeast ribosomal protein genes are duplicated and hence have to be distinguished by adding an `A' or `B', we have avoided the use of an additional `a' as occasionally applied in the rat rp-nomenclature. This also allowed us to fill in the gaps that exist in the numbering of the rat ribosomal proteins.
We urge our colleagues to use the new nomenclature in all papers to be submitted after January 1, 1998. To facilitate the changeover, it is advisable to add, between brackets, the previously used designations for a period of at least 1 year.
The genes should be indicated as, e.g., RPS6A, RPS6B, RPL26A, etc., the proteins as rpS6A, rpS6B, rpL26A, etc. In cases where the duplicate copies of a ribosomal protein are, despite strong structural similarity, not completely functionally equivalent [as for instance the acidic ribosomal proteins P1 and P2 (7 )] the alternative use of Greek letters to distinguish these protein copies (rpP1[alpha], rpP1[beta]) can be considered.
The list of yeast cytoplasmic ribosomal protein genes can be found at MIPS Website (http://www.mips.biochem.mpg.de/mips/yeast/index.html).
1 Kruiswijk,T. and Planta,R.J. (1974) Mol. Biol. Rep. 1, 409-415.
2 Warner,J.R. and Gorenstein,C.G. (1978) In Prescott,D.M. (ed.) Methods in Cell Biology, Academic Press, New York, Vol. 20, pp. 45-60.
3 Otaka,E. and Osawa,S. (1981) Mol. Gen. Genet., 181, 176-182.
4 Michel,S., Traut,R.R. and Lee,J.C. (1983). Mol. Gen. Genet., 191, 251-256.
5 Planta,R.J. and Mager,W.H. (1997) Yeast , in press.
6 Wool,I.G., Chan,Y-L. and Glück,A. (1995) Biochem. Cell Biol., 73, 933-947.
7 Remacha,M., Jimenez-Diaz,A., Bermejo,B., Rodriguez-Gabriel,M.A., Guarinos,E. and Ballesta,J.P.G. (1995) Mol. Cell. Biol., 15, 4754-4762.
*To whom correspondence should be addressed. Tel: +31 20 444 7548; Fax: +31 20 444 7553; Email: brink{at}chem.vu.nl
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