Nomenclature for bacterial genes coding for class-II restriction endonucleases and modification methyltransferases

APPENDICES

219

Gene. 74 (1988) 279-280 Elsevier GEN 02779

Nomenclature for bacterial genes coding for class-II restriction endonucleases and modification methyltransferases * (Recombinant DNA; R-M enzymes; gene cloning; alleles; mutants; polypeptide subunits)

W. Szybalski *, R.M. Blumenthal b, J.E. Brooks c, S. Hattman d and E.A. Raleigh e a McArdle Laboratoryfor Cancer Research, Universityof Wisconsin,Madison, WI 53706 (U.S.A.); b Medical College of Ohio, C.S. No. 10008, Toledo, OH 43699 (U.S.A.) Tel. (419)381-5422;‘New England Biolabs. Beverly, MA 01915-9990 (U.S.A.) Tel. (800)632-5227; d Biology Department, Universityof Rochester, Rochester, NY 14627 (U.S.A.) Tel. (716)275-3846 Received 20 July 1988 Accepted 9 September 1988 Received by publisher 19 September 1988

A system of nomenclature for DNA restriction and modification enzymes was proposed by Smith and Nathans (1973) and has been generally accepted with only minor exceptions. Under these rules, the first three letters (in italics) reflect the genus and species name (e.g., Eco corresponds to Escherichia and Hpa corresponds to Haemophilus coli, paraintuenzae) and are followed (without any intervening space) by roman numerals (I, II, III etc.), which indicate different enzymes produced by the same strain. The enzyme name might include additional symbols before the reman numerals corresponding to the particular strain designations. In the original proposal, the capital letter R or M (followed by a raised dot, i.e., R-, MS) was placed in front of the enzyme symbol, to specify the restriction endonuclease or modification methyltransferase, respectively. However, in the current short-hand usage

Correspondence to: Dr. W. Szybalski, McArdle Laboratory, University of Wisconsin, Madison, WI 53706 (U.S.A.) Tel. (608)262-1259, Fax (608)262-2824. * Prepared by the Editors of the New England Biolabs Workshop on Biological DNA Modification, Gloucester, MA (U.S.A.) 20-23 May, 1988, in consultation with: Drs. W. Arber, F. Barany, T.A. Bickle, C. Kessler, N.E. Murray, D. Nathans, A.J. Podhajska, R.J. Roberts, I. Schildkraut, H.O. Smith and T.A. Trautner. This proposal was adopted for this issue of Gene. The question of nomenclature was not discussed at the Workshop. The authors recognize the need for a more comprehensive system than that proposed here. 0378-l 119/88/$03.50

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the letter R* is used rarely; thus the symbol, HpaII denotes the restriction endonuclease, whereas M * HpaII designates the corresponding modification methyltransferase. There exist extensive compilations of the restriction and modification enzymes, and they generally follow the original Smith and Nathans (1973) proposal (Roberts, 1988; Kessler and Holtke, 1986). Because of recent interest in the cloning of genes coding for restriction and modification enzymes, produced by a great variety of species, there appears to be a need for a simple and informative genetic nomenclature, which in general should reflect the original Demerec et al. (1966) proposal (see also Bachmann, 1983; Bhagwat and Person, 1981; Novick et al., 1976). This is the first attempt to name the genes, according only to their specific products, and without regard to the species. The present proposal applies to all prokaryotes and eukaryotes producing class-II restriction-modification enzymes. The first three letters of the gene designation according to the rules of Demerec et al. (1966) should all be in lower-case italicized letters (e.g., lac), and they usually relate to the general function of the gene or its product. The fourth letter (capital, italics, e.g., in lacZ) identifies the specific gene function and is followed by an allele or mutant number; this fourth letter is sometimes replaced by a hyphen. Strict adherence to these conventions is not possible in the case of the restriction-modification systems, if clarity usuaIIy

Division)

280 TABLE I Examples of gene designations for the class-11 restriction and modification enzymes Restriction enzyme a

Gene

Modification enzyme *

Gene

Alar1 Eco241 Eco47I &04X1 EcoRI EwRV Hind111 Suu 3AI 7?hHB81

aluIR eco24IR eco47iR ew47IIR ecoRiR ecoRYR AindIHR sau3AIR tthH38IR

M.AlUI

aluIM

not described not described not described M *EcoRI M *EcoRV M *HindIII M *Snu3AI M +TthHB81

eco24IM ew47IM eco47IIM

ecoRIM ecoRVM hindIIIM sau3AIM tthHI38IM

* See Kessler and HBltke (1986) and Roberts (1988).

and generality are desired for genes of many species coding for a multitude of already described enzymes. We propose instead that the gene should be named by a combination of the Demerec et al. (1966) rules and the conventions presently used to name the class-II restriction enzymes, but with the following changes: (I) the entire gene designation will be italicized; (2) the first letter will be in lower case; (3) the capital letters R or M (referring to the restriction endonuclease or modification methyltransferase) will follow, rather than precede, the rest of the gene designation. Examples of gene designations are listed in Table I. Thus the last symbol (right ‘boundary’) of the gene designation will be letter R or A4, which will then be followed by a non-italicized arabic number indicating the allele or mutant. This will help to distinguish clearly between the gene symbol and the allele or mutant designation. It is hoped that some strain-related designations (symbols between the first three letters and the letter R or M) could be simplified, and gene designations

could be incorporated into future editions of the compilations by Roberts and by Kessler and his colleagues (Roberts, 1988; Kessler and Holtke, 1986). Our proposal does not include any specilic suggestions how to simplify the enzyme (and gene) designations, but we realize that these are urgently needed. We propose that any generally accepted changes in restriction enzyme nomenclature should be automatic~y translated into corresponding changes in the gene nomenclature, as per the above guidelines. The principle of this nomenclature could be extended to genes coding for the class-I, class-III and other restriction and/or modification enzymes, including phage/~rus-coded and other (e.g., Dam and Dcm) DNA modification methyltransferases (without cognate restriction endonucleases), but it is necessary to take into consideration that some of these are composed of different polypeptide subunits and already have an established genetic nomenclature.

REFERENCES Bachmann, B.J.: Linkage map ofE~cheti&o co&K-12, edition 7. Microb. Rev. 47 (1983) 180-230. Bhagwat, A.S. and Person, S.: Structure and properties of the region ofhomology between plasmids pMB 1 and ColE 1. Mol. Gen. Genet. 182 (1981) 505-507. Demerec, M., Adelberg, E.A., Clark, A.J. and Hartman, P.E.: A proposal for a uniform nomenclature in bacterial genetics. Genetics 54 (1966) 61-76. Kessler, C. and Holtke, H.-J.: Specificity of restriction endonucleases and methylases - a review (Edition 2). Gene 47 (1986) l-153. Novick, R.P., Cloves, R.C., Cohen, S.N., Curtiss, III, R., Datta, N. and Falkow, S.: Uniform nomenclature for bacterial plasmids, a proposal. Bacterial. Rev. 40 (1976) 168-189. Roberts, R.J.: Restriction enzymes and their isoschizomers, Nucleic Acids Res. 16 (1988) r271-r313. Smith, H.O. and Nathans, D.: A suggested nomenclature for bacterial host modification and restriction systems and their enzymes. J. Mol. Biol. 81 (1973) 419-423.