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Nomenclature of Transposable Elements in Prokaryotesl

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Nomenclature of Transposable Elements in Prokaryotesl PLASMID 2, 466-473 (1979) Nomenclature of Transposable Elements in Prokaryotesl A. CAMPBELL P. STARLINGER Department of Biological Sciences, Stanford lnstitut fur Genetik, Universitiit zu Koln, University, Stanford California 94305 D-500 Koln, West Germany D. E. BERG D. BOTSTEIN Department of Microbiology and Immunology, Department of Biology, Massachusetts Washington University, St. Louis, Institute of Technology, Cambridge, Missouri 63110 Massachusetts 02139 E. M. LEDERBERG R. P. NOVICK Department of Medical Microbiology, Public Health Research Institute of the City of Stanford University School of New York, New York, New York 10016 Medicine, Stanford, California 94305 AND W. SZYBALSKI McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin 53706 ReceivedMarch 21, 1979 Transposable elements are defined as specific DNA segments that can repeatedly insert into a few or many sites in a genome. They are classified as simple IS elements, more complex Tn transposons, and self-replicating episomes. Definitions and nomenclature rules for these three classes of prokaryotic transposable elements are specified. I. INTRODUCTION modified in light of more recent develop- ments. The most important relevant tech- At the Cold Spring Harbor meeting on nical advances have been in the area of DNA insertions, a committee was elected nucleotide sequencing. In 1977, it seemed to draft a set of rules for nomenclature necessary that the primary operational (Campbell et al., 1977), These rules were definition for relatedness of two genetic based on discussions held at the meeting elements should be descent from a common and on previously accepted conventions for ancestor. Two elements should be identical the Mu prophage (Howe and Bade, 1975), (or at least very similar) if descended in the for bacterial plasmids (Novick et al., 1976), laboratory from the same natural source. for bacteriophage A (Hershey, 1971), and for They are potentially different if derived bacterial genetics (Demerec et al., 1966). from different sources. Common descent This article is a revised version of the becomes superhuous when complete nucleo- original report (Campbell et al., 1977) tide sequences of both elements are known (except insofar as the sequence of the ele- I In order to obtain wide distribution, this paper is ment used in a given experiment is gen- being published concurrently in Gene, Vol. 5 (1979) No. 4. Suggestions for changes and amendments in erally inferred from that of some ancestor future versions of theserules should be directed to the on which the sequencing was performed). first author. Elements known to be identical in sequence 0147-619X/79/030466-08$02.00/0 466 Copyright 0 1979 by Academic Press, Inc. All rights of reproduction in any form reserved. NOMENCLATURE OF TRANSPOSABLE ELEMENTS 467 clearly should have the same name, even at random, to phage h, which usually, but when independently derived. not always, inserts at a single site in the Because of the range in size of known Escherichiu coli genome. Some (such as transposable elements (from 0.8 kb for IS2 A) have free phases that have been iden- to over 100 kb for some of the conjugative tified (e.g. intracellular replicons or extra- plasmids) we can anticipate an extended cellular viruses), whereas others (such as interval in which some of the shorter ele- the IS or Tn elements) are presently known ments (and perhaps numerous isolates only in the inserted state. thereof) will have been completely se- quenced, while sequence data on the larger III. CLASSES OF TRANSPOSABLE elements is still incomplete. We therefore ELEMENTS retain common descent as the only cri- terion for relatedness that is directly ap- ZZZ.A-l. IS Elements plicable to all transposable elements recog- nizing where appropriate the implications IS (Simple Insertion Sequences) elements of sequence information. contain no known genes unrelated to in- In the following report, the rules are pre- sertion function and are generally shorter sented in boldface type. Adherence to these than 2 kb. rules in all publications about inserting ele- ments is highly desirable. Interspersed with ZZZ.A-2. Symbols the rules are some comments, which include ISI, IQ, 1!33, I!34, IS5, etc. with the discussion and explanation of the rules, and also suggestions for possible usage in some numbers italicized. (Fiandt et al., 1972; Hirsch et al., 1972; MaIamy et al., 1972). cases not covered by the rules. The rules are intended to be minimal and applica- ZZZ.A-3. Comments ble to current or clearly imminent situations. We have not tried to anticipate problems At present, the IS elements listed above that may arise far in the future. We have are not known to contain any genes, either also avoided prescribing rules for problems related or unrelated to insertion function. that arise currently but rarely. Many of these Our intention in specifying “genes un- are best treated on an individual basis related to insertion function” is that even relevant to specific needs. if insertion genes should be discovered in some IS elements, they still would be II. TRANSPOSABLE ELEMENTS classified as simple insertion sequences. ZZ. A. Definition The term “gene” as used here means a DNA segment coding for a functional Transposable elements2 are specific DNA product and does not include, e.g., the “stop segmentsthat can repeatedly insert into a few signals” responsible for polar effects of IS or many sites in a genome. elements or promoters allowing IS elements to turn on adjacent genes. ZZ. B. Comments Operationally, the failure to detect other The definition applies to elements rang- genes in IS elements is closely tied to the ing from phage Mu, which seems to insert absence of a recognizable phenotype con- ferred by their presence. The only ob- served consequences of IS insertion are * The term “transposable element” is derived from cis-specific effects, such as changes in gene the work of McClintock (1952) on mobile genetic ele- ments in maize. In prokaryotes, an acceptable expression due to insertion within an operon, synonym is “translocation sequence” (Novick et or the rate of incidence of adjacent dele- al., 1976). tions. Effects other than c&specific ones 468 CAMPBELL ET AL. are expected to be unobservable because complete base sequence of an IS insert has of the endogenous origin of IS elements. been determined, either it will prove They are always present in the cell, not only identical to some previously sequenced at the site under examination, but at other, insert or else minor variations in base generally unidentified sites as well. One or sequence may come to light. Here again it is more copy of each of the common IS ele- desirable to assign specific designations so ments is present in the E. coli genome. The that all inserts with identical sequences have phenotype of E. co/i lacking, for example, the same designation and are distinguished IS1 is unknown. from those known to differ from them. Because several copies of each element are present in the genome, it is currently ZZZ.B-l. Tn Elements (transposons) impossible to trace the lineage of a given IS element. When IS2 appears at a new site, Tn are more complex transposable ele- we cannot say which of the several pre- ments, often containing two IS elements. existing IS2s is ancestral to it. It must They behave formally like IS elements but therefore clearly be borne in mind that a are generally larger than 2 kb and contain name such as IS2 is a generic term referring additional genes unrelated to insertion to all insertions that appear indistinguish- function. able by hybridization, heteroduplexing, or restriction analysis, but which could have 111.B-2. Symbols individual differences in base sequence and Tnl , Tn2, Tnl, etc. with the numbers which might have undergone mutations or italicized. A different number is assigned to rearrangements in the laboratory (see IV. E) . each independent isolate from nature even if There is presently no advantage to giving it is apparently identical to some previous each IS2 in a different location a specific isolate by criteria other than direct de- as well as a generic name. Such a designa- termination of nucleotide sequence. If the tion would provide no additional informa- complete nucleotide sequenceof a new isolate tion not already given by the mutation is shown to be identical to that of some pre- number (see below) that identifies the in- vious isolate, the element should be designated sertion event. This situation may change in by the symbol assigned to the first isolate the future for two reasons: (1) IS2 elements with that sequence. If useful in a particular may be introduced into species from which context, genes carried by a Tn element may they are naturally absent. IS2, for example, be indicated following the name; e.g., Tn9 is said to be absent from Salmonella cam+ [Tn9 is a transposable element that typhimurium. If a single copy of IS2 is intro- confers chloramphenicol resistance (cam+)]. duced into S. typhimurium, then all sub- Mutations in Tn elements are designated by sequent transpositions within that species standard genetic symbols following the name must be derived from that specific IS2. If of the element, e.g., Tn!J cam4 is a particular and when such experiments are performed, mutant of Tn9 that no longer confers all IS2s derived from an identified IS2 in- chloramphenicol resistance. sertion should be assigned a specific desig- nation (e.g., IS2.1) to distinguish them from ZZZ.B-3. Comments IS2 insertions derived from another, po- tentially different source. (2) Laboratory Unlike IS elements, the lineage of Tn mutants of IS elements recognizably dif- elements generally can be followed unam- ferent from wild type have been isolated. biguously. Hence TnZ , Tn2, etc. are specific For example, Tomich and Friedman (1977) rather than generic terms.
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