Elsevier

Plasmid

Volume 60, Issue 3, November 2008, Pages 167-173
Plasmid

Review
Revised nomenclature for transposable genetic elements

https://doi.org/10.1016/j.plasmid.2008.08.001Get rights and content

Abstract

Transposable DNA elements occur naturally in the genomes of nearly all species of prokaryotes. A proposal for a uniform transposable element nomenclature was published prominently in the 1970s but is not, at present, available online even in abstract form, and many of the newly discovered elements have been named without reference to it. We propose here an updated version of the original nomenclature system for all of the various types of prokaryotic, autonomous, transposable elements excluding insertion sequences, for which a nomenclature system already exists. The use of this inclusive and sequential Tn numbering system for transposable elements, as described here, recognizes the ease of interspecies spread of individual elements, and allows for the naming of mosaic elements containing segments from two or more previously described types of transposons or plasmids. It will guard against any future need to rename elements following changes in bacterial nomenclature which occurs constantly with our increased understanding of bacterial phylogenies and taxonomic groupings. It also takes into account the increasing importance of metagenomic sequencing projects and the continued identification of new mobile elements from unknown hosts.

Introduction

Reports of prokaryotic transposable elements proven by experiment or inferred from sequence homology or their diverse positions in prokaryotic genomes (bacterial and archaeal) have proliferated dramatically in the last two decades (Berg and Howe, 1989, Craig et al., 2002). Although classical elements, such as insertion sequences (IS), comprise only a small fraction (less than 1–2%) of the genomes of Escherichia coli and many other microbial species, no obvious uniform rule appears to determine their distribution; for example early studies showed that IS1-like elements were far more abundant in certain strains of Shigella than in closely related E. coli strains (Ohtsubo et al., 1981). When all potential mobile elements or foreign DNA within a particular genome are considered, they can make up much of that genome. For example, sequencing projects have revealed that mobile elements comprise approximately 11% and 25% of the genome of strains of Clostridium difficile and Enterococcus faecalis, respectively (Sebaihia et al., 2006, Paulsen et al., 2003). Recently analysis of the genome sequence of Orientia tsutsugamushi revealed that 46.7% of the genome was occupied by sequences derived from an integrative and conjugative element (ICE), 10 types of transposable element and other repetitive regions of unknown origin (Nakayama et al., 2008).

Transposons are borne both by plasmids and the chromosome and have an enormous variation in their genetic organization, the genes responsible for their insertion and excision and in the accessory or passenger genes they carry. Transposable elements are also able to interact, by recombination between elements and/or by transposition into other elements, forming novel chimeric elements.

Given the many genome sequencing projects now underway or planned, there is good reason to believe that new transposable elements will continue to be discovered. Although a proposal for a uniform bacterial transposable element nomenclature had been developed and published 30 years ago (Campbell et al., 1979a, Campbell et al., 1979b), that proposal is not available online and many newly discovered elements have been named without reference to it. In consequence, a myriad of systems have been devised for naming newly discovered prokaryotic transposable elements, which has resulted in a complex and potentially confusing array of names. Much as at the beginning of the transposable element era, nearly 40 years ago, we believe that scientific understanding would benefit from re-implementation of a universal system for naming new transposable elements.

Section snippets

A historical perspective

A committee assembled during the meeting on DNA Insertions at Cold Spring Harbor in 1976 proposed a set of rules to be used for the nomenclature of transposable elements. These rules were themselves modified from an initial proposal from D.E. Berg and W. Szybalski (Department of Biochemistry and the McArdle Laboratory for Cancer Research, respectively, University of Wisconsin, USA; Campbell et al., 1977). They were revised further to cope with, and include, the then recent development of DNA

Definition of transposable elements

Transposable elements will be defined as “specific DNA segments that can repeatedly insert into one or more sites in one or more genomes”. This definition is modified from that used in the original nomenclature proposal (Campbell et al., 1979a, Campbell et al., 1979b) to allow it to include the many different types of transposable elements that have been discovered since that proposal was published.

The movement of most of the elements used in formulating the original definition was mediated by

Proposed nomenclature system

It is proposed that newly discovered bacterial and archaeal autonomous transposable elements (unit and composite transposons, mobilizable transposons/integrative mobilizable elements, conjugative transposons/integrative conjugative elements and mobile genomic islands; see Table 1 for definitions) be designated with a sequential Tn number, written in italics to conform with previous guidelines, e.g. Tn3 or Tn5397. A registry for the assignment of Tn numbers has been set up on the UCL website (//www.ucl.ac.uk/eastman/tn/

Conclusions and perspectives

The issue of nomenclature for any group of entities, transposable elements included, is often subject to lively discussion. In an earlier system for new integrative and conjugative elements, Burrus et al. (2002) proposed to use the prefix ICE followed by the initials of the name of the bacterial genus and species and a number corresponding to the rank of the discovery (e.g. ICESt1 for the first ICE found in Streptococcus thermophilus). Subsequently, Burrus et al. (2006a) further proposed

Acknowledgments

The authors dedicate this review to the memory of Dr. Esther Lederberg.

We thank M. Osborn, A. Salyers, V. Burrus and numerous colleagues for helpful and insightful suggestions and discussions regarding the nomenclature system and the website. Special thanks to S. Jancich and K. Widdowson for the setting up of the Transposon Registry Web pages.

The following funding is gratefully acknowledged: US National Institutes of Health (DK63041; D.E. Berg); CNRS intramural funding (M. Chandler); BBSRC, MRC

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