J. Mol. Biol. (1982) 159, 557-580 Structure and Stability of Transposon 5-Mediated Cointegrates BERNARD J. HIRSCHEL, DAVII) J. GAI,Ast Division of Infectious Diseases, Department of Medicine University Hospital, 1211 Geneva 4, Switzerland DOVGLAS E. BEKC: Department of Microbiology and Immunology Washington University, St Louis MO. 63110, U.S.A. ANI) MICHAEL CHANDLER Zjepartment of Molecular Biology, University of Geneva Geneva. Switzerland (Received I1 January 1982) We have determined the structure of a set of independently derived. TnS-mediated cointegrates and examined the stability of several examples. A variety of cointegrate structures was found, including those mediated by the entire compound transposon, and those mediated by a single flanking IS50 element, which was always ISSO-R, and never ISSO-L. 1&50-R but not ISSO-L is reported to code for a protein(s) required for transposition. This finding confirms that ISSO-L is relatively inactive and suggests that the active transposition protein(s) acts largely in cis on IS50-R. Another class of cointegrate was created by inverse transposition of Tn5 (using the inside ends of the flanking elements). In addition, we found an unexpectedly large set of cointegrates, in which the joint between the two plasmids was not adjacent to the transposon. All cointegrates analysed were found to be stable. This suggests that Tn5, unlike the transposon Tn3, does not transpose via an obligate cointegrate intermediate. This finding is compared to previous results with Tn5 and Tn9, and is discussed in terms of current models of transposition. 1. Introduction In addition to their ability to insert at different locations in the genomes of bacteria and phage, transposable elements are capable of mediating the fusion of replicons (cointegrate formation; Faelen et al., 1975; Gill et al., 1978; Ohtsubo et al., 1980). Cointegrates have a single copy of the element, in directly repeated orientation, at each juncture of the fused plasmids. Shapiro (1979) and Arthur & Sherratt (1979) have proposed that cointegrates are essential intermediates in transposition of an t Present address: Molecular Biology, ACBR 126, University of Southern California, Los Angeles. Calif. 90@07. V.S.A. 557 0022-2836/82/240557-24 $03.00/O 19 0 1982 Academic Press Inc. (London) LM.