The F plasmid CcdB protein induces efficient ATP-dependent DNA cleavage by gyrase.

DNA topoisomerases perform essential roles in DNA replication, gene transcription, and chromosome segregation. Recently, we identified a new type of topoisomerase II poison: the CcdB protein of plasmid F. When its action is not prevented by CcdA protein, the CcdB protein is a potent cytotoxin. In this paper, using purified CcdB, CcdA and gyrase, we show that CcdB protein efficiently traps gyrase in a cleavable complex. The CcdA protein not only prevents the gyrase poisoning activity of CcdB but also reverses its effect on gyrase. The mechanism by which the CcdB protein induces DNA strand breakage is closely related to the action of quinolone antibiotics. However, the ATP dependence of the CcdB cleavage process differentiates the CcdB mechanism from quinolone-dependent reactions because the quinolone antibiotics stimulate efficient DNA breakage, whether or not ATP is present. We previously showed that bacteria resistant to quinolone antibiotics are sensitive to CcdB and vice versa. Elucidation of the mechanism of action of CcdB protein may permit the design of drugs targeting gyrase so as to take advantage of this new poisoning mechanism.Journal ArticleResearch Support, Non-U.S. Gov'tSCOPUS: ar.jinfo:eu-repo/semantics/publishe

Pattern Matching for k-Track Permutations

International audienceGiven permutations τ and π, the permutation pattern (PP) problem is to decide whether π occurs in τ as an order-isomorphic subsequence. Although an FPT algorithm is known for PP parameterized by the size of the pattern |π| [Guillemot and Marx 2014], the high complexity of this algorithm makes it impractical for most instances. In this paper we approach the PP problem from k-track permutations, i.e. those permutations that are the union of k increasing patterns or, equivalently, those permutation that avoid the decreasing pattern (k+1)k…1. Recently, k-track permutations have been shown to be central combinatorial objects in the study of the PP problem. Indeed, the PP problem is NP-complete when π is 321-avoiding and τ is 4321-avoiding but is solvable in polynomial-time if both π and τ avoid 321. We propose and implement an exact algorithm, FPT for parameters k and |π|, which allows to solve efficiently some large instances