Conformational Toggling Controls Target Site Choice for the Heteromeric Transposase Element Tn7

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2015 Sep 19

PMID 26384427

Citations 15

Authors

Qiaojuan Shi

Marco R Straus

Jeremy J Caron

Huasheng Wang

Yu Seon Chung

Alba Guarne

Joseph E Peters

Affiliations

Soon will be listed here.

Abstract

The bacterial transposon Tn7 facilitates horizontal transfer by directing transposition into actively replicating DNA with the element-encoded protein TnsE. Structural analysis of the C-terminal domain of wild-type TnsE identified a novel protein fold including a central V-shaped loop that toggles between two distinct conformations. The structure of a robust TnsE gain-of-activity variant has this loop locked in a single conformation, suggesting that conformational flexibility regulates TnsE activity. Structure-based analysis of a series of TnsE mutants relates transposition activity to DNA binding stability. Wild-type TnsE appears to naturally form an unstable complex with a target DNA, whereas mutant combinations required for large changes in transposition frequency and targeting stabilized this interaction. Collectively, our work unveils a unique structural proofreading mechanism where toggling between two conformations regulates target commitment by limiting the stability of target DNA engagement until an appropriate insertion site is identified.

Citing Articles

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Structure of TnsABCD transpososome reveals mechanisms of targeted DNA transposition.

Wang S, Siddique R, Hall M, Rice P, Chang L Cell. 2024; 187(24):6865-6881.e16.

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References

Rao J, Craig N . Selective recognition of pyrimidine motif triplexes by a protein encoded by the bacterial transposon Tn7. J Mol Biol. 2001; 307(5):1161-70. DOI: 10.1006/jmbi.2001.4553. View

Holm L, Rosenstrom P . Dali server: conservation mapping in 3D. Nucleic Acids Res. 2010; 38(Web Server issue):W545-9. PMC: 2896194. DOI: 10.1093/nar/gkq366. View

Finn J, Parks A, Peters J . Transposon Tn7 directs transposition into the genome of filamentous bacteriophage M13 using the element-encoded TnsE protein. J Bacteriol. 2007; 189(24):9122-5. PMC: 2168609. DOI: 10.1128/JB.01451-07. View

Wolkow C, Deboy R, Craig N . Conjugating plasmids are preferred targets for Tn7. Genes Dev. 1996; 10(17):2145-57. DOI: 10.1101/gad.10.17.2145. View

Parks A, Li Z, Shi Q, Owens R, Jin M, Peters J . Transposition into replicating DNA occurs through interaction with the processivity factor. Cell. 2009; 138(4):685-95. PMC: 2752310. DOI: 10.1016/j.cell.2009.06.011. View

Fodje M, Grochulski P, Janzen K, Labiuk S, Gorin J, Berg R . 08B1-1: an automated beamline for macromolecular crystallography experiments at the Canadian Light Source. J Synchrotron Radiat. 2014; 21(Pt 3):633-7. DOI: 10.1107/S1600577514005578. View

Krissinel E, Henrick K . Inference of macromolecular assemblies from crystalline state. J Mol Biol. 2007; 372(3):774-97. DOI: 10.1016/j.jmb.2007.05.022. View

Haines A, Jones K, Batt S, Kosheleva I, Thomas C . Sequence of plasmid pBS228 and reconstruction of the IncP-1alpha phylogeny. Plasmid. 2007; 58(1):76-83. DOI: 10.1016/j.plasmid.2007.01.001. View

Flores C, Qadri M, Lichtenstein C . DNA sequence analysis of five genes; tnsA, B, C, D and E, required for Tn7 transposition. Nucleic Acids Res. 1990; 18(4):901-11. PMC: 330344. DOI: 10.1093/nar/18.4.901. View

10.

McKown R, Waddell C, Arciszewska L, Craig N . Identification of a transposon Tn7-dependent DNA-binding activity that recognizes the ends of Tn7. Proc Natl Acad Sci U S A. 1987; 84(22):7807-11. PMC: 299398. DOI: 10.1073/pnas.84.22.7807. View

11.

Peters J, Fricker A, Kapili B, Petassi M . Heteromeric transposase elements: generators of genomic islands across diverse bacteria. Mol Microbiol. 2014; 93(6):1084-92. DOI: 10.1111/mmi.12740. View

12.

Rao J, Miller P, Craig N . Recognition of triple-helical DNA structures by transposon Tn7. Proc Natl Acad Sci U S A. 2000; 97(8):3936-41. PMC: 18120. DOI: 10.1073/pnas.080061497. View

13.

Yang F, Yang J, Zhang X, Chen L, Jiang Y, Yan Y . Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res. 2005; 33(19):6445-58. PMC: 1278947. DOI: 10.1093/nar/gki954. View

14.

Roche D, Flechard M, Lallier N, Reperant M, Bree A, Pascal G . ICEEc2, a new integrative and conjugative element belonging to the pKLC102/PAGI-2 family, identified in Escherichia coli strain BEN374. J Bacteriol. 2010; 192(19):5026-36. PMC: 2944505. DOI: 10.1128/JB.00609-10. View

15.

Fricker A, Peters J . Vulnerabilities on the lagging-strand template: opportunities for mobile elements. Annu Rev Genet. 2014; 48:167-86. DOI: 10.1146/annurev-genet-120213-092046. View

16.

Chivers P, Sauer R . NikR repressor: high-affinity nickel binding to the C-terminal domain regulates binding to operator DNA. Chem Biol. 2002; 9(10):1141-8. DOI: 10.1016/s1074-5521(02)00241-7. View

17.

Peters J, Craig N . Tn7 recognizes transposition target structures associated with DNA replication using the DNA-binding protein TnsE. Genes Dev. 2001; 15(6):737-47. PMC: 312648. DOI: 10.1101/gad.870201. View

18.

Peters J . Tn7. Microbiol Spectr. 2015; 2(5). DOI: 10.1128/microbiolspec.MDNA3-0010-2014. View

19.

Yamauchi M, Baker T . An ATP-ADP switch in MuB controls progression of the Mu transposition pathway. EMBO J. 1998; 17(18):5509-18. PMC: 1170876. DOI: 10.1093/emboj/17.18.5509. View

20.

Ramirez M, Quiroga C, Centron D . Novel rearrangement of a class 2 integron in two non-epidemiologically related isolates of Acinetobacter baumannii. Antimicrob Agents Chemother. 2005; 49(12):5179-81. PMC: 1315932. DOI: 10.1128/AAC.49.12.5179-5181.2005. View