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Mechanistic basis of plasmid-specific DNA binding of the F plasmid regulatory protein, TraM

  • Author / Creator
    Peng, Yun
  • The conjugative transfer of bacterial F plasmids relies on TraM, a plasmid-encoded protein that recognizes multiple DNA sites to recruit the plasmid to the conjugative pore. In spite of the high degree of amino acid sequence conservation between TraM proteins, many of these proteins have markedly different DNA binding specificities that ensure the selective recruitment of a plasmid to its cognate pore. Here we present the structure of F TraM RHH (ribbon-helix-helix) domain bound to its sbmA site. The structure indicates a pair of TraM tetramers cooperatively binds an underwound sbmA site that contains 12 base pairs/turn. The sbmA is composed of 4 copies of a 5 base pair motif, each of which is recognized by an RHH domain. The structure reveals that a single conservative amino acid difference in the RHH β-ribbon between F and pED208 TraM changes its specificity for its cognate 5 base pair sequence motif. Specificity is also dictated by the positioning of 2 base pair spacer elements within sbmA; in F sbmA, the spacers are positioned between motifs 1 and 2 and motifs 3 and 4, whereas in pED208 sbmA there is a single spacer between motifs 2 and 3. We also demonstrate that a pair of F TraM tetramers can cooperatively bind its sbmC site with an affinity similar to that of sbmA, in spite of a lack of sequence similarity between these DNA elements. These results provide a basis for the prediction of the DNA binding properties of the family of TraM proteins.

  • Subjects / Keywords
  • Graduation date
    2014-11
  • Type of Item
    Thesis
  • Degree
    Master of Science
  • DOI
    https://doi.org/10.7939/R3TM28
  • License
    This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
  • Language
    English
  • Institution
    University of Alberta
  • Degree level
    Master's
  • Department
    • Department of Biochemistry
  • Supervisor / co-supervisor and their department(s)
    • Glover, Mark
  • Examining committee members and their departments
    • MacMillan, Andrew (Biochemistry)
    • Fahlman, Richard (Biochemistry)
    • Raivio, Tracy (Biological Sciences)