The role of g-quadruplex DNA in borrelia burgdorferi antigenic variation

The National Institute of Allergy and Infectious Diseases awarded Northeastern University $100,228 on December 1, 2026, under the Allergy and Infectious Diseases Research program (CFDA 93.855) to investigate the role of G-quadruplex DNA structures in the antigenic variation mechanism of Borrelia burgdorferi, the causative agent of Lyme disease.

The research addresses the molecular mechanism by which B. burgdorferi evades host adaptive immune defenses through antigenic variation—reshaping outer surface epitopes during mammalian infection to hinder antibody-mediated clearance and enable persistent infection. The project implements the first tractable mutagenesis method for the vlse gene to reveal how B. burgdorferi mediates antigenic variation through genetic recombination. Work will quantify vlse gene conversion dynamics following genetic perturbations targeting G4 structures to determine their function in recombination. Proximity labeling in live B. burgdorferi cells identified DksA as a candidate vlse recombination factor; the research investigates whether G4s participate in antigenic variation by recruiting DksA to mediate vlse gene conversion.

Performance occurs in Boston, Massachusetts. The period of performance runs from December 1, 2026, through June 3, 2028. This is a Project Grant, a form of assistance funding supporting biomedical research in infectious diseases and related areas at public and private nonprofit institutions.

Abstract

To evade host adaptive immune defenses, pathogens such as borrelia burgdorferi, the agent of lyme disease, undergo antigenic variation by reshaping outer surface epitopes during mammalian infections. This process hinders antibody-mediated clearance and enables persistent infection. Lyme disease is the most prevalent vector-borne disease in the united states, and antigenic variation is crucial for b. Burgdorferi's transmission cycle in nature and chronic pathogenicity in humans. However, the molecular mechanism underlying antigenic variation in b. Burgdorferi remains unknown, presenting a critical research GAP with significant implications towards public health. B. Burgdorferi mediate antigenic variation through genetic recombination of the vlse gene, which encodes a key surface lipoprotein; multiple polymorphic VLS cassettes donate mutations into the vlse coding sequence to generate diverse antigenic isoforms. Interestingly, b. Burgdorferi contains a ~100-fold enrichment of g- quadruplex (G4) DNA sequences at the VLS locus over the rest of the genome. G4S are secondary nucleic acid structures that fold via hoogsteen base-pairing of guanines and are implicated in DNA recombination in bacteria, eukaryotes, and viruses, alike. Here, the principle investigator will implement the first method for tractable mutagenesis of vlse to reveal the molecular mechanism underlying b. Burgdorferi antigenic variation. Vlse gene conversion dynamics will be quantified following genetic perturbations targeting G4S to determine the function of these structures in recombination. Further, G4-targeted proximity labeling in live b. Burgdorferi cells identified dksa as a strong candidate vlse recombination factor. Therefore, G4S are hypothesized to participate in b. Burgdorferi antigenic variation via recruitment of dksa to mediate vlse gene conversion. The work proposed here investigates the coordinated activity of G4 DNA and dksa in vlse recombination. Aim 1 seeks to demonstrate the relationship between vlse G4 loci and recombination events to elucidate the mechanistic function of these structures. Aim 2 will test dksa's involvement in antigenic variation and G4-binding activity. Collectively, these aims will help uncover the molecular mechanism of antigenic variation in b. Burgdorferi, addressing a long-standing GAP in the knowledge of this bacterium's pathogenic mechanisms. The research in this training plan will be conducted under CO-mentorship by DR. Tovah day and DR. Constantin n. Takacs, experts in G4 biology and b. Burgdorferi genetics, respectively. This partnership was specifically established to answer this research question, which requires their specialized expertise across both of these distinct fields. Therefore, the research environment is uniquely suited to facilitate completion of the proposed training plan.