Skip to main content

National Institutes of Health

Eunice Kennedy Shriver National Institute of Child Health and Human Development

2023 Annual Report of the Division of Intramural Research

RNA–Mediated Gene Regulation in the Lyme Disease Pathogen

Philip Adams
  • Philip P. Adams, PhD, Head, Group on Gene Regulation in Bacterial Pathogens
  • Ryan Fishman, BS, Postbaccalaureate Intramural Research Training Award Fellow
  • Emily Petroni, BS, Postbaccalaureate Intramural Research Training Award Fellow
  • Julia Silberman, BS, Postbaccalaureate Intramural Research Training Award Fellow
  • Daniel Soliman, BS, Postbaccalaureate Intramural Research Training Award Fellow

The goal of this research is to identify and characterize gene regulation in the spirochete Borrelia burgdorferi, the causative agent of Lyme disease. We use genetics, RNA sequencing, and murine infection models to pinpoint genes for mechanistic study.

Lyme disease is a re-emerging infectious disease and the foremost vector-borne bacterial infection in the world. Given that B. burgdorferi inhabits tick and mammalian hosts, environments with very different temperatures, immune responses, and sources of metabolites, the bacterium must harbor robust gene-regulatory mechanisms in order to survive. Yet, fundamental aspects of gene expression have not been studied extensively B. burgdorferi.

We recognize the importance of mapping RNA boundaries (their 5′ and 3′ ends) in bacteria, which is critical for gene annotation, the discovery of novel transcripts, and mechanistic characterization of genes. Several RNA-seq approaches have been developed to globally determine RNA boundaries: 5′ RNA-seq identifies and distinguishes transcription starts sites (TSSs) from 5′ processed ends; total RNA-seq sequences genes in their entirety; 3′ RNA-seq captures termination events and identifies RNA 3′ ends. As proof of concept, we first applied these sequencing approaches to the model organism Escherichia coli [Reference 1]. In doing so, we identified numerous E. coli RNA fragments derived from 5′ regions of mRNAs and internal to open reading frames (ORFs). We documented regulation for multiple transcripts and identified a function for an E. coli small RNA encoded internal to an essential cell-division gene.

We next performed 5′, total and 3′ RNA-seq on RNA isolated from B. burgdorferi grown in culture [Reference 2]. This identified complex gene arrangements and operons, untranslated regions, and small RNAs. Remarkably, 63% of RNA 3′ ends mapped upstream or internal to open reading frames (ORFs), including genes involved in the unique infectious cycle of B. burgdorferi. We hypothesize these RNAs result from premature termination and regulatory events such as cis-acting RNA regulation. Our findings uncovered an abundance of potential RNA regulators for future study in B. burgdorferi.

In a separate study, we compared identified 5′ ends to transcriptionally active sequences on the B. burgdorferi genome during a mouse infection. One gene identified by our approach, bb0562, was an annotated hypothetical protein. Targeted deletion of bb0562 revealed that the gene encodes a protein important for disseminated infection in mice by needle inoculation and tick bite transmission. We identified two canonical lipase motifs within BB0562 and demonstrated in vitro lipolytic activity with purified BB0562 protein. Collectively, the work established bb0562 as a novel B. burgdorferi nutritional virulence determinant [Reference 3].

Ongoing work in our lab has been focused on characterization and the physiological roles of other B. burgdorferi genes, particularly regulatory RNAs, and regulatory networks, particularly those that regulate motility.

Figure 1.

Figure 1

Click image to view.

Rendering of the Lyme bacterium Borrelia burgdorferi, its genome, and various RNA transcripts

Additional Funding

  • NICHD Early Career Award (2023) to Philip Adams, concluded


  1. Adams PP, Baniulyte G, Esnault C, Chegireddy K, Singh N, Monge M, Dale RK, Storz G, Wade JT. Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping. eLife 2021 10:e62438.
  2. Petroni E, Esnault C, Tetreault D, Dale RK, Storz G, Adams PP. Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi. Nat Commun 2023 14(1):3931.
  3. Kuhn HW, Lasseter A, Adams PP, Flores Avile C, Stone BL, Akins DR, Jewett TJ, Jewett MW. BB0562 is a nutritional virulence determinant with lipase activity important for Borrelia burgdorferi infection and survival in fatty acid deficient environments. PLoS Pathog 2021 17(8):e1009869.


  • Ryan Dale, PhD, Computer Support Services Core, NICHD, Bethesda, MD
  • Aravind Iyer, PhD, National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD
  • Mollie Jewett, PhD, University of Central Florida, Orlando, FL
  • Jun Liu, PhD, Yale School of Medicine, New Haven, CT
  • Gisela Storz, PhD, Section on Environmental Gene Regulation, NICHD, Bethesda, MD
  • Joseph Wade, PhD, Wadsworth Center, New York State Department of Health, Albany, NY


For more information, email or visit

Top of Page