Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi

Emily Petroni, Caroline Esnault, Daniel Tetreault, Ryan K. Dale, Gisela Storz and Philip P. Adams ()
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Emily Petroni: Eunice Kennedy Shriver National Institute of Child Health and Human Development
Caroline Esnault: Eunice Kennedy Shriver National Institute of Child Health and Human Development
Daniel Tetreault: Eunice Kennedy Shriver National Institute of Child Health and Human Development
Ryan K. Dale: Eunice Kennedy Shriver National Institute of Child Health and Human Development
Gisela Storz: Eunice Kennedy Shriver National Institute of Child Health and Human Development
Philip P. Adams: Eunice Kennedy Shriver National Institute of Child Health and Human Development

Nature Communications, 2023, vol. 14, issue 1, 1-23

Abstract: Abstract Transcription termination is an essential and dynamic process that can tune gene expression in response to diverse molecular signals. Yet, the genomic positions, molecular mechanisms, and regulatory consequences of termination have only been studied thoroughly in model bacteria. Here, we use several RNA-seq approaches to map RNA ends for the transcriptome of the spirochete Borrelia burgdorferi – the etiological agent of Lyme disease. We identify complex gene arrangements and operons, untranslated regions and small RNAs. We predict intrinsic terminators and experimentally test examples of Rho-dependent transcription termination. Remarkably, 63% of RNA 3′ ends map upstream of or internal to open reading frames (ORFs), including genes involved in the unique infectious cycle of B. burgdorferi. We suggest these RNAs result from premature termination, processing and regulatory events such as cis-acting regulation. Furthermore, the polyamine spermidine globally influences the generation of truncated mRNAs. Collectively, our findings provide insights into transcription termination and uncover an abundance of potential RNA regulators in B. burgdorferi.

Date: 2023
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DOI: 10.1038/s41467-023-39576-1

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