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

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.

PIPETS: A statistically informed, gene-annotation agnostic analysis method to study bacterial termination using 3’-end sequencing

“…Initial studies using 3’-seq focused on identifying regulatory elements in the 5’UTRs of annotated genes by focusing exclusively on signal in the 5’- and 3’-UTRs of these genes (Dar et al ., 2016, Dar and Sorek, 2018; Konikkat et al ., 2021. This analysis methodology was used or closely mirrored by several studies afterwards, many of which noted an abundance of 3’-seq signal in other genomic regions of the data (Warrier et al ., 2018; Millman et al ., 2017; Petroni et al ., 2023). Other studies created their own custom analysis methods to study 3’-seq data in order to study specific regulatory signals or to add additional sequencing information (Ju et al ., 2019; Mandell et al ., 2021).…”