RNA-Seq of Borrelia burgdorferi in Multiple Phases of Growth Reveals Insights into the Dynamics of Gene Expression, Transcriptome Architecture, and Noncoding RNAs

Abstract

Borrelia burgdorferi, the agent of Lyme disease, differentially expresses numerous genes and proteins as it cycles between mammalian hosts and tick vectors. Insights on regulatory mechanisms have been provided by earlier studies that examined B. burgdorferi gene expression patterns during cultivation. However, prior studies examined bacteria at only a single time point of cultivation, providing only a snapshot of what is likely a dynamic transcriptional program driving B. burgdorferi adaptations to changes during culture growth phases. To address that concern, we performed RNA sequencing (RNA-Seq) analysis of B. burgdorferi cultures at early-exponential, mid-exponential, and early-stationary phases of growth. We found that expression of nearly 18% of annotated B. burgdorferi genes changed significantly during culture maturation. Moreover, genome-wide mapping of the B. burgdorferi transcriptome in different growth phases enabled insight on transcript boundaries, operon structures, and identified numerous putative non-coding RNAs. These RNA-Seq data are discussed and presented as a resource for the community of researchers seeking to better understand B. burgdorferi biology and pathogenesis.

Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans

“…The relatively high number of sRNAs found in our study is likely due to differences in regards to library preparation strategies and the dRNA-seq approach used. A recent study in B. burgdorferi , which is one-third the size of the genome of L. interrogans , identified 351 putative sRNAs (Arnold et al, 2016), suggesting that spirochetes transcribe numerous noncoding RNAs which are harnessed to control transcriptional and post-transcriptional processes.…”

A Dual Luciferase Reporter System for B. burgdorferi Measures Transcriptional Activity during Tick-Pathogen Interactions

“…The same rluc Bb -expressing clones, were also incubated with luciferin and relative Fluc Bb units were determined by normalizing to OD 600 (Figure 3B). All fluc Bb promoter fusions displayed the expected relative Fluc Bb units/OD 600 , given the known expression patterns of their corresponding mRNA during logarithmic and stationary phase growth (Arnold et al, 2016). Both the flaB (+pCFA801) and ospA (+pCFA802) promoters demonstrated significant activity above the promoterless fluc Bb control (+pCFA701) for both logarithmic and stationary phase growth.…”

The Lyme disease spirochete's BpuR DNA/RNA‐binding protein is differentially expressed during the mammal–tick infectious cycle, which affects translation of the SodA superoxide dismutase

“…Bacteria were cultured in complete BSK‐II medium at 35°C, with or without added IPTG, then total RNA was purified and assayed by RNA‐Seq. Levels of all transcripts were analyzed, including coding and noncoding RNAs (Arnold et al , ; ). Under those culture conditions, we found only two transcripts that met the commonly used criteria for differential expression (2X expression and padj <0.05) (Supplemental Fig.…”

“…Illumina cDNA libraries were generated using the RNAtag‐Seq protocol (Shishkin et al , ; Arnold et al , ; ), with minor modifications. Briefly, 840 ng of total RNA was fragmented, depleted of genomic DNA, dephosphorylated, then ligated to DNA adapter barcodes.…”