Transcriptomic insights on the virulence-controlling CsrA, BadR, RpoN, and RpoS regulatory networks in the Lyme disease spirochete

Abstract

Borrelia burgdorferi, the causative agent of Lyme disease, survives in nature through a cycle that alternates between ticks and vertebrates. To facilitate this defined lifestyle, B. burgdorferi has evolved a gene regulatory network that ensures transmission between those hosts, along with specific adaptations to niches within each host. Several regulatory proteins are known to be essential for the bacterium to complete these critical tasks, but interactions between regulators had not previously been investigated in detail, due to experimental uses of different strain backgrounds and growth conditions. To address that deficit in knowledge, the transcriptomic impacts of four critical regulatory proteins were examined in a uniform strain background. Pairs of mutants and their wild-type parent were grown simultaneously under a single, specific culture condition, permitting direct comparisons between the mutant strains. Transcriptomic analyses were strand-specific, and assayed both coding and noncoding RNAs. Intersection analyses identified regulatory overlaps between regulons, including transcripts involved in carbohydrate and polyamine metabolism. In addition, it was found that transcriptional units such as ospC and dbpBA, which were previously observed to be affected by alternative sigma factors, are transcribed by RNA polymerase using the housekeeping sigma factor, RpoD.

DNA Methylation by Restriction Modification Systems Affects the Global Transcriptome Profile in Borrelia burgdorferi

“…Interestingly, the "canonical" RpoS-dependent gene ospC was upregulated in both MTase mutants. The ospC gene contains a unique operator region located immediately upstream of its RpoS-dependent promoter that is hypothesized to allow input from additional gene regulatory networks in order to independently repress ospC expression while continuing to express the RpoS regulon during persistent infection (62,63). Thus, it is possible that any decrease in ospC expression in the MTase mutants due to the downregulation of rpoS is offset by an even larger derepression or activation by dysregulation of some yet-unidentified regulatory network.…”

The Functional and Molecular Effects of Doxycycline Treatment on Borrelia burgdorferi Phenotype

“…The use of RNASeq to study adaptation (Drecktrah et al, 2015; Arnold et al, 2016, 2018) has led to significant understanding of the changes in gene expression associated with growth phase and illumination of regulatory pathways. In this report, we add to this understanding through the analysis of the response to antibiotic, and elucidate possible antigenic targets (Oms28, OspA and several Erp proteins) for improved therapeutic intervention.…”

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.…”