The regulatory landscape of the Spirochaeta africana transcription system

Abstract

Spirochetes constitute a phylum of prokaryotic bacteria, primarily distinguished by their unique helical or corkscrew shape. Spirochetes are also known for causing life-threatening diseases in humans, namely syphilis, Lyme disease, and leptospirosis. The transcription systems of model organisms such as Escherichia coli and Bacillus subtilis have been studied in detail, but relatively little is known about transcription regulation in spirochetes. Spirochaeta africana provides a feasible model for spirochetal transcription, as it is non-pathogenic and relatively easy to culture. To study the transcriptional regulation in S. africana, we isolated total RNA from S. africana, sequenced the transcriptome, and analysed the expression profile of the transcription system. We sequenced six RNA samples, quantified the cellular transcripts, and performed a comprehensive analysis of transcripts encoding proteins that regulate transcription. To assess the integrity of the genome, a reference-based genome assembly was conducted. The analysis indicates that the rates of transcription and translation are heavily moderated in S. africana, and both processes are limited as growth reaches saturation. RNA polymerase transcripts are three times more abundant during logarithmic growth compared to early saturation. The transcript counts of identified translation factors, ribosomal proteins, and proteins involved in ribosomal biogenesis had a statistically significant equivalent decrease in early saturation. The analysis also suggests that alternative sigma factors play a dominant role in S. africana, as RNA encoding the primary sigma factor represented only 7 % of all sigma-encoding RNAs during the exponential growth phase and only 1 % in early saturation. As a result of this study, multiple levels of transcriptional regulation in S. africana, such as operons, metabolic pathways, anti-sigma networks, sRNAs, and transcription factors, are established and investigated.