Direct RNA Sequencing Unfolds the Complex Transcriptome of Vibrio parahaemolyticus

概要

〔目的(Purpose)〕
Vibrio parahaemolyticus is a halophilic bacterium found in the marine environment. Upon ingestion by humans—often through the consumption of raw or undercooked seafood—E parahaemolyticus senses the host environment and expresses numerous genes, the products of which synergize to synthesize and secrete toxins that can cause acute gastroenteritis. To understand the regulation of such adaptive response, mRNA transcripts must be mapped accurately. However, due to the limitations of common sequencing methods, not all features of bacterial transcriptomes are always reported. In this study we aim to map the full features of the transcriptome of Vibrio parahaemolyticus to enhance our understanding of gene regulation in this bacterium and provide a dataset for future work.　Additionally, we aimed to reveals a deeper view of a complicated transcriptome landscape, demonstrating the importance of applying such methods to other bacterial models.

〔方法ならびに成績(Methods/ResuIts)〕
Vibrio parahaemolyticus was grown in LB medium with and without bile salts (0.4%). RNA was isolated and polyadenylated to be sequenced using Direct RNA sequencing kit. A total of 4.103 TSSs were identified. In comparison to short-read sequencing, full-length information provided a deeper view of TSS classification, showing that most internal and antisense TSSs were actually a result of gene　overlap. Several non-coding genes were discovered. Sequencing the transcriptome of K parahaemolyticus grown with bile al lowed us to study the landscape of pathogenicity island Vp-PAI. Some genes in this region were reannotated, providing more accurate annotation to increase precision in their characterization. Quantitative detection of operons in V. parahaemolyticus showed high complexity in some operons, shedding light on a greater extent of regulation within the same operon. Our study using direct RNA sequencing provides a quantitative and high-resolution landscape of the V. parahaemolyticus transcriptome.

〔総括(Conclusion)〕
Mapping the full features of the transcriptome of V. parahaemolyticus provided rich information and led to more accurate annotation. It also unraveled the complexity of some operons. Our results support the application of long-read sequencing for analyzing and annotating other bacterial models.