# High quality transcriptome profiling confirms the transcriptional landscape of Treponema pallidum subsp. pallidum

## TL;DR

This study provides a detailed map of gene activity in the syphilis-causing bacterium, confirming many previously unknown genes and offering insights for vaccine development.

## Contribution

The study experimentally validates in silico predicted genes in Treponema pallidum subsp. pallidum using RNA-sequencing.

## Key findings

- Many hypothetical genes in TPA are actively transcribed.
- Transcriptomic data revealed gene organization into transcription units and anti-sense RNAs.
- Transcripts were identified from intergenic regions, suggesting previously unknown gene activity.

## Abstract

Syphilis remains a critical global health challenge due to its potential for severe complications and the increase in its incidence rate over recent years. Until recently, the infectious agent of syphilis, Treponema pallidum subsp. pallidum (TPA), could not be cultured in vitro. Advances in co-culture techniques have enabled the effective long-term cultivation of TPA, providing a platform for studying its biology. Limited transcriptional data from TPA have been reported, and many genes in treponemal genomes are annotated based on in silico prediction of putative coding sequences without functional validation. To inform future syphilis vaccine development, experimental validation of in silico predicted genes coupled with functional annotation is necessary. This study used strand-specific RNA-sequencing to reconstruct a high-quality transcriptome profile of TPA, confirming the active transcription of genes previously annotated as hypothetical, paving the way for more accurate identification of vaccine target candidates. Our transcriptomic data also revealed, for the first time, the organization of genes into transcription units, an abundance of anti-sense RNAs, and transcripts from intergenic regions, providing crucial insights for future functional genomics studies of TPA.

The online version contains supplementary material available at 10.1038/s41598-025-06583-9.