Exploring temperature-dependent transcriptomic adaptations in Yersinia pestis using direct cDNA sequencing by Oxford Nanopore Technologies
Abstract Transcriptomics is key to understanding how bacterial pathogens adapt and cause disease, but remains constrained by cost, technical, and biosafety issues, especially for highly virulent and/or regulated pathogens. Here, we present a streamlined and cost-effective RNA-Seq workflow using Oxfo...
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Nature Portfolio
2025-07-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-025-05662-1 |
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| author | Brandon Robin Alexandre Baillez Servane Le Guillouzer Cécile Lecoeur Florent Sebbane Sébastien Bontemps-Gallo |
| author_facet | Brandon Robin Alexandre Baillez Servane Le Guillouzer Cécile Lecoeur Florent Sebbane Sébastien Bontemps-Gallo |
| author_sort | Brandon Robin |
| collection | DOAJ |
| description | Abstract Transcriptomics is key to understanding how bacterial pathogens adapt and cause disease, but remains constrained by cost, technical, and biosafety issues, especially for highly virulent and/or regulated pathogens. Here, we present a streamlined and cost-effective RNA-Seq workflow using Oxford Nanopore Technologies for direct cDNA sequencing, suitable for complete in-house implementation. This method avoids PCR bias, enables multiplexing, and includes built-in quality controls and alignment benchmarking. Applied to Yersinia pestis (the causative agent of plague), the workflow produced an experimentally validated operon map and revealed novel transcriptional units, including within the pathogenicity island. Transcriptomic profiling at 21 °C and 37 °C, modeling the flea and mammalian environments, highlighted temperature-driven metabolic shifts, notably the upregulation of sulfur metabolism and the dmsABCD operon. These findings provide insights into Y. pestis adaptation and illustrate how long-read RNA-Seq can support operon discovery, genome annotation, and gene regulation studies in high-risk or understudied bacterial pathogens. |
| format | Article |
| id | doaj-art-48d16c0b93134b3da1f3d976f28e269b |
| institution | DOAJ |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj-art-48d16c0b93134b3da1f3d976f28e269b2025-08-20T03:03:40ZengNature PortfolioScientific Reports2045-23222025-07-0115111110.1038/s41598-025-05662-1Exploring temperature-dependent transcriptomic adaptations in Yersinia pestis using direct cDNA sequencing by Oxford Nanopore TechnologiesBrandon Robin0Alexandre Baillez1Servane Le Guillouzer2Cécile Lecoeur3Florent Sebbane4Sébastien Bontemps-Gallo5Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of LilleUniv. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of LilleUniv. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of LilleUniv. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of LilleUniv. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of LilleUniv. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of LilleAbstract Transcriptomics is key to understanding how bacterial pathogens adapt and cause disease, but remains constrained by cost, technical, and biosafety issues, especially for highly virulent and/or regulated pathogens. Here, we present a streamlined and cost-effective RNA-Seq workflow using Oxford Nanopore Technologies for direct cDNA sequencing, suitable for complete in-house implementation. This method avoids PCR bias, enables multiplexing, and includes built-in quality controls and alignment benchmarking. Applied to Yersinia pestis (the causative agent of plague), the workflow produced an experimentally validated operon map and revealed novel transcriptional units, including within the pathogenicity island. Transcriptomic profiling at 21 °C and 37 °C, modeling the flea and mammalian environments, highlighted temperature-driven metabolic shifts, notably the upregulation of sulfur metabolism and the dmsABCD operon. These findings provide insights into Y. pestis adaptation and illustrate how long-read RNA-Seq can support operon discovery, genome annotation, and gene regulation studies in high-risk or understudied bacterial pathogens.https://doi.org/10.1038/s41598-025-05662-1Oxford Nanopore TechnologyRNA-SeqYersinia pestisOperons mappingTemperature adaptation |
| spellingShingle | Brandon Robin Alexandre Baillez Servane Le Guillouzer Cécile Lecoeur Florent Sebbane Sébastien Bontemps-Gallo Exploring temperature-dependent transcriptomic adaptations in Yersinia pestis using direct cDNA sequencing by Oxford Nanopore Technologies Scientific Reports Oxford Nanopore Technology RNA-Seq Yersinia pestis Operons mapping Temperature adaptation |
| title | Exploring temperature-dependent transcriptomic adaptations in Yersinia pestis using direct cDNA sequencing by Oxford Nanopore Technologies |
| title_full | Exploring temperature-dependent transcriptomic adaptations in Yersinia pestis using direct cDNA sequencing by Oxford Nanopore Technologies |
| title_fullStr | Exploring temperature-dependent transcriptomic adaptations in Yersinia pestis using direct cDNA sequencing by Oxford Nanopore Technologies |
| title_full_unstemmed | Exploring temperature-dependent transcriptomic adaptations in Yersinia pestis using direct cDNA sequencing by Oxford Nanopore Technologies |
| title_short | Exploring temperature-dependent transcriptomic adaptations in Yersinia pestis using direct cDNA sequencing by Oxford Nanopore Technologies |
| title_sort | exploring temperature dependent transcriptomic adaptations in yersinia pestis using direct cdna sequencing by oxford nanopore technologies |
| topic | Oxford Nanopore Technology RNA-Seq Yersinia pestis Operons mapping Temperature adaptation |
| url | https://doi.org/10.1038/s41598-025-05662-1 |
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