IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-58329-w.html
   My bibliography  Save this article

Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni

Author

Listed:
  • Kathrin Froschauer

    (Department of Molecular Infection Biology II)

  • Sarah L. Svensson

    (Department of Molecular Infection Biology II
    Chinese Academy of Sciences)

  • Rick Gelhausen

    (University of Freiburg)

  • Elisabetta Fiore

    (Department of Molecular Infection Biology II)

  • Philipp Kible

    (Department of Molecular Infection Biology II)

  • Alicia Klaude

    (Institute for Microbiology
    Helmholtz Centre for Infection Research (HZI))

  • Martin Kucklick

    (Institute for Microbiology
    Helmholtz Centre for Infection Research (HZI))

  • Stephan Fuchs

    (Methodenentwicklung und Forschungsinfrastruktur (MF))

  • Florian Eggenhofer

    (University of Freiburg)

  • Chao Yang

    (Chinese Academy of Sciences)

  • Daniel Falush

    (Chinese Academy of Sciences)

  • Susanne Engelmann

    (Institute for Microbiology
    Helmholtz Centre for Infection Research (HZI))

  • Rolf Backofen

    (University of Freiburg
    University of Freiburg)

  • Cynthia M. Sharma

    (Department of Molecular Infection Biology II)

Abstract

In contrast to transcriptome maps, bacterial small protein (≤50-100 aa) coding landscapes, including overlapping genes, are poorly characterized. However, an emerging number of small proteins have crucial roles in bacterial physiology and virulence. Here, we present a Ribo-seq-based high-resolution translatome map for the major foodborne pathogen Campylobacter jejuni. Besides conventional Ribo-seq, we employed translation initiation site (TIS) profiling to map start codons and also developed a translation termination site (TTS) profiling approach, which revealed stop codons not apparent from the reference genome in virulence loci. Our integrated approach combined with independent validation expanded the small proteome by two-fold, including CioY, a new 34 aa component of the CioAB oxidase. Overall, our study generates a high-resolution annotation of the C. jejuni coding landscape, provided in an interactive browser, and showcases a strategy for applying integrated Ribo-seq to other species to enrich our understanding of small proteomes.

Suggested Citation

  • Kathrin Froschauer & Sarah L. Svensson & Rick Gelhausen & Elisabetta Fiore & Philipp Kible & Alicia Klaude & Martin Kucklick & Stephan Fuchs & Florian Eggenhofer & Chao Yang & Daniel Falush & Susanne , 2025. "Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58329-w
    DOI: 10.1038/s41467-025-58329-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-58329-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-025-58329-w?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Cynthia M. Sharma & Steve Hoffmann & Fabien Darfeuille & Jérémy Reignier & Sven Findeiß & Alexandra Sittka & Sandrine Chabas & Kristin Reiche & Jörg Hackermüller & Richard Reinhardt & Peter F. Stadler, 2010. "The primary transcriptome of the major human pathogen Helicobacter pylori," Nature, Nature, vol. 464(7286), pages 250-255, March.
    2. J. Parkhill & B. W. Wren & K. Mungall & J. M. Ketley & C. Churcher & D. Basham & T. Chillingworth & R. M. Davies & T. Feltwell & S. Holroyd & K. Jagels & A. V. Karlyshev & S. Moule & M. J. Pallen & C., 2000. "The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences," Nature, Nature, vol. 403(6770), pages 665-668, February.
    3. Muhammad Aammar Tufail & Britta Jordan & Lydia Hadjeras & Rick Gelhausen & Liam Cassidy & Tim Habenicht & Miriam Gutt & Lisa Hellwig & Rolf Backofen & Andreas Tholey & Cynthia M. Sharma & Ruth A. Schm, 2024. "Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Fabian König & Sarah L. Svensson & Cynthia M. Sharma, 2024. "Interplay of two small RNAs fine-tunes hierarchical flagella gene expression in Campylobacter jejuni," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    2. Amir Bar & Liron Argaman & Michal Eldar & Hanah Margalit, 2023. "TRS: a method for determining transcript termini from RNAtag-seq sequencing data," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    3. Emily Petroni & Caroline Esnault & Daniel Tetreault & Ryan K. Dale & Gisela Storz & Philip P. Adams, 2023. "Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
    4. Martin Ackermann & Lin Chao, 2006. "DNA Sequences Shaped by Selection for Stability," PLOS Genetics, Public Library of Science, vol. 2(2), pages 1-7, February.
    5. Martina O. Chukwu & Akebe Luther King Abia & Eunice Ubomba-Jaswa & Lawrence Obi & John Barr Dewar, 2019. "Characterization and Phylogenetic Analysis of Campylobacter Species Isolated from Paediatric Stool and Water Samples in the Northwest Province, South Africa," IJERPH, MDPI, vol. 16(12), pages 1-22, June.
    6. Mateusz Noszka & Agnieszka Strzałka & Jakub Muraszko & Rafał Kolenda & Chen Meng & Christina Ludwig & Kerstin Stingl & Anna Zawilak-Pawlik, 2023. "Profiling of the Helicobacter pylori redox switch HP1021 regulon using a multi-omics approach," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    7. Christopher Ruis & Aaron Weimann & Gerry Tonkin-Hill & Arun Prasad Pandurangan & Marta Matuszewska & Gemma G. R. Murray & Roger C. Lévesque & Tom L. Blundell & R. Andres Floto & Julian Parkhill, 2023. "Mutational spectra are associated with bacterial niche," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    8. Daniel G. Mediati & Julia L. Wong & Wei Gao & Stuart McKellar & Chi Nam Ignatius Pang & Sylvania Wu & Winton Wu & Brandon Sy & Ian R. Monk & Joanna M. Biazik & Marc R. Wilkins & Benjamin P. Howden & T, 2022. "RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3′UTR required for intermediate vancomycin resistance," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    9. Alejandro Tejada-Arranz & Aleksei Lulla & Maxime Bouilloux-Lafont & Evelyne Turlin & Xue-Yuan Pei & Thibaut Douché & Mariette Matondo & Allison H. Williams & Bertrand Raynal & Ben F. Luisi & Hilde Reu, 2023. "Acetylation regulates the oligomerization state and activity of RNase J, the Helicobacter pylori major ribonuclease," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58329-w. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.