Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni
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.
Authors
- Susanne Engelmann (ORCID: https://orcid.org/0000-0002-1201-3488)
- Rolf Backofen (ORCID: https://orcid.org/0000-0001-8231-3323)
- Martin Kucklick (ORCID: https://orcid.org/0000-0002-7289-3915)
- Stephan Fuchs (ORCID: https://orcid.org/0000-0002-1338-2699)
- Cynthia M. Sharma (ORCID: https://orcid.org/0000-0002-2321-9705)
- Alicia Klaude
- Florian Eggenhofer (ORCID: https://orcid.org/0000-0001-9564-7525)
- Kathrin Froschauer (ORCID: https://orcid.org/0000-0001-5288-4440)
- Rick Gelhausen (ORCID: https://orcid.org/0000-0003-4161-4394)
- Daniel Falush (ORCID: https://orcid.org/0000-0002-2956-0795)
- Philipp Kible (ORCID: https://orcid.org/0000-0001-6955-2645)
- Elisabetta Fiore (ORCID: https://orcid.org/0000-0002-2419-2794)
- Sarah L. Svensson (ORCID: https://orcid.org/0000-0002-3183-6084)
- Chao Yang (ORCID: https://orcid.org/0000-0003-0626-0586)
Institutions
- University of Freiburg (DE)
- Robert Koch Institute (DE)
- University of Würzburg (DE)
- Helmholtz Centre for Infection Research (DE)
- Technische Universität Braunschweig (DE)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-03-30
- DOI
- https://doi.org/10.1038/s41467-025-58329-w
- Citations
- 12
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 8.06
Funders
- Deutsche Forschungsgemeinschaft