Article | Published:

The primary transcriptome of the major human pathogen Helicobacter pylori

Nature volume 464, pages 250255 (11 March 2010) | Download Citation

Abstract

Genome sequencing of Helicobacter pylori has revealed the potential proteins and genetic diversity of this prevalent human pathogen, yet little is known about its transcriptional organization and noncoding RNA output. Massively parallel cDNA sequencing (RNA-seq) has been revolutionizing global transcriptomic analysis. Here, using a novel differential approach (dRNA-seq) selective for the 5′ end of primary transcripts, we present a genome-wide map of H. pylori transcriptional start sites and operons. We discovered hundreds of transcriptional start sites within operons, and opposite to annotated genes, indicating that complexity of gene expression from the small H. pylori genome is increased by uncoupling of polycistrons and by genome-wide antisense transcription. We also discovered an unexpected number of 60 small RNAs including the ε-subdivision counterpart of the regulatory 6S RNA and associated RNA products, and potential regulators of cis- and trans-encoded target messenger RNAs. Our approach establishes a paradigm for mapping and annotating the primary transcriptomes of many living species.

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Data deposits

Raw data are available from the NCBI Short Read Archive (http://www.ncbi.nlm.nih.gov/Traces/sra) under accession number SRA010186.

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Acknowledgements

We thank F. Seifert; H. Hamoutene and B. Timmermann for technical support; M. Schmid for mass spectrometry analysis; H. De Reuse, A. van Vliet and M. K. Waldor for discussions; F. Thümmler for library preparation; M. Droege for pyrosequencing support. J.V. and R.R. are supported by NGFN+ grants (BMBF, Germany), and J.V. and P.F.S. by DFG Priority Program SPP1258 Sensory and Regulatory RNAs in Prokaryotes (Grants VO8751/2, VO8751/4; STA850/7-1). S.H. was supported by a formel.1 grant of the University of Leipzig, the Freistaat Sachsen (LIFE project), the German Research Foundation IZBI (BIZ6/1-4) and Volkswagen Stiftung (I/82 720). F.D. is supported by the French Agence Nationale de la Recherche (ANR-07-JCJC-0104-01), the French Association de la Recherche contre le Cancer (ARC) and La Ligue Nationale contre le Cancer (LNCC). We thank D. Rose for his supporting work and S. Washietl for a pre-release of the RNAcode software.

Author Contributions C.M.S., F.D., P.F.S. and J.V. designed the research; C.M.S., F.D., A.S., J.R., J.V. and S.C. performed all wet lab work. C.M.S., S.H., S.F., K.R., J.H. and P.F.S. conducted biocomputational analyses; R.R. carried out sequencing. J.V. wrote the manuscript, which all authors commented on, and supervised the project. Author information and raw data are available from C.M.S, P.F.S. and J.V.

Author information

Affiliations

  1. Max Planck Institute for Infection Biology, RNA Biology Group, D-10117 Berlin, Germany

    • Cynthia M. Sharma
    • , Alexandra Sittka
    •  & Jörg Vogel
  2. University of Leipzig, Department of Computer Science & Interdisciplinary Centre for Bioinformatics, D-04107 Leipzig, Germany

    • Steve Hoffmann
    • , Sven Findeiß
    •  & Peter F. Stadler
  3. INSERM U869 and,

    • Fabien Darfeuille
    • , Jérémy Reignier
    •  & Sandrine Chabas
  4. Université de Bordeaux, F-33076 Bordeaux Cedex, France

    • Fabien Darfeuille
    • , Jérémy Reignier
    •  & Sandrine Chabas
  5. Fraunhofer Institute for Cell Therapy and Immunology, RNomics Group, D-04103 Leipzig, Germany

    • Kristin Reiche
    • , Jörg Hackermüller
    •  & Peter F. Stadler
  6. Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany

    • Richard Reinhardt
  7. Max Planck Institute for the Mathematics in Sciences, D-04103 Leipzig, Germany

    • Peter F. Stadler
  8. University of Vienna, Institute for Theoretical Chemistry, A-1090 Vienna, Austria

    • Peter F. Stadler
  9. The Santa Fe Institute, Santa Fe, 87501 New Mexico, USA

    • Peter F. Stadler
  10. University of Würzburg, Institute for Molecular Infection Biology, D-97080 Würzburg, Germany

    • Jörg Vogel

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Corresponding author

Correspondence to Jörg Vogel.

Supplementary information

PDF files

  1. 1.

    Supplementary Methods

    This file contains Supplementary Methods and Supplementary References.

  2. 2.

    Supplementary Figures

    This file contains Supplementary Figures 1-23 with Legends and Supplementary References.

  3. 3.

    Supplementary Tables

    This file contains Supplementary Tables 1-3, 6 -11, 14, and 17-18 and Supplementary References. See separate files for Tables 4, 5, 12, 13, 15 and 16.

Excel files

  1. 1.

    Supplementary Table 4

    This file contains a TSS table.

  2. 2.

    Supplementary Table 5

    This file contains an operon map of H. pylori.

  3. 3.

    Supplementary Table 12

    This file contains a reannotation of genes.

  4. 4.

    Supplementary Table 13

    This file contains the putative sRNA and antisense RNA TSS.

  5. 5.

    Supplementary Table 15

    This file contains the predicted small ORFs in Helicobacter pylori 26695.

  6. 6.

    Supplementary Table 16

    This file contains the expression differences at primary TSS.

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DOI

https://doi.org/10.1038/nature08756

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