Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

The primary transcriptome of the major human pathogen Helicobacter pylori

Nature volume 464, pages 250–255 (2010)Cite this article

Subjects

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.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it

$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Figure 1: H. pylori TSS revealed by dRNA-seq.
Figure 2: TSS annotation and 5′ mRNA structure.
Figure 3: Discovery of H. pylori sRNAs including 6S RNA.
Figure 4: Trans and cis regulatory sRNAs.

Accession codes

Data deposits

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

References

  1. Cover, T. L. & Blaser, M. J. Helicobacter pylori in health and disease. Gastroenterology 136, 1863–1873 (2009)

    Article  CAS  Google Scholar 

  2. Suerbaum, S. & Michetti, P. Helicobacter pylori infection. N. Engl. J. Med. 347, 1175–1186 (2002)

    Article  CAS  Google Scholar 

  3. Tomb, J. F. et al. The complete genome sequence of the gastric pathogen Helicobacter pylori . Nature 388, 539–547 (1997)

    Article  ADS  CAS  Google Scholar 

  4. Alm, R. A. et al. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori . Nature 397, 176–180 (1999)

    Article  ADS  Google Scholar 

  5. Waters, L. S. & Storz, G. Regulatory RNAs in bacteria. Cell 136, 615–628 (2009)

    Article  CAS  Google Scholar 

  6. Majdalani, N., Vanderpool, C. K. & Gottesman, S. Bacterial small RNA regulators. Crit. Rev. Biochem. Mol. Biol. 40, 93–113 (2005)

    Article  CAS  Google Scholar 

  7. Valentin-Hansen, P., Eriksen, M. & Udesen, C. The bacterial Sm-like protein Hfq: a key player in RNA transactions. Mol. Microbiol. 51, 1525–1533 (2004)

    Article  CAS  Google Scholar 

  8. Sorek, R. & Cossart, P. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nature Rev. Genet. 11, 9–16 (2010)

    Article  CAS  Google Scholar 

  9. Sharma, C. M. & Vogel, J. Experimental approaches for the discovery and characterization of regulatory small RNA. Curr. Opin. Microbiol. 12, 536–546 (2009)

    Article  CAS  Google Scholar 

  10. Wen, Y. et al. Acid-adaptive genes of Helicobacter pylori . Infect. Immun. 71, 5921–5939 (2003)

    Article  CAS  Google Scholar 

  11. Merrell, D. S., Goodrich, M. L., Otto, G., Tompkins, L. S. & Falkow, S. pH-regulated gene expression of the gastric pathogen Helicobacter pylori . Infect. Immun. 71, 3529–3539 (2003)

    Article  CAS  Google Scholar 

  12. Bury-Moné, S. et al. Responsiveness to acidity via metal ion regulators mediates virulence in the gastric pathogen Helicobacter pylori . Mol. Microbiol. 53, 623–638 (2004)

    Article  Google Scholar 

  13. Shirai, M., Fujinaga, R., Akada, J. K. & Nakazawa, T. Activation of Helicobacter pylori ureA promoter by a hybrid Escherichia coli–H. pylori rpoD gene in E. coli . Gene 239, 351–359 (1999)

    Article  CAS  Google Scholar 

  14. Spohn, G. & Scarlato, V. Motility of Helicobacter pylori is coordinately regulated by the transcriptional activator FlgR, an NtrC homolog. J. Bacteriol. 181, 593–599 (1999)

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Spohn, G., Beier, D., Rappuoli, R. & Scarlato, V. Transcriptional analysis of the divergent cagAB genes encoded by the pathogenicity island of Helicobacter pylori . Mol. Microbiol. 26, 361–372 (1997)

    Article  CAS  Google Scholar 

  16. Thompson, L. J. et al. Gene expression profiling of Helicobacter pylori reveals a growth-phase-dependent switch in virulence gene expression. Infect. Immun. 71, 2643–2655 (2003)

    Article  CAS  Google Scholar 

  17. Mao, F., Dam, P., Chou, J., Olman, V. & Xu, Y. DOOR: a database for prokaryotic operons. Nucleic Acids Res. 37, D459–D463 (2009)

    Article  CAS  Google Scholar 

  18. Beier, D., Spohn, G., Rappuoli, R. & Scarlato, V. Identification and characterization of an operon of Helicobacter pylori that is involved in motility and stress adaptation. J. Bacteriol. 179, 4676–4683 (1997)

    Article  CAS  Google Scholar 

  19. Burgess, R. R. & Anthony, L. How sigma docks to RNA polymerase and what sigma does. Curr. Opin. Microbiol. 4, 126–131 (2001)

    Article  CAS  Google Scholar 

  20. Forsyth, M. H. & Cover, T. L. Mutational analysis of the vacA promoter provides insight into gene transcription in Helicobacter pylori . J. Bacteriol. 181, 2261–2266 (1999)

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Petersen, L., Larsen, T. S., Ussery, D. W., On, S. L. & Krogh, A. RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box. J. Mol. Biol. 326, 1361–1372 (2003)

    Article  CAS  Google Scholar 

  22. Selinger, D. W. et al. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nature Biotechnol. 18, 1262–1268 (2000)

    Article  CAS  Google Scholar 

  23. Gressmann, H. et al. Gain and loss of multiple genes during the evolution of Helicobacter pylori . PLoS Genet. 1, e43 (2005)

    Article  Google Scholar 

  24. Saunders, N. J., Peden, J. F., Hood, D. W. & Moxon, E. R. Simple sequence repeats in the Helicobacter pylori genome. Mol. Microbiol. 27, 1091–1098 (1998)

    Article  CAS  Google Scholar 

  25. Appelmelk, B. J. et al. Phase variation in Helicobacter pylori lipopolysaccharide. Infect. Immun. 66, 70–76 (1998)

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Wang, G., Rasko, D. A., Sherburne, R. & Taylor, D. E. Molecular genetic basis for the variable expression of Lewis Y antigen in Helicobacter pylori: analysis of the α(1,2) fucosyltransferase gene. Mol. Microbiol. 31, 1265–1274 (1999)

    Article  CAS  Google Scholar 

  27. Ramakrishnan, V. Ribosome structure and the mechanism of translation. Cell 108, 557–572 (2002)

    Article  CAS  Google Scholar 

  28. Vanet, A., Marsan, L., Labigne, A. & Sagot, M. F. Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori σ80 family of promoter signals. J. Mol. Biol. 297, 335–353 (2000)

    Article  CAS  Google Scholar 

  29. Yada, T., Totoki, Y., Takagi, T. & Nakai, K. A novel bacterial gene-finding system with improved accuracy in locating start codons. DNA Res. 8, 97–106 (2001)

    Article  CAS  Google Scholar 

  30. Rodionov, D. A., Vitreschak, A. G., Mironov, A. A. & Gelfand, M. S. Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J. Biol. Chem. 277, 48949–48959 (2002)

    Article  CAS  Google Scholar 

  31. Weinberg, Z. et al. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res. 35, 4809–4819 (2007)

    Article  ADS  CAS  Google Scholar 

  32. Brock, J. E., Pourshahian, S., Giliberti, J., Limbach, P. A. & Janssen, G. R. Ribosomes bind leaderless mRNA in Escherichia coli through recognition of their 5′-terminal AUG. RNA 14, 2159–2169 (2008)

    Article  CAS  Google Scholar 

  33. Boneca, I. G. et al. A revised annotation and comparative analysis of Helicobacter pylori genomes. Nucleic Acids Res. 31, 1704–1714 (2003)

    Article  CAS  Google Scholar 

  34. Lenz, D. H. et al. The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae . Cell 118, 69–82 (2004)

    Article  CAS  Google Scholar 

  35. Barrick, J. E., Sudarsan, N., Weinberg, Z., Ruzzo, W. L. & Breaker, R. R. 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. RNA 11, 774–784 (2005)

    Article  CAS  Google Scholar 

  36. Wassarman, K. M. & Storz, G. 6S RNA regulates E. coli RNA polymerase activity. Cell 101, 613–623 (2000)

    Article  CAS  Google Scholar 

  37. Wassarman, K. M. & Saecker, R. M. Synthesis-mediated release of a small RNA inhibitor of RNA polymerase. Science 314, 1601–1603 (2006)

    Article  ADS  CAS  Google Scholar 

  38. Tjaden, B. et al. Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Res. 34, 2791–2802 (2006)

    Article  CAS  Google Scholar 

  39. Wang, Z. & Wang, G. APD: the Antimicrobial Peptide Database. Nucleic Acids Res. 32, D590–D592 (2004)

    Article  ADS  CAS  Google Scholar 

  40. Phadnis, S. H. et al. Surface localization of Helicobacter pylori urease and a heat shock protein homolog requires bacterial autolysis. Infect. Immun. 64, 905–912 (1996)

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Fujita, Y. et al. A novel mechanism of autolysis in Helicobacter pylori: possible involvement of peptidergic substances. Helicobacter 10, 567–576 (2005)

    Article  CAS  Google Scholar 

  42. Fozo, E. M., Hemm, M. R. & Storz, G. Small toxic proteins and the antisense RNAs that repress them. Microbiol. Mol. Biol. Rev. 72, 579–589 (2008)

    Article  CAS  Google Scholar 

  43. Rain, J. C. et al. The protein–protein interaction map of Helicobacter pylori . Nature 409, 211–215 (2001)

    Article  ADS  CAS  Google Scholar 

  44. Salama, N. R., Shepherd, B. & Falkow, S. Global transposon mutagenesis and essential gene analysis of Helicobacter pylori . J. Bacteriol. 186, 7926–7935 (2004)

    Article  CAS  Google Scholar 

  45. Jenks, P. J., Chevalier, C., Ecobichon, C. & Labigne, A. Identification of nonessential Helicobacter pylori genes using random mutagenesis and loop amplification. Res. Microbiol. 152, 725–734 (2001)

    Article  CAS  Google Scholar 

  46. Croxen, M. A., Ernst, P. B. & Hoffman, P. S. Antisense RNA modulation of alkyl hydroperoxide reductase levels in Helicobacter pylori correlates with organic peroxide toxicity but not infectivity. J. Bacteriol. 189, 3359–3368 (2007)

    Article  CAS  Google Scholar 

  47. Shi, Y., Tyson, G. W. & DeLong, E. F. Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column. Nature 459, 266–269 (2009)

    Article  ADS  CAS  Google Scholar 

  48. Kodzius, R. et al. CAGE: cap analysis of gene expression. Nature Methods 3, 211–222 (2006)

    Article  CAS  Google Scholar 

  49. Akada, J. K., Shirai, M., Takeuchi, H., Tsuda, M. & Nakazawa, T. Identification of the urease operon in Helicobacter pylori and its control by mRNA decay in response to pH. Mol. Microbiol. 36, 1071–1084 (2000)

    Article  CAS  Google Scholar 

  50. Pflock, M., Kennard, S., Delany, I., Scarlato, V. & Beier, D. Acid-induced activation of the urease promoters is mediated directly by the ArsRS two-component system of Helicobacter pylori . Infect. Immun. 73, 6437–6445 (2005)

    Article  CAS  Google Scholar 

Download references

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

Authors and Affiliations

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

    Cynthia M. Sharma, Alexandra Sittka & Jörg Vogel

  2. Department of Computer Science & Interdisciplinary Centre for Bioinformatics, University of Leipzig, 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

Authors
  1. Cynthia M. Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Steve Hoffmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Fabien Darfeuille
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jérémy Reignier
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Sven Findeiß
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Alexandra Sittka
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Sandrine Chabas
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Kristin Reiche
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Jörg Hackermüller
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Richard Reinhardt
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Peter F. Stadler
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Jörg Vogel
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jörg Vogel.

Supplementary information

Supplementary Methods

This file contains Supplementary Methods and Supplementary References. (PDF 288 kb)

Supplementary Figures

This file contains Supplementary Figures 1-23 with Legends and Supplementary References. (PDF 4224 kb)

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. (PDF 439 kb)

Supplementary Table 4

This file contains a TSS table. (XLS 582 kb)

Supplementary Table 5

This file contains an operon map of H. pylori. (XLS 102 kb)

Supplementary Table 12

This file contains a reannotation of genes. (XLS 34 kb)

Supplementary Table 13

This file contains the putative sRNA and antisense RNA TSS. (XLS 383 kb)

Supplementary Table 15

This file contains the predicted small ORFs in Helicobacter pylori 26695. (XLS 45 kb)

Supplementary Table 16

This file contains the expression differences at primary TSS. (XLS 136 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Sharma, C., Hoffmann, S., Darfeuille, F. et al. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464, 250–255 (2010). https://doi.org/10.1038/nature08756

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature08756

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing