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Screening and identification of natural antisense transcripts in Helicobacter pylori by a novel approach based on RNase I protection assay

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Abstract

Natural antisense transcripts (NATs) are endogenous RNA molecules that exhibit partial or complete complementarity to other RNAs. Studies have shown that NATs may participate in a broad range of gene regulatory events. The identification of NATs in human, mouse and Escherichia coli has revealed their widespread occurrence in both eukaryotic and prokaryotic life. However, little is known about NATs in Helicobacter pylori (H. pylori), a human pathogen which is associated with gastric diseases. Here we systematically screened NATs in H. pylori by a novel experimental strategy based on RNase I protection assay. We successfully constructed a cDNA library of NATs and developed a novel poly(A)-tailed RT-PCR method to monitor the expression of NATs. After sequencing, bioinformatic analysis and expression detection, two novel NATs (NAT-39 and NAT-67) were confirmed. They were, respectively, complementary to the following genes: iron-regulated outer membrane protein (frpB) and periplasmic iron-binding protein (ceuE). Taken together, the results suggest that NAT-39 and NAT-67 may participate in the regulation of iron homeostasis in H. Pylori in a sequence complementary manner with target mRNAs.

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References

  1. Lavorgna G, Dahary D, Lehner B, Sorek R, Sanderson CM, Casari G (2004) In search of antisense. Trends Biochem Sci 29:88–94. doi:10.1016/j.tibs.2003.12.002

    Article  PubMed  CAS  Google Scholar 

  2. Wagner EG, Flardh K (2002) Antisense RNAs everywhere? Trends Genet 18:223–226. doi:10.1016/S0168-9525(02)02658-6

    Article  PubMed  CAS  Google Scholar 

  3. Wagner EG, Altuvia S, Romby P (2002) Antisense RNAs in bacteria and their genetic elements. Adv Genet 46:361–398. doi:10.1016/S0065-2660(02)46013-0

    Article  PubMed  CAS  Google Scholar 

  4. Gottesman S, McCullen CA, Guillier M, Vanderpool CK, Majdalani N, Benhammou J et al (2006) Small RNA regulators and the bacterial response to stress. Cold Spring Harb Symp Quant Biol 71:1–11. doi:10.1101/sqb.2006.71.016

    Article  PubMed  CAS  Google Scholar 

  5. Ramani N, Hedeshian M, Freundlich M (1994) micF antisense RNA has a major role in osmoregulation of OmpF in Escherichia coli. J Bacteriol 176:5005–5010

    PubMed  CAS  Google Scholar 

  6. Gottesman S (2005) Micros for microbes: non-coding regulatory RNAs in bacteria. Trends Genet 21:399–404. doi:10.1016/j.tig.2005.05.008

    Article  PubMed  CAS  Google Scholar 

  7. Goodwin CS (1997) Helicobacter pylori gastritis, peptic ulcer, and gastric cancer: clinical and molecular aspects. Clin Infect Dis 25:1017–1019. doi:10.1086/516077

    Article  PubMed  CAS  Google Scholar 

  8. Scarlato V, Delany I, Spohn G, Beier D (2001) Regulation of transcription in Helicobacter pylori: simple systems or complex circuits? Int J Med Microbiol 291:107–117. doi:10.1078/1438-4221-00107

    Article  PubMed  CAS  Google Scholar 

  9. Fu H, Tie Y, Xu C, Zhang Z, Zhu J, Shi Y et al (2005) Identification of human fetal liver miRNAs by a novel method. FEBS Lett 579:3849–3854. doi:10.1016/j.febslet.2005.05.064

    Article  PubMed  CAS  Google Scholar 

  10. Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD et al (1997) The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388:539–547. doi:10.1038/41483

    Article  PubMed  CAS  Google Scholar 

  11. Alm RA, Ling LS, Moir DT, King BL, Brown ED, Doig PC et al (1999) Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397:176–180. doi:10.1038/16495

    Article  PubMed  Google Scholar 

  12. Oh JD, Kling-Backhed H, Giannakis M, Xu J, Fulton RS, Fulton LA et al (2006) The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression. Proc Natl Acad Sci USA 103:9999–10004. doi:10.1073/pnas.0603784103

    Article  PubMed  CAS  Google Scholar 

  13. Masse E, Gottesman S (2002) A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci USA 99:4620–4625. doi:10.1073/pnas.032066599

    Article  PubMed  CAS  Google Scholar 

  14. Lehner B, Williams G, Campbell RD, Sanderson CM (2002) Antisense transcripts in the human genome. Trends Genet 18:63–65. doi:10.1016/S0168-9525(02)02598-2

    Article  PubMed  CAS  Google Scholar 

  15. Shendure J, Church GM (2002) Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol 3:RESEARCH0044

    Article  PubMed  Google Scholar 

  16. Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jager JG, Huttenhofer A et al (2003) RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. Nucleic Acids Res 31:6435–6443. doi:10.1093/nar/gkg867

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

We would like to thank Dr Y. Zhaohui (Department of Microbiology, Third Military Medical University, China) for technical assistance in construction of cDNA library. This work was supported by Chinese National Natural Science Foundation project (30770113).

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Authors and Affiliations

  1. Department of Clinical Microbiology and Immunology, Faculty of Medical Laboratory Science, Third Military Medical University, Chongqing, 400038, People’s Republic of China

    Bin Xiao, Wei Li, Gang Guo, Bo-Sheng Li, Zhen Liu, Bin Tang, Xu-Hu Mao & Quan-Ming Zou

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  1. Bin Xiao
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  2. Wei Li
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  3. Gang Guo
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  4. Bo-Sheng Li
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  5. Zhen Liu
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  6. Bin Tang
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  7. Xu-Hu Mao
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  8. Quan-Ming Zou
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Correspondence to Xu-Hu Mao or Quan-Ming Zou.

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Xiao, B., Li, W., Guo, G. et al. Screening and identification of natural antisense transcripts in Helicobacter pylori by a novel approach based on RNase I protection assay. Mol Biol Rep 36, 1853–1858 (2009). https://doi.org/10.1007/s11033-008-9390-5

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  • DOI: https://doi.org/10.1007/s11033-008-9390-5

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