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Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase


Horizontal gene transfer permits rapid dissemination of genetic elements between individuals in bacterial populations. Transmitted DNA sequences may encode favourable traits. However, if the acquired DNA has an atypical base composition, it can reduce host fitness. Consequently, bacteria have evolved strategies to minimize the harmful effects of foreign genes. Most notably, xenogeneic silencing proteins bind incoming DNA that has a higher AT content than the host genome. An enduring question has been why such sequences are deleterious. Here, we showed that the toxicity of AT-rich DNA in Escherichia coli frequently results from constitutive transcription initiation within the coding regions of genes. Left unchecked, this causes titration of RNA polymerase and a global downshift in host gene expression. Accordingly, a mutation in RNA polymerase that diminished the impact of AT-rich DNA on host fitness reduced transcription from constitutive, but not activator-dependent, promoters.

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Figure 1: Characterization of the yccE locus.
Figure 2: H-NS represses intragenic yccE transcription and associated fitness costs.
Figure 3: H-NS represses intragenic transcription and associated fitness costs at many loci.
Figure 4: Most transcription is uniformly downregulated in cells lacking H-NS.


  1. 1

    Soucy, S. M., Huang, J. & Gogarten, J. P. Horizontal gene transfer: building the web of life. Nat. Rev. Genet. 16, 472–482 (2015).

    CAS  Article  Google Scholar 

  2. 2

    Doyle, M. et al. An H-NS-like stealth protein aids horizontal DNA transmission in bacteria. Science 315, 251–252 (2007).

    CAS  Article  Google Scholar 

  3. 3

    Popa, O., Hazkani-Covo, E., Landan, G., Martin, W. & Dagan, T. Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res. 21, 599–609 (2011).

    CAS  Article  Google Scholar 

  4. 4

    Popa, O. & Dagan, T. Trends and barriers to lateral gene transfer in prokaryotes. Curr. Opin. Microbiol. 145, 615–623 (2011).

    Article  Google Scholar 

  5. 5

    Raghavan, R., Kelkar, Y. D. & Ochman, H. A selective force favoring increased G+C content in bacterial genes. Proc. Natl Acad. Sci. USA 109, 14504–14507 (2012).

    CAS  Article  Google Scholar 

  6. 6

    Baltrus, D. A. Exploring the costs of horizontal gene transfer. Trends Ecol. Evol. 8, 489–495 (2013).

    Article  Google Scholar 

  7. 7

    Dorman, C. J. H-NS, the genome sentinel. Nat. Rev. Microbiol. 5, 157–161 (2007).

    CAS  Article  Google Scholar 

  8. 8

    Singh, K., Milstein, J. N. & Navarre, W. W. Xenogeneic silencing and its impact on bacterial genomes. Annu. Rev. Microbiol. 70, 199–213 (2016).

    CAS  Article  Google Scholar 

  9. 9

    Navarre, W. W. et al. Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella. Science 313, 236–238 (2006).

    CAS  Article  Google Scholar 

  10. 10

    Lucchini, S. et al. H-NS mediates the silencing of laterally acquired genes in bacteria. PLoS Pathogens 28, e81 (2006).

    Article  Google Scholar 

  11. 11

    Smits, W. K. & Grossman, A. D. The transcriptional regulator Rok binds A+T-rich DNA and is involved in repression of a mobile genetic element in Bacillus subtilis. PLoS Genet. 6, e1001207 (2010).

    Article  Google Scholar 

  12. 12

    Gordon, B. R. et al. Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes in Mycobacterium tuberculosis. Proc. Natl Acad. Sci. USA 107, 5154–5159 (2010).

    CAS  Article  Google Scholar 

  13. 13

    Dorman, C. J. H-NS-like nucleoid-associated proteins, mobile genetic elements and horizontal gene transfer in bacteria. Plasmid 75, 1–11 (2014).

    CAS  Article  Google Scholar 

  14. 14

    Bouffartigues, E., Buckle, M., Badaut, C., Travers, A. & Rimsky, S. H-NS cooperative binding to high-affinity sites in a regulatory element results in transcriptional silencing. Nat. Struct. Mol. Biol. 14, 441–418 (2007).

    CAS  Article  Google Scholar 

  15. 15

    Gordon, B. R. et al. Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins. Proc. Natl Acad. Sci. USA 108, 10690–10695 (2011).

    CAS  Article  Google Scholar 

  16. 16

    Arold, S. T., Leonard, P. G., Parkinson, G. N. & Ladbury, J. E. H-NS forms a superhelical protein scaffold for DNA condensation. Proc. Natl Acad. Sci. USA 107, 15728–15732 (2010).

    CAS  Article  Google Scholar 

  17. 17

    Amit, R., Oppenheim, A. B. & Stavans, J. Increased bending rigidity of single DNA molecules by H-NS, a temperature and osmolarity sensor. Biophys. J. 84, 2467–2473 (2003).

    CAS  Article  Google Scholar 

  18. 18

    Dame, R. T., Noom, M. C. & Wuite, G. J. Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation. Nature 444, 387–390 (2006).

    CAS  Article  Google Scholar 

  19. 19

    Liu, Y., Chen, H., Kenney, L. J. & Yan, J. A divalent switch drives H-NS/DNA-binding conformations between stiffening and bridging modes. Genes Dev. 24, 339–344 (2010).

    CAS  Article  Google Scholar 

  20. 20

    Landick, R., Wade, J. T. & Grainger, D. C. H-NS and RNA polymerase: a love–hate relationship? Curr. Opin. Microbiol. 24, 53–59 (2015).

    CAS  Article  Google Scholar 

  21. 21

    Winardhi, R. S., Yan, J. & Kenney, L. J. H-NS regulates gene expression and compacts the nucleoid: insights from single-molecule experiments. Biophys. J. 109, 1321–1329 (2015).

    CAS  Article  Google Scholar 

  22. 22

    Dame, R. T., Wyman, C., Wurm, R., Wagner, R. & Goosen, N. Structural basis for H-NS-mediated trapping of RNA polymerase in the open initiation complex at the rrnB P1. J. Biol. Chem. 277, 2146–2150 (2002).

    CAS  Article  Google Scholar 

  23. 23

    Huang, Q. et al. High-density transcriptional initiation signals underline genomic islands in bacteria. PLoS ONE 7, e33759 (2012).

    CAS  Article  Google Scholar 

  24. 24

    Singh, S. S. & Grainger, D. C. H-NS can facilitate specific DNA-binding by RNA polymerase in AT-rich gene regulatory regions. PLoS Genet. 9, e1003589 (2013).

    CAS  Article  Google Scholar 

  25. 25

    Singh, S. S. et al. Widespread suppression of intragenic transcription initiation by H NS. Genes Dev. 28, 214–219 (2014).

    CAS  Article  Google Scholar 

  26. 26

    Lam, K. N. & Charles, T. C. Strong spurious transcription likely contributes to DNA insert bias in typical metagenomic clone libraries. Microbiome 3, 22 (2015).

    Article  Google Scholar 

  27. 27

    Kahramanoglou, C. et al. Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res. 39, 2073–2091 (2011).

    CAS  Article  Google Scholar 

  28. 28

    Chintakayala, K. et al. E. coli Fis protein insulates the cbpA gene from uncontrolled transcription. PLoS Genet. 9, e1003152 (2013).

    CAS  Article  Google Scholar 

  29. 29

    Wade, J. T. et al. Extensive functional overlap between σ factors in Escherichia coli. Nat. Struct. Mol. Biol. 13, 806–814 (2006).

    CAS  Article  Google Scholar 

  30. 30

    Haycocks, J. R., Sharma, P., Stringer, A. M., Wade, J. T. & Grainger, D. C. The molecular basis for control of ETEC enterotoxin expression in response to environment and host. PLoS Pathogens 11, e1004605 (2015).

    Article  Google Scholar 

  31. 31

    Piper, S. E., Mitchell, J. E., Lee, D. J. & Busby, S. J. A global view of Escherichia coli Rsd protein and its interactions. Mol. Biosyst. 5, 1943–1947 (2009).

    CAS  Article  Google Scholar 

  32. 32

    Srinivasan, R., Scolari, V. F., Lagomarsino, M. C. & Seshasayee, A. S. The genome-scale interplay amongst xenogene silencing, stress response and chromosome architecture in Escherichia coli. Nucleic Acids Res. 43, 295–308 (2015).

    CAS  Article  Google Scholar 

  33. 33

    Oshima, T., Ishikawa, S., Kurokawa, K., Aiba, H. & Ogasawara, N. Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase. DNA Res. 13, 141–153 (2006).

    CAS  Article  Google Scholar 

  34. 34

    Lovén, J. et al. Revisiting global gene expression analysis. Cell 151, 476–482 (2012).

    Article  Google Scholar 

  35. 35

    Lawrence, J. G. & Ochman, H. Molecular archaeology of the Escherichia coli genome. Proc. Natl Acad. Sci. USA 95, 9413–9417 (1998).

    CAS  Article  Google Scholar 

  36. 36

    Zarei, M., Sclavi, B. & Cosentino Lagomarsino, M. Gene silencing and large-scale domain structure of the E. coli genome. Mol. Biosyst. 9, 758–767 (2013).

    CAS  Article  Google Scholar 

  37. 37

    Dame, R. T., Kalmykowa, O. J. & Grainger, D. C. Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in Gram negative bacteria. PLoS Genet. 7, e1002123 (2011).

    CAS  Article  Google Scholar 

  38. 38

    Junier, I., Boccard, F. & Espéli, O. Polymer modeling of the E. coli genome reveals the involvement of locus positioning and macrodomain structuring for the control of chromosome conformation and segregation. Nucleic Acids Res. 42, 1461–1473 (2014).

    CAS  Article  Google Scholar 

  39. 39

    Youngren, B., Nielsen, H. J., Jun, S. & Austin, S. The multifork Escherichia coli chromosome is a self-duplicating and self-segregating thermodynamic ring polymer. Genes Dev. 28, 71–84 (2014).

    CAS  Article  Google Scholar 

  40. 40

    Stracy, M. et al. Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid. Proc. Natl Acad. Sci. USA 112, E4390–E4399 (2015).

    CAS  Article  Google Scholar 

  41. 41

    Ali, S. S. et al. Silencing by H-NS potentiated the evolution of Salmonella. PLoS Pathogens 10, e1004500 (2014).

    Article  Google Scholar 

  42. 42

    Lee, D. J., Minchin, S. D. & Busby, S. J. Activating transcription in bacteria. Annu. Rev. Microbiol. 66, 125–152 (2012).

    CAS  Article  Google Scholar 

  43. 43

    Miroslavova, N. S. & Busby, S. J. Investigations of the modular structure of bacterial promoters. Biochem. Soc. Symp. 73, 1–10 (2006).

    CAS  Article  Google Scholar 

  44. 44

    Castang, S., McManus, H. R., Turner, K. H. & Dove, S. L. H-NS family members function coordinately in an opportunistic pathogen. Proc. Natl Acad. Sci. USA 105, 18947–18952 (2008).

    CAS  Article  Google Scholar 

  45. 45

    Li, C., Wally, H., Miller, S. J. & Lu, C. D. The multifaceted proteins MvaT and MvaU, members of the H-NS family, control arginine metabolism, pyocyanin synthesis, and prophage activation in Pseudomonas aeruginosa PAO1. J. Bacteriol. 191, 6211–6218 (2009).

    CAS  Article  Google Scholar 

  46. 46

    Kotlajich, M. V. et al. Bridged filaments of histone-like nucleoid structuring protein pause RNA polymerase and aid termination in bacteria. eLife 4, e04970 (2015).

    Article  Google Scholar 

  47. 47

    Page, L., Griffiths, L. & Cole, J. A. Different physiological roles of two independent pathways for nitrite reduction to ammonia by enteric bacteria. Arch. Microbiol. 154, 349–354 (1990).

    CAS  Article  Google Scholar 

  48. 48

    Keseler, I. M., et al. EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res. 41, D605–D612 (2013).

    CAS  Article  Google Scholar 

  49. 49

    Lee, D. J. et al. Gene doctoring: a method for recombineering in laboratory and pathogenic Escherichia coli strains. BMC Microbiol. 9, 252 (2009).

    Article  Google Scholar 

  50. 50

    Rhodius, V. A. & Busby, S. J. Interactions between activating region 3 of the Escherichia coli cyclic AMP receptor protein and region 4 of the RNA polymerase σ70 subunit: application of suppression genetics. J. Mol. Biol. 299, 311–324 (2000).

    CAS  Article  Google Scholar 

  51. 51

    Lodge, J., Fear, J., Busby, S., Gunasekaran, P. & Kamini, N. R. Broad host range plasmids carrying the Escherichia coli lactose and galactose operons. FEMS Microbiol. Lett. 74, 271–276 (1992).

    CAS  Article  Google Scholar 

  52. 52

    Miller, J. H. Experiments in Molecular Genetics (Cold Spring Harbor Laboratory Press, 1972).

    Google Scholar 

  53. 53

    Grainger, D. C., Goldberg, M. D., Lee, D. J. & Busby, S. J. Selective repression by Fis and H-NS at the Escherichia coli dps promoter. Mol. Microbiol. 68, 1366–1377 (2008).

    CAS  Article  Google Scholar 

  54. 54

    Grainger, D. C., Belyaeva, T. A., Lee, D. J., Hyde, E. I. & Busby, S. J. Transcription activation at the Escherichia coli melAB promoter: interactions of MelR with the C-terminal domain of the RNA polymerase α subunit. Mol. Microbiol. 51, 1311–1320 (2004).

    CAS  Article  Google Scholar 

  55. 55

    Savery, N. J. et al. Transcription activation at Class II CRP-dependent promoters: identification of determinants in the C-terminal domain of the RNA polymerase α subunit. EMBO J. 17, 3439–3447 (1998).

    CAS  Article  Google Scholar 

  56. 56

    Kolb, A., Kotlarz, D., Kusano, S. & Ishihama, A. Selectivity of the Escherichia coli RNA polymerase Eσ38 for overlapping promoters and ability to support CRP activation. Nucleic Acids Res. 23, 819–826 (1995).

    CAS  Article  Google Scholar 

  57. 57

    Stringer, A. M. et al. Genome-scale analyses of Escherichia coli and Salmonella enterica AraC reveal noncanonical targets and an expanded core regulon. J. Bacteriol. 196, 660–671 (2014).

    Article  Google Scholar 

  58. 58

    Endesfelder, U. et al. Multiscale spatial organization of RNA polymerase in Escherichia coli. Biophys. J. 105, 172–181 (2013).

    CAS  Article  Google Scholar 

  59. 59

    Zawadzki, P. et al. The localization and action of topoisomerase IV in Escherichia coli chromosome segregation is coordinated by the SMC complex, MukBEF. Cell Rep. 13, 2587–2596 (2015).

    CAS  Article  Google Scholar 

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This work was funded by a Leverhulme Trust project grant (RPG-2013-147) and Wellcome Trust Career Development Fellowship (WT085092MA) awarded to D.C.G. Support for J.T.W. was a National Institutes of Health Director's New Innovator Award (1DP2OD007188). A.N.K. and M.S. were supported by a Biotechnology and Biological Sciences Research Council grant (BB/N018656/1, to A.N.K. and M.S.) and a Wellcome Trust Investigatorship (110164/Z/15/Z, to A.N.K.). We thank J. Hinton for the gift of anti-H-NS antiserum.

Author information




D.C.G. and J.T.W. designed the study and wrote the manuscript. L.E.L., G.B., S.S.S., A.M.S., R.P.B. and M.S. generated the data and prepared it for publication. M.S. and A.N.K. provided new analytical tools and critically discussed the manuscript with D.C.G. and J.T.W. All authors contributed to data analysis and interpretation.

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Correspondence to David C. Grainger.

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The authors declare no competing financial interests.

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Supplementary Figures 1–7, Supplementary Table 1. (PDF 1114 kb)

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Lamberte, L., Baniulyte, G., Singh, S. et al. Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase. Nat Microbiol 2, 16249 (2017).

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