Silencing of foreign DNA by the H-NS like proteins of bacteria


The bacteria behind the most devastating human disease epidemics have profoundly shaped human history.  In the middle ages bubonic plague killed 1/3 to 1/2 of Europe and Asia in just 8 years (1346-1353). Cholera has caused numerous pandemics throughout our history that have resulted in millions of deaths, and severe outbreaks have occurred recently in Haiti and Africa.  Tuberculosis, currently the number one bacterial cause of death, infects one-third of the people on the planet.  Surprisingly all of these pathogens evolved from non-pathogenic bacteria that can be found in soil or water.  How do new pathogens arise, seemingly from nowhere?  How do they adapt to the human host after evolving for millenia in non-host environments?

During infection of an animal host, pathogens like Salmonella are brought in contact with a wide variety of hostile environments.  Successful pathogens have evolved sophisticated mechanisms that enable them to withstand the harmful effectors of the immune response and thrive in places where most non-pathogens are easily eliminated.  


Not all environments are equal within the host and the way a pathogen survives in one environment (e.g. the stomach) may be detrimental in another (e.g. the large intestine).  Bacterial pathogens have therefore evolved to regulate particular virulence genes in response to cues they detect in their local environment.  In this way they ensure that the proper genes are expressed at the appropriate time and place.  The details of what host signals are being sensed and exactly how this information is integrated into an effective response is an area of intense research.

The virulence genes that many pathogens use to cause disease are often recent additions to the bacterial genome, having been acquired from a foreign source via a process known as horizontal (or lateral) transfer.  Virulence and antibiotic resistance genes are frequently carried on phages, plasmids, and transposable elements.  These include genes found in pathogenic E. coli, Salmonella, Vibrio, Yersinia, Bacillus anthracis, Staphylococcus and Franciscella.  One question is how a bacterial cell can evolve to properly regulate a gene it acquired from a foreign source.

figure 5

Often foreign genes look different than the other resident genes in the genome and are more AT-rich than the other genes in the genome in a surprising majority of cases. We discovered the H-NS protein of Salmonella and E. coli, selectively silences the expression of AT-rich genes.  This includes about 15-20% of the genome including almost every gene involved in virulence.  Because of this H-NS is the master virulence regulator of the cell that also protects the cell from the detrimental consequences that could occur when newly acquired genes integrate into the resident genome.  H-NS silenced genes need to be expressed (counter-silenced) at specific times during infection and projects are underway to explore the different mechanisms by which counter-silencing can occur.  In collaboration with Dr. Jun Liu we have also explored the function of Ls32, an H-NS like molecule from Mycobacteria, the causative agent of tuberculosis.


Ali, S.S., Soo, J., Rao, C., Leung, A.S., Ngai, D.H-M., Ensminger, A.W., and W.W. Navarre. (2014) Silencing by H-NS potentiated the evolution of Salmonella.  PLoS Pathogens (in press)

Wang, H., Epstein, S., Ali, S.S., Navarre, W.W. and J. Milstein (2014) A biomechanical mechanism for initiating DNA packaging.  Nucleic Acids Research doi: 10.1093/nar/gku896

Ali, S.S., Whitney, J.C., Stevenson, J., Robinson, H., Howell, P.L., and W.W. Navarre (2013) Structural Insights into the Regulation of Foreign Genes in Salmonella by the Hha/H-NS Complex. Journal of Biological Chemistry 288(19):13356-13369.

Ali, S.S., Xia, B., Liu, J., and W. W. Navarre (2012) Silencing of foreign DNA in bacteria. Current Opinion in Microbiology 15(2):175-181

Ali, S.S., Beckett, E., Bae, S.J., and W.W. Navarre (2011) The 5.5 protein of phage T7 inhibits H-NS through interactions with the central oligomerization domain. Journal of Bacteriology, 193(18):4881-4892

Gordon, B.R., Li, Y., Cote, A., Weirauch, M., Ding, P., Hughes, T., Navarre, W.W., Xia, B. and J. Liu (2011) Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins.  Proc. Natl. Acad. Sci. USA. 108(26):10690-10695

Protein Translation in Control of Virulence Gene Expression

Navarre NIH lambda

art by Hervé Roy

During a screen for Salmonella mutants that are unable to cause disease in mice we discovered that deletion of two closely linked genes, poxA and yjeK, led to a severe defect in Salmonella virulence. The protein encoded by the poxA gene is related to the lysyl-tRNA synthetase family of enzymes (i.e. the enzymes that charge tRNAs with the amino acid lysine).  YjeK encodes an enzyme that converts lysine to an unusual molecule called beta-lysine.  We have determined that PoxA and YjeK act in a common pathway to modify another protein called EF-P (elongation factor P).  The addition of beta-lysine to EF-P by PoxA and YjeK represents an entirely new mechanism of post-translational modification.

In the absence of the PoxA, YjeK, or EF-P, Salmonella cells are susceptible to a number of different forms of cellular stress.  Notably these mutant cells display increased sensitivity to several classes of antibiotics.  They also display unusual metabolic hyperactivity.  This pathway could be a novel target for new antimicrobial compounds.


Hersch, S.J., Elgamal, S., Katz, A., Ibba, M., and W.W. Navarre (2014) Translation Initiation Rate Determines the Impact of Ribosome Stalling on Bacterial Protein Synthesis. Journal of Biological Chemistry 289(41):28160-28171

Elgamal, S., Katz, A., Hersch, S.J., Newsom, D., White, P., Navarre, W.W. and M. Ibba (2014) EF-P dependent pauses integrate proximal and distal signals during translation. PLoS Genetics 10(8):e1004553. doi:10.1371/journal.pgen.1004553

Katz, A., Solden, L., Zou, S.B., Navarre W.W., and M. Ibba (2014) Molecular evolution of protein-RNA mimicry as a mechanism for translational control. Nucleic Acids Research 42(5):3261-3271.

Hersch, S.J., Wang, M., Zou, S.B., Moon, K-M., Foster, L.J., Ibba, M., and W.W. Navarre (2013) Divergent protein motifs direct EF-P mediated translational regulation in Salmonella and E. coli.  mBio 4(2) e00180-13.  doi: 10.1128/mBio.00180-13.

Zou, S.B., Hersch, S.J., Roy, H., Wiggers, J.B., Leung, A.L., Buranyi, S.G., Xie, J.L., Dare, K., Ibba, M., and W.W. Navarre (2012) Loss of elongation factor P disrupts bacterial outer membrane integrity. Journal of Bacteriology 194(2):413-425    * Note: Authors correction in Journal of Bacteriology (2012), 194(16):4484.

Roy, H., Zou S.B., Bullwinkle, T.B., Wolfe, B.S., Gilreath, M.S., Forsyth, C.J., Navarre, W.W., and M. Ibba  (2011) The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-β-lysine. Nature Chemical Biology, 7(10):667-669

Navarre lab - university of Toronto