University of Illinois at Chicago
Nucl. Acids Res.-2012-Lim-3316-28.pdf (6.8 MB)

Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility

Download (6.8 MB)
journal contribution
posted on 2013-11-07, 00:00 authored by Ci Ji Lim, Yixun R. Whang, Linda J. Kenney, Jie Yan
Nucleoid-associated proteins are bacterial proteins that are responsible for chromosomal DNA compaction and global gene regulation. One such protein is Escherichia coli Histone-like nucleoid structuring protein (H-NS) which functions as a global gene silencer. Whereas the DNA-binding mechanism of H-NS is well-characterized, its paralogue, StpA which is also able to silence genes is less understood. Here we show that StpA is similar to H-NS in that it is able to form a rigid filament along DNA. In contrast to H-NS, the StpA filament interacts with a naked DNA segment to cause DNA bridging which results in simultaneous stiffening and bridging of DNA. DNA accessibility is effectively blocked after the formation of StpA filament on DNA, suggesting rigid filament formation is the important step in promoting gene silencing. We also show that >1mM magnesium promotes higher order DNA condensation, suggesting StpA may also play a role in chromosomal DNA packaging.


The Ministry of Education of Singapore (R144000251112 to J.Y.); the Mechanobiology Institute, Singapore (R714005007271 and R714015007271 to J.Y.); the Veterans Administration (101BX000372 to L.J.K.). Funding for open access charge: Mechanobiology Institute of Singapore (R144000251112 to J.Y.).


Publisher Statement

© The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Nucleic Acids Research following peer review. The definitive publisher-authenticated version Lim, C. J., Y. X. R. Whang, et al. (2012). "Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility." Nucleic Acids Research 40(8): 3316-3328.DOI: 10.1093/nar/gkr1247 is available online at: DOI: 10.1093/nar/gkr1247


Oxford University Press


  • en_US



Issue date


Usage metrics


    No categories selected



    Ref. manager