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Nucleic Acids Research Advance Access originally published online on April 29, 2008
Nucleic Acids Research 2008 36(10):3463-3473; doi:10.1093/nar/gkn199
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Nucleic Acids Research, 2008, Vol. 36, No. 10 3463-3473
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Insights into anti-termination regulation of the hut operon in Bacillus subtilis: importance of the dual RNA-binding surfaces of HutP

Subash C. B. Gopinath1, Dhakshnamoorthy Balasundaresan1, Thirumananseri Kumarevel2, Tomoko S. Misono1, Hiroshi Mizuno1 and Penmetcha K. R. Kumar*

1Functional Nucleic Acids Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba City 305-8566, Ibaraki and 2Biometal Science Laboratory & Protein Crystallography Research Group, RIKEN Spring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan

*To whom correspondence should be addressed. Tel: +81 298 61 6085; Fax: +81 298 61 6095; Email: pkr-kumar{at}aist.go.jp

Received February 18, 2008. Revised April 1, 2008. Accepted April 2, 2008.

The anti-termination protein, HutP, regulates the gene expression of the hut (histidine utilization) operon of Bacillus subtilis, by destabilizing the hut terminator RNA located upstream of the coding region encoding L-histidine degradation enzymes. On the basis of biochemical, in vivo and X-ray structural analyses, we now report that HutP uses its dual RNA-binding surfaces to access two XAG-rich regions (sites I and II) within the terminator RNA to mediate the destabilization process. In this process, HutP initiates destabilization at the 5'-end of its mRNA by binding to the first XAG-rich region (site I) and then accesses the second XAG-rich region (site II), located downstream of the stable G-C-rich segment of the terminator stem. By this action, HutP appears to disrupt the G-C-rich terminator stem, and thus prevents premature termination of transcription in the RNA segment preceding the regions encoding for the histidine degradation enzymes.


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