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Updated: Aug 14, 2026

An Assay for Quantifying Protein-RNA Binding in Bacteria
Published on: June 12, 2019
Crystal structure of the restriction-modification system control element C.Bcll and mapping of its binding site
Michael R Sawaya1, Zhenyu Zhu, Fana Mersha
1UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, 205 Boyer Hall, Box 951570, Los Angeles, California 90095, USA.
Abstract:
Protection from DNA invasion is afforded by restriction-modification systems in many bacteria. The efficiency of protection depends crucially on the relative expression levels of restriction versus methytransferase genes. This regulation is provided by a controller protein, named C protein. Studies of the Bcll system in E. coli suggest that C.Bcll functions as a negative regulator for M.Bcll expression, implying that it plays a role in defense against foreign DNA during virus infection. C.Bcll binds (Kd = 14.3 nM) to a 2-fold symmetric C box DNA sequence that overlaps with the putative -35 promoter region upstream of the bcllM and bcllC genes. The C.Bcll fold comprises five alpha helices: two helices form a helix-turn-helix motif, and the remaining three helices form the extensive dimer interface. The C.Bcll-DNA model proposed suggests that DNA bending might play an important role in gene regulation, and that Glu27 and Asp31 in C.Bcll might function critically in the regulation.
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