Department of Chemistry and Biochemistry, Biophysics Graduate Program, and Center for RNA Biology, College of Pharmacy, The Ohio State University, Columbus, OH 43210.
Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3442-7. doi: 10.1073/pnas.1315281111. Epub 2014 Feb 18.
The control of tryptophan production in Bacillus is a paradigmatic example of gene regulation involving the interplay of multiple protein and nucleic acid components. Central to this combinatorial mechanism are the homo-oligomeric proteins TRAP (trp RNA-binding attenuation protein) and anti-TRAP (AT). TRAP forms undecameric rings, and AT assembles into triskelion-shaped trimers. Upon activation by tryptophan, the outer circumference of the TRAP ring binds specifically to a series of tandem sequences present in the 5' UTR of RNA transcripts encoding several tryptophan metabolism genes, leading to their silencing. AT, whose expression is up-regulated upon tryptophan depletion to concentrations not exceeding a ratio of one AT trimer per TRAP 11-mer, restores tryptophan production by binding activated TRAP and preventing RNA binding. How the smaller AT inhibitor prevents RNA binding at such low stoichiometries has remained a puzzle, in part because of the large RNA-binding surface on the tryptophan-activated TRAP ring and its high affinity for RNA. Using X-ray scattering, hydrodynamic, and mass spectrometric data, we show that the polydentate action of AT trimers can condense multiple intact TRAP rings into large heterocomplexes, effectively reducing the available contiguous RNA-binding surfaces. This finding reveals an unprecedented mechanism for substoichiometric inhibition of a gene-regulatory protein, which may be a widespread but underappreciated regulatory mechanism in pathways that involve homo-oligomeric or polyvalent components.
色氨酸生产的控制是涉及多个蛋白质和核酸成分相互作用的基因调控的典范例子。这种组合机制的核心是同型寡聚蛋白 TRAP（色氨酸 RNA 结合衰减蛋白）和抗 TRAP（AT）。TRAP 形成十一聚体环，而 AT 组装成三叶草形三聚体。在色氨酸激活后，TRAP 环的外周长特异性结合 RNA 转录物 5'UTR 中存在的一系列串联序列，这些序列编码几种色氨酸代谢基因，导致它们沉默。AT 的表达在色氨酸耗尽时被上调，以不超过每个 TRAP 十一聚体 1 个 AT 三聚体的比例，通过结合激活的 TRAP 并阻止 RNA 结合来恢复色氨酸的产生。较小的 AT 抑制剂如何在如此低的化学计量比下防止 RNA 结合一直是一个谜，部分原因是色氨酸激活的 TRAP 环具有大的 RNA 结合表面及其与 RNA 的高亲和力。使用 X 射线散射、流体动力学和质谱数据，我们表明 AT 三聚体的多齿作用可以将多个完整的 TRAP 环凝聚成大的杂合复合物，有效地减少可用的连续 RNA 结合表面。这一发现揭示了一种前所未有的亚化学计量抑制基因调控蛋白的机制，这可能是涉及同型寡聚体或多价成分的途径中的一种广泛但未被充分认识的调控机制。
