Regulatory features of the trp operon and the crystal structure of the trp RNA-binding attenuation protein from Bacillus stearothermophilus.

Characterization of both the cis and trans -acting regulatory elements indicates that the Bacillus stearothermophilustrp operon is regulated by an attenuation mechanism similar to that which controls the trp operon in Bacillus subtilis. Secondary structure predictions indicate that the leader region of the trp mRNA is capable of folding into terminator and anti- terminator RNA structures. B. stearothermophilus also encodes an RNA-binding protein with 77% sequence identity with the RNA-binding protein (TRAP) that regulates attenuation in B. subtilis. The X-ray structure of this protein has been determined in complex with L-tryptophan at 2.5 A resolution. Like the B. subtilis protein, B. stearothermophilus TRAP has 11 subunits arranged in a ring-like structure. The central cavities in these two structures have different sizes and opposite charge distributions, and packing within the B. stearothermophilus TRAP crystal form does not generate the head-to-head dimers seen in the B. subtilis protein, suggesting that neither of these properties is functionally important. However, the mode of L-tryptophan binding and the proposed RNA binding surfaces are similar, indicating that both proteins are activated by l -tryptophan and bind RNA in essentially the same way. As expected, the TRAP:RNA complex from B. stearothermophilus is significantly more thermostable than that from B. subtilis, with optimal binding occurring at 70 degrees C.     

Effects of mutations in the L-tryptophan binding pocket of the Trp RNA-binding attenuation protein of Bacillus subtilis

The Bacillus subtilis tryptophan biosynthetic genes are regulated by the trp RNA-binding attenuation protein (TRAP). Cooperative binding of L-tryptophan activates TRAP so that it can bind to RNA. The crystal structure revealed that L-tryptophan forms nine hydrogen bonds with various amino acid residues of TRAP. We performed site-directed mutagenesis to determine the importance of several of these hydrogen bonds in TRAP activation. We tested both alanine substitutions as well as substitutions more closely related to the natural amino acid at appropriate positions. Tryptophan binding mutations were identified in vivo having unchanged, reduced, or completely eliminated repression activity. Several of the in vivo defective TRAP mutants exhibited reduced affinity for tryptophan in vitro but did not interfere with RNA binding at saturating tryptophan concentrations. However, a 10-fold decrease in TRAP affinity for tryptophan led to an almost complete loss of regulation, whereas increased TRAP affinity for tryptophan had little or no effect on the in vivo regulatory activity of TRAP. One hydrogen bond was found to be dispensable for TRAP activity, whereas two others appear to be essential for TRAP function. Another mutant protein exhibited tryptophan-independent RNA binding activity. We also found that trp leader RNA increases the affinity of TRAP for tryptophan.     

色氨酸操纵子调控机理详析

色氨酸操纵子是最早被研究的细菌合成代谢调控、基因表达调控的模型之一。其中阻遏蛋白对转录起始的抑制作用、色氨酸作为辅阻遏物的作用以及通过定点突变揭示的弱化作用的分子机制已基本被阐明。此外,色氨酸操纵子RNA结合弱化蛋白、NusA、NusG、TrpY等调节蛋白对细菌色氨酸操纵子弱化作用的调节机制也在近年来得到进一步揭示。特别是在枯草芽孢杆菌中,色氨酸操纵子主要依赖于转录衰减机制调控,包括由色氨酸激活的色氨酸操纵子RNA结合弱化蛋白与新生转录产物结合形成内部终止子,导致5′非翻译区（5′UTR）转录终止。NusA、NusG通过刺激RNA聚合酶在5′UTR的U107和U144位点暂停,释放出RNA聚合酶,最终造成转录终止。不同的是,在U144位点NusA参与的转录弱化机制依赖其发夹结构,且NusA与RNA聚合酶作用促进了RNA结合弱化蛋白与新生转录产物的结合,使转录终止。而NusG是通过与非模板DNA链中的一段富含T碱基序列和RNA聚合酶同时互作,阻止了RNA聚合酶向下游移动,从而引起RNA聚合酶高效停滞。但在细菌操纵子中,绝大多数调节因子参与的弱化机制最终依赖于ρ因子,从而导致多达一半的转录终止事件发生。近年来,随着学科的发展,越来越多关于色氨酸操纵子调节机制新概念被挖掘报道,这也使人类对色氨酸操纵子的表达调控机制的认知愈加详尽。