Indirect DNA readout by an H-NS related protein: structure of the DNA complex of the C-terminal domain of Ler.
Indirect DNA readout by an H-NS related protein: structure of the DNA complex of the C-terminal domain of Ler.
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DOI：
10.1371/journal.ppat.1002380
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发表时间：
2011-11
期刊：
影响因子：
6.7
通讯作者：
Pons M
中科院分区：
文献类型：
--
作者：
Cordeiro TN;Schmidt H;Madrid C;Juárez A;Bernadó P;Griesinger C;García J;Pons M
Ler是H-NS蛋白家族的一员，是致病性大肠杆菌菌株LEE致病性岛的主要调控因子。在这里，我们确定了Ler的DNA结合域（CT-Ler）和15-mer DNA双链之间的复合物的结构。CT-Ler识别DNA小凹槽中预先存在的结构模式，由两个连续区域形成，分别比标准B-DNA更窄和更宽。与at链相关的压缩区域被Arg90侧链感知，其突变会消除Ler结合DNA的能力。扩展槽允许进入Arg90所在的回路。这是第一个关于包含H-NS家族蛋白质的DNA复合体的实验结构的报告。间接读出机制不仅解释了H-NS和其他H-NS家族成员调节大量基因表达的能力，也解释了Ler所表现出的特异性的来源。我们的研究结果指出了一种普遍的机制，通过这种机制，水平获得的基因可能被H-NS家族成员特异性识别。致病性大肠杆菌菌株和其他肠杆菌携带通过水平基因转移过程从其他细菌获得的基因。对特定时刻表达的基因进行适当的调控对细菌的成功至关重要。蛋白质H-NS是一种结合DNA的全局调节剂，在需要之前保持大量基因沉默，例如，维持细菌在新宿主的定植。Ler是H-NS家族的一员，与H-NS竞争激活一组水平获得基因的表达，这些基因编码大肠杆菌用来感染人类细胞的分子机器。Ler和H-NS具有相似的DNA结合结构域，可以结合不同的DNA序列。在这里，我们展示了Ler的DNA结合域和天然DNA片段之间的复合物结构。这种结构揭示了Ler识别特定的DNA形状，解释了它调节不同序列基因的能力。单个精氨酸残基是识别DNA狭窄小槽的关键，这是H-NS和Ler识别的DNA形状的标志之一，尽管不是唯一的标志。
Ler, a member of the H-NS protein family, is the master regulator of the LEE pathogenicity island in virulent Escherichia coli strains. Here, we determined the structure of a complex between the DNA-binding domain of Ler (CT-Ler) and a 15-mer DNA duplex. CT-Ler recognizes a preexisting structural pattern in the DNA minor groove formed by two consecutive regions which are narrower and wider, respectively, compared with standard B-DNA. The compressed region, associated with an AT-tract, is sensed by the side chain of Arg90, whose mutation abolishes the capacity of Ler to bind DNA. The expanded groove allows the approach of the loop in which Arg90 is located. This is the first report of an experimental structure of a DNA complex that includes a protein belonging to the H-NS family. The indirect readout mechanism not only explains the capacity of H-NS and other H-NS family members to modulate the expression of a large number of genes but also the origin of the specificity displayed by Ler. Our results point to a general mechanism by which horizontally acquired genes may be specifically recognized by members of the H-NS family. Pathogenic Escherichia coli strains and other enterobacteria carry genes acquired from other bacteria by a process known as horizontal gene transfer. Proper regulation of the genes that are expressed in a given moment is crucial for the success of the bacteria. The protein H-NS is a global regulator that binds DNA and maintains a large number of genes silent until they are required, for example, to sustain the bacteria's colonization of a new host. Ler is a member of the H-NS family that competes with H-NS to activate the expression of a group of horizontally acquired genes that encode for a molecular machine used by E. coli to infect human cells. Ler and H-NS share a similar DNA-binding domain and can bind to different DNA sequences. Here, we present the structure of a complex between the DNA-binding domain of Ler and a natural DNA fragment. This structure reveals that Ler recognizes specific DNA shapes, explaining its capacity to regulate genes with different sequences. A single arginine residue is key for the recognition of a DNA narrow minor groove, which is one of, though not the only, hallmarks of the DNA shapes that are recognized by H-NS and Ler.
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影响因子：
14.9
作者：
Lang B;Blot N;Bouffartigues E;Buckle M;Geertz M;Gualerzi CO;Mavathur R;Muskhelishvili G;Pon CL;Rimsky S;Stella S;Babu MM;Travers A
通讯作者：
Travers A
影响因子：
3.6
作者：
Friedberg, D;Umanski, T;Rosenshine, I
通讯作者：
Rosenshine, I
DOI：
10.1073/pnas.0913551107
发表时间：
2010-03-16
影响因子：
11.1
作者：
Gordon, Blair R. G.;Li, Yifei;Liu, Jun
通讯作者：
Liu, Jun
影响因子：
6.1
作者：
Konarev, PV;Volkov, VV;Svergun, DI
通讯作者：
Svergun, DI
DOI：
10.1107/s0907444998003254
发表时间：
1998-09-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Brunger, AT;Adams, PD;Warren, GL
通讯作者：
Warren, GL