Sanchez-Alberola Neus, Campoy Susana, Emerson David, Barbé Jordi, Erill Ivan
Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA.
Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain.
J Bacteriol. 2015 Aug;197(16):2622-30. doi: 10.1128/JB.00035-15. Epub 2015 May 18.
The SOS response is a transcriptional regulatory network governed by the LexA repressor that activates in response to DNA damage. In the Betaproteobacteria, LexA is known to target a palindromic sequence with the consensus sequence CTGT-N8-ACAG. We report the characterization of a LexA regulon in the iron-oxidizing betaproteobacterium Sideroxydans lithotrophicus. In silico and in vitro analyses show that LexA targets six genes by recognizing a binding motif with the consensus sequence GAACGaaCGTTC, which is strongly reminiscent of the Bacillus subtilis LexA-binding motif. We confirm that the closely related Gallionella capsiferriformans shares the same LexA-binding motif, and in silico analyses indicate that this motif is also conserved in the Nitrosomonadales and the Methylophilales. Phylogenetic analysis of LexA and the alpha subunit of DNA polymerase III (DnaE) reveal that the organisms harboring this noncanonical LexA form a compact taxonomic cluster within the Betaproteobacteria. However, their lexA gene is unrelated to the standard Betaproteobacteria lexA, and there is evidence of its spread through lateral gene transfer. In contrast to other reported cases of noncanonical LexA-binding motifs, the regulon of S. lithotrophicus is comparable in size and function to that of many other Betaproteobacteria, suggesting that a convergent SOS regulon has reevolved under the control of a new LexA protein. Analysis of the DNA-binding domain of S. lithotrophicus LexA reveals little sequence similarity with that of other LexA proteins targeting similar binding motifs, suggesting that network structure may limit site evolution or that structural constrains make the B. subtilis-type motif an optimal interface for multiple LexA sequences.
Understanding the evolution of transcriptional systems enables us to address important questions in microbiology, such as the emergence and transfer potential of different regulatory systems to regulate virulence or mediate responses to stress. The results reported here constitute the first characterization of a noncanonical LexA protein regulating a standard SOS regulon. This is significant because it illustrates how a complex transcriptional program can be put under the control of a novel transcriptional regulator. Our results also reveal a substantial degree of plasticity in the LexA recognition domain, raising intriguing questions about the space of protein-DNA interfaces and the specific evolutionary constrains faced by these elements.
SOS应答是一种由LexA阻遏物调控的转录调控网络，它在DNA损伤时被激活。在β-变形菌纲中，已知LexA靶向具有共有序列CTGT-N8-ACAG的回文序列。我们报道了铁氧化β-变形菌嗜铁氧化硫杆菌中LexA调控子的特征。计算机模拟和体外分析表明，LexA通过识别具有共有序列GAACGaaCGTTC的结合基序来靶向六个基因，这与枯草芽孢杆菌的LexA结合基序非常相似。我们证实密切相关的荚膜嘉利翁氏菌具有相同的LexA结合基序，并且计算机模拟分析表明该基序在亚硝化单胞菌目和嗜甲基菌目中也保守。对LexA和DNA聚合酶III的α亚基（DnaE）的系统发育分析表明，携带这种非典型LexA的生物体在β-变形菌纲中形成了一个紧密的分类学簇。然而，它们的lexA基因与标准的β-变形菌纲lexA无关，并且有证据表明它是通过横向基因转移传播的。与其他报道的非典型LexA结合基序的情况不同，嗜铁氧化硫杆菌的调控子在大小和功能上与许多其他β-变形菌纲的调控子相当，这表明一个趋同的SOS调控子在一种新的LexA蛋白的控制下重新进化。对嗜铁氧化硫杆菌LexA的DNA结合结构域的分析表明，它与靶向相似结合基序的其他LexA蛋白的序列相似性很小，这表明网络结构可能限制位点进化，或者结构限制使枯草芽孢杆菌型基序成为多个LexA序列的最佳界面。
了解转录系统的进化使我们能够解决微生物学中的重要问题，例如不同调控系统调节毒力或介导应激反应的出现和转移潜力。这里报道的结果构成了对调控标准SOS调控子的非典型LexA蛋白的首次表征。这很重要，因为它说明了一个复杂的转录程序如何能够置于一种新型转录调节因子的控制之下。我们的结果还揭示了LexA识别结构域有很大程度的可塑性，这就提出了关于蛋白质-DNA界面空间以及这些元件所面临的特定进化限制的有趣问题。
