Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
Department of Biochemistry, University of Washington, Seattle, Washington, USA.
mBio. 2019 Mar 5;10(2):e00009-19. doi: 10.1128/mBio.00009-19.
Gene duplication and subsequent evolutionary divergence have allowed conserved proteins to develop unique roles. The MarR family of transcription factors (TFs) has undergone extensive duplication and diversification in bacteria, where they act as environmentally responsive repressors of genes encoding efflux pumps that confer resistance to xenobiotics, including many antimicrobial agents. We have performed structural, functional, and genetic analyses of representative members of the SlyA/RovA lineage of MarR TFs, which retain some ancestral functions, including repression of their own expression and that of divergently transcribed multidrug efflux pumps, as well as allosteric inhibition by aromatic carboxylate compounds. However, SlyA and RovA have acquired the ability to countersilence horizontally acquired genes, which has greatly facilitated the evolution of by horizontal gene transfer. SlyA/RovA TFs in different species have independently evolved novel regulatory circuits to provide the enhanced levels of expression required for their new role. Moreover, in contrast to MarR, SlyA is not responsive to copper. These observations demonstrate the ability of TFs to acquire new functions as a result of evolutionary divergence of both -regulatory sequences and in interactions with modulatory ligands. Bacteria primarily evolve via horizontal gene transfer, acquiring new traits such as virulence and antibiotic resistance in single transfer events. However, newly acquired genes must be integrated into existing regulatory networks to allow appropriate expression in new hosts. This is accommodated in part by the opposing mechanisms of xenogeneic silencing and countersilencing. An understanding of these mechanisms is necessary to understand the relationship between gene regulation and bacterial evolution. Here we examine the functional evolution of an important lineage of countersilencers belonging to the ancient MarR family of classical transcriptional repressors. We show that although members of the SlyA lineage retain some ancestral features associated with the MarR family, their -regulatory sequences have evolved significantly to support their new function. Understanding the mechanistic requirements for countersilencing is critical to understanding the pathoadaptation of emerging pathogens and also has practical applications in synthetic biology.
基因复制和随后的进化分歧使保守蛋白具有独特的功能。MarR 家族转录因子（TFs）在细菌中经历了广泛的复制和多样化，它们作为环境响应的负调控因子，抑制编码外排泵的基因，使细菌对抗生素等外源性化合物产生抗性，包括许多抗菌剂。我们对 MarR TF 的 SlyA/RovA 谱系的代表性成员进行了结构、功能和遗传分析，这些成员保留了一些祖先功能，包括对自身表达和转录方向不同的多药外排泵的表达的抑制，以及芳香羧酸化合物的变构抑制。然而，SlyA 和 RovA 获得了抑制水平获得的基因的能力，这极大地促进了通过水平基因转移的进化。不同物种中的 SlyA/RovA TF 独立进化出了新的调控回路，为其新功能提供了所需的表达水平的提高。此外，与 MarR 不同，SlyA 对铜没有反应。这些观察结果表明，TFs 能够通过进化分歧获得新的功能，包括 -调节序列和与调节配体的相互作用。细菌主要通过水平基因转移进化，在单个转移事件中获得新的特征，如毒力和抗生素抗性。然而，新获得的基因必须整合到现有的调控网络中，以允许在新宿主中适当表达。这在一定程度上是通过异种基因沉默和反沉默的相反机制来实现的。了解这些机制对于理解基因调控与细菌进化之间的关系是必要的。在这里，我们研究了属于经典转录阻遏物古老 MarR 家族的重要反沉默因子谱系的功能进化。我们表明，尽管 SlyA 谱系的成员保留了与 MarR 家族相关的一些祖先特征，但它们的 -调节序列已经发生了显著进化，以支持它们的新功能。了解反沉默的机制要求对于理解新兴病原体的病理适应至关重要，并且在合成生物学中也具有实际应用。
