Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies et Biotechnologie, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France.
Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.
mBio. 2023 Feb 28;14(1):e0300122. doi: 10.1128/mbio.03001-22. Epub 2023 Jan 19.
Myxococcus xanthus possesses two Fe-S cluster biogenesis machineries, ISC (iron-sulfur cluster) and SUF (sulfur mobilization). Here, we show that in comparison to the phylogenetically distant Enterobacteria, which also have both machineries, M. xanthus evolved an independent transcriptional scheme to coordinately regulate the expression of these machineries. This transcriptional response is directed by RisR, which we show to belong to a phylogenetically distant and biochemically distinct subgroup of the Rrf2 transcription factor family, in comparison to IscR that regulates the and operons in Enterobacteria. We report that RisR harbors an Fe-S cluster and that holo-RisR acts as a repressor of both the and operons, in contrast to Escherichia coli, where holo-IscR represses the operon whereas apo-IscR activates the operon. In addition, we establish that the nature of the cluster and the DNA binding sites of RisR, in the and operons, diverge from those of IscR. We further show that in M. xanthus, the two machineries appear to be fully interchangeable in maintaining housekeeping levels of Fe-S cluster biogenesis and in synthesizing the Fe-S cluster for their common regulator, RisR. We also demonstrate that in response to oxidative stress and iron limitation, transcriptional upregulation of the M. xanthus and operons was mediated solely by RisR and that the contribution of the SUF machinery was greater than the ISC machinery. Altogether, these findings shed light on the diversity of homeostatic mechanisms exploited by bacteria to coordinately use two Fe-S cluster biogenesis machineries. Fe-S proteins are ubiquitous and control a wide variety of key biological processes; therefore, maintaining Fe-S cluster homeostasis is an essential task for all organisms. Here, we provide the first example of how a bacterium from the Deltaproteobacteria branch coordinates expression of two Fe-S cluster biogenesis machineries. The results revealed a new model of coordination, highlighting the unique and common features that have independently emerged in phylogenetically distant bacteria to maintain Fe-S cluster homeostasis in response to environmental changes. Regulation is orchestrated by a previously uncharacterized transcriptional regulator, RisR, belonging to the Rrf2 superfamily, whose members are known to sense diverse environmental stresses frequently encountered by bacteria. Understanding how M. xanthus maintains Fe-S cluster homeostasis via RisR regulation revealed a strategy reflective of the aerobic lifestyle of this organsim. This new knowledge also paves the way to improve production of Fe-S-dependent secondary metabolites using M. xanthus as a chassis.
黄色粘球菌拥有两种铁硫簇生物发生机制，ISC（铁硫簇）和 SUF（硫动员）。在这里，我们表明，与具有这两种机制的系统发育上较远的 Enterobacteria 相比，黄色粘球菌进化出了一种独立的转录方案来协调调节这些机制的表达。这种转录反应是由 RisR 介导的，我们发现它属于 Rrf2 转录因子家族的一个系统发育上较远且生化上不同的亚群，而不是调节 Enterobacteria 中 和 操纵子的 IscR。我们报告说，RisR 含有一个铁硫簇，并且全酶 RisR 作为 和 操纵子的抑制剂，与大肠杆菌中的 holo-IscR 抑制 操纵子而 apo-IscR 激活 操纵子形成对比。此外，我们确定了 RisR 在 和 操纵子中的簇性质和 DNA 结合位点与 IscR 不同。我们进一步表明，在黄色粘球菌中，这两种机制似乎在维持铁硫簇生物发生的管家水平以及为其共同调节剂 RisR 合成铁硫簇方面是完全可互换的。我们还证明，在应对氧化应激和铁限制时，黄色粘球菌 和 操纵子的转录上调仅由 RisR 介导，并且 SUF 机制的贡献大于 ISC 机制。总之，这些发现揭示了细菌协调使用两种铁硫簇生物发生机制的多种体内平衡机制的多样性。Fe-S 蛋白无处不在，控制着广泛的关键生物学过程；因此，维持 Fe-S 簇的体内平衡是所有生物体的一项基本任务。在这里，我们提供了第一个例子，说明来自 Delta-proteobacteria 分支的细菌如何协调表达两种铁硫簇生物发生机制。结果揭示了一种新的协调模式，突出了在系统发育上相距较远的细菌中独立出现的独特和共同特征，以响应环境变化维持 Fe-S 簇的体内平衡。调节是由以前未被表征的转录调节剂 RisR 协调的，该调节剂属于 Rrf2 超家族，其成员已知可以感知细菌经常遇到的各种环境压力。了解黄色粘球菌如何通过 RisR 调节维持 Fe-S 簇的体内平衡，揭示了一种反映该生物体有氧生活方式的策略。这一新的认识也为使用黄色粘球菌作为底盘来提高 Fe-S 依赖性次生代谢产物的产量铺平了道路。
