Guío J, Peleato M L, Fillat M F, Sevilla E
Department of Biochemistry & Molecular and Cellular Biology, University of Zaragoza, Zaragoza, Spain.
Institute for Biocomputation and Physics of Complex Systems (BIFI), Zaragoza, Spain.
mSystems. 2025 Jun 25:e0037325. doi: 10.1128/msystems.00373-25.
FUR proteins in sp. PCC 7120 (FurA/Fur, FurB/Zur, and FurC/PerR) are a family of transcriptional regulators involved in the control of highly important metabolic processes such as the maintenance of metal homeostasis, the regulation of oxidative stress response, and the adaptation to nitrogen starvation. Previous RNAseq analyses of FUR misregulation strains revealed a broad panel of genes directly modulated by these transcriptional regulators. However, the expression of several regulatory proteins was also altered, indicating that FUR proteins could extend their influence by exerting a second level of regulation through some members of their regulons. In this work, by combining differential gene expression data and electrophoretic mobility shift assays (EMSAs), we sought to identify novel direct targets of FUR proteins with regulatory functions, namely, transcriptional regulators, two-component systems, sigma factors, and other proteins with regulatory functions such as serine/threonine kinases. This allowed us to build a network composed of these regulatory proteins that are directly modulated by FUR proteins. In addition, taking into account the role of FUR proteins in the regulation of nitrogen metabolism, the overlap between FUR and NtcA regulatory networks was studied, revealing that an important part of the FUR network is coregulated by NtcA. These results unveil a complex network in in which regulatory proteins hierarchically below FUR or NtcA proteins could be controlling the expression of several genes, connecting the integration of stress signaling performed by FUR and NtcA to a wide set of cyanobacterial transcriptional responses.IMPORTANCEFUR proteins in sp. PCC 7120 are a family of global transcriptional regulators that control several cellular processes ranging from metal homeostasis to nitrogen metabolism. Apart from directly regulating their target genes, the differential expression of several regulatory genes in RNAseq analyses of FUR misregulation strains suggests that these transcriptional regulators could also control the expression of many targets indirectly. Here, we report that FUR proteins from sp. PCC 7120 directly modulate the expression of transcriptional regulators, two-component systems, sigma factors, and serine/threonine kinases, revealing that these regulators indirectly modulate a wide number of genes and cellular processes through this regulatory network. Besides, it was found that an important part of this network is co-regulated by NtcA, connecting the integration of FUR and NtcA stress signals and suggesting that the FUR regulatory network could be involved in the adaptive responses to nitrogen deficiency.
集胞藻PCC 7120中的FUR蛋白（FurA/Fur、FurB/Zur和FurC/PerR）是一类转录调节因子，参与控制高度重要的代谢过程，如维持金属稳态、调节氧化应激反应以及适应氮饥饿。先前对FUR失调菌株的RNA测序分析揭示了一系列受这些转录调节因子直接调控的基因。然而，几种调节蛋白的表达也发生了改变，这表明FUR蛋白可能通过其调控子中的一些成员施加第二层调节来扩大其影响。在这项工作中，通过结合差异基因表达数据和电泳迁移率变动分析（EMSA），我们试图鉴定具有调节功能的FUR蛋白的新型直接靶标，即转录调节因子、双组分系统、σ因子以及其他具有调节功能的蛋白，如丝氨酸/苏氨酸激酶。这使我们构建了一个由受FUR蛋白直接调控的这些调节蛋白组成的网络。此外，考虑到FUR蛋白在氮代谢调节中的作用，研究了FUR和NtcA调控网络之间的重叠，发现FUR网络的一个重要部分受NtcA共同调控。这些结果揭示了一个复杂的网络，其中在FUR或NtcA蛋白之下分层的调节蛋白可能控制着多个基因的表达，将FUR和NtcA进行的应激信号整合与广泛的蓝藻转录反应联系起来。
重要性
集胞藻PCC 7120中的FUR蛋白是一类全局转录调节因子，控制从金属稳态到氮代谢等多个细胞过程。除了直接调控其靶基因外，在FUR失调菌株的RNA测序分析中几种调节基因的差异表达表明，这些转录调节因子也可能间接控制许多靶标的表达。在此，我们报道集胞藻PCC 7120中的FUR蛋白直接调节转录调节因子、双组分系统、σ因子和丝氨酸/苏氨酸激酶的表达，揭示这些调节因子通过这个调控网络间接调节大量基因和细胞过程。此外，发现该网络的一个重要部分受NtcA共同调控，将FUR和NtcA应激信号的整合联系起来，并表明FUR调控网络可能参与对氮缺乏 的适应性反应。
