Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA.
Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.
Microbiol Spectr. 2022 Oct 26;10(5):e0235422. doi: 10.1128/spectrum.02354-22. Epub 2022 Sep 15.
We recently described a new member of the CRP (cyclic AMP receptor protein)/FNR (fumarate and nitrate reductase regulatory protein) family called RedB, an acronym for redox brake, that functions to limit the production of ATP and NADH. This study shows that the RedB regulon significantly overlaps the FnrL regulon, with 199 genes being either directly or indirectly regulated by both of these global regulatory proteins. Among these 199 coregulated genes, 192 are divergently regulated, indicating that RedB functions as an antagonist of FnrL. Chromatin immunoprecipitation sequencing (ChIP-seq) analysis indicates that RedB and Fnr directly coregulate only 4 out of 199 genes. The primary mechanism for the divergent regulation of target genes thus involves indirect regulation by both RedB and FnrL (156 cases). Additional regulation involves direct binding by RedB and indirect regulation by FnrL (36 cases) or direct binding by FnrL and indirect regulation by RedB (3 cases). Analysis of physiological pathways under direct and indirect control by these global regulators demonstrates that RedB functions primarily to limit energy production, while FnrL functions to enhance energy production. This regulation includes glycolysis, gluconeogenesis, photosynthesis, hydrogen oxidation, electron transport, carbon fixation, lipid biosynthesis, and protein synthesis. Finally, we show that 75% of genomes from diverse species that code for RedB proteins also harbor genes coding for FNR homologs. This cooccurrence indicates that RedB likely has an important role in buffering FNR-mediated energy production in a broad range of species. The CRP/FNR family of regulatory proteins constitutes a large collection of related transcription factors, several of which globally regulate cellular energy production. A well-characterized example is FNR (called FnrL in Rhodobacter capsulatus), which is responsible for regulating the expression of numerous genes that promote maximal energy production and growth under anaerobic conditions. In a companion article (N. Ke, J. E. Kumka, M. Fang, B. Weaver, et al., Microbiol Spectr 10:e02353-22, 2022, https://doi.org/10.1128/Spectrum02353-22), we identified a new subgroup of the CRP/FNR family and demonstrated that a member of this new subgroup, called RedB, has a role in limiting cellular energy production. In this study, we show that numerous genes encompassing the RedB regulon significantly overlap genes that are members of the FnrL regulon. Furthermore, 97% of the genes that are members of both the RedB and FnrL regulons are divergently regulated by these two transcription factors. RedB thus functions as a buffer limiting the amount of energy production that is promoted by FnrL.
我们最近描述了 CRP（环磷酸腺苷受体蛋白）/FNR（延胡索酸和硝酸盐还原酶调节蛋白）家族的一个新成员，称为 RedB，是 redox brake 的缩写，它的功能是限制 ATP 和 NADH 的产生。这项研究表明，RedB 调控组与 FnrL 调控组有很大的重叠，这两个全局调控蛋白直接或间接调控了 199 个基因。在这 199 个共同调控的基因中，有 192 个是差异调控的，这表明 RedB 作为 FnrL 的拮抗剂发挥作用。染色质免疫沉淀测序（ChIP-seq）分析表明，RedB 和 Fnr 仅直接共同调控了 199 个基因中的 4 个。因此，靶基因差异调控的主要机制涉及 RedB 和 FnrL 的间接调控（156 种情况）。其他调控涉及 RedB 的直接结合和 FnrL 的间接调控（36 种情况）或 FnrL 的直接结合和 RedB 的间接调控（3 种情况）。对这些全局调控因子直接和间接调控的生理途径的分析表明，RedB 的主要功能是限制能量产生，而 FnrL 的功能是增强能量产生。这种调节包括糖酵解、糖异生、光合作用、氢气氧化、电子传递、碳固定、脂质生物合成和蛋白质合成。最后，我们表明，来自编码 RedB 蛋白的不同物种的 75%的基因组也编码 FNR 同源物。这种共存表明，RedB 可能在广泛的物种中对缓冲 FNR 介导的能量产生起着重要作用。CRP/FNR 家族的调节蛋白构成了一大类相关的转录因子，其中有几个因子可全局调节细胞的能量产生。一个很好的例子是 FNR（在荚膜红细菌中称为 FnrL），它负责调节许多基因的表达，这些基因在厌氧条件下促进最大的能量产生和生长。在一篇配套文章（N. Ke、J. E. Kumka、M. Fang、B. Weaver 等人，Microbiol Spectr 10:e02353-22，2022，https://doi.org/10.1128/Spectrum02353-22）中，我们确定了 CRP/FNR 家族的一个新亚群，并表明该新亚群的一个成员，称为 RedB，在限制细胞能量产生方面发挥作用。在这项研究中，我们表明，RedB 调控组中的许多基因与 FnrL 调控组中的基因有显著重叠。此外，这两个转录因子共同调控的 97%的基因是由这两个转录因子差异调控的。因此，RedB 作为一种缓冲剂，限制了 FnrL 促进的能量产生量。
