Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, California, USA.
Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, California, USA.
J Biol Chem. 2022 Oct;298(10):102410. doi: 10.1016/j.jbc.2022.102410. Epub 2022 Aug 22.
NAD is a cellular redox cofactor involved in many essential processes. The regulation of NAD metabolism and the signaling networks reciprocally interacting with NAD-producing metabolic pathways are not yet fully understood. The NAD-dependent histone deacetylase (HDAC) Hst1 has been shown to inhibit de novo NAD synthesis by repressing biosynthesis of nicotinic acid (BNA) gene expression. Here, we alternatively identify HDAC Rpd3 as a positive regulator of de novo NAD metabolism in the budding yeast Saccharomyces cerevisiae. We reveal that deletion of RPD3 causes marked decreases in the production of de novo pathway metabolites, in direct contrast to deletion of HST1. We determined the BNA expression profiles of rpd3Δ and hst1Δ cells to be similarly opposed, suggesting the two HDACs may regulate the BNA genes in an antagonistic fashion. Our chromatin immunoprecipitation analysis revealed that Rpd3 and Hst1 mutually influence each other's binding distribution at the BNA2 promoter. We demonstrate Hst1 to be the main deacetylase active at the BNA2 promoter, with hst1Δ cells displaying increased acetylation of the N-terminal tail lysine residues of histone H4, H4K5, and H4K12. Conversely, we show that deletion of RPD3 reduces the acetylation of these residues in an Hst1-dependent manner. This suggests that Rpd3 may function to oppose spreading of Hst1-dependent heterochromatin and represents a unique form of antagonism between HDACs in regulating gene expression. Moreover, we found that Rpd3 and Hst1 also coregulate additional targets involved in other branches of NAD metabolism. These findings help elucidate the complex interconnections involved in effecting the regulation of NAD metabolism.
NAD 是一种参与许多基本过程的细胞氧化还原辅助因子。NAD 代谢的调节和与产生 NAD 的代谢途径相互作用的信号网络尚未完全理解。已经表明，依赖 NAD 的组蛋白去乙酰化酶 (HDAC) Hst1 通过抑制烟酸 (BNA) 基因表达的生物合成来抑制从头合成 NAD。在这里，我们将 HDAC Rpd3 鉴定为酿酒酵母芽殖酵母中从头 NAD 代谢的正向调节剂。我们揭示 RPD3 的缺失导致从头途径代谢物的产生明显减少，这与 HST1 的缺失直接相反。我们确定 rpd3Δ 和 hst1Δ 细胞的 BNA 表达谱相似，表明这两种 HDAC 可能以拮抗方式调节 BNA 基因。我们的染色质免疫沉淀分析表明，Rpd3 和 Hst1 相互影响彼此在 BNA2 启动子上的结合分布。我们证明 Hst1 是在 BNA2 启动子上起主要去乙酰化酶作用的酶，hst1Δ 细胞显示组蛋白 H4、H4K5 和 H4K12 的 N 端尾巴赖氨酸残基乙酰化增加。相反，我们表明 RPD3 的缺失以 Hst1 依赖性方式降低这些残基的乙酰化。这表明 Rpd3 可能起作用以反对 Hst1 依赖性异染色质的扩散，并代表了在调节基因表达中 HDAC 之间的一种独特形式的拮抗作用。此外，我们发现 Rpd3 和 Hst1 还共同调节其他 NAD 代谢分支中涉及的其他靶标。这些发现有助于阐明影响 NAD 代谢调节的复杂相互联系。
