Department of Biology, University of Iowa, Iowa City, IA, United States of America.
PLoS One. 2019 Aug 1;14(8):e0220447. doi: 10.1371/journal.pone.0220447. eCollection 2019.
NAD kinase (NADK) is the sole enzyme that phosphorylates nicotinamide adenine dinucleotide (NAD+/NADH) into NADP+/NADPH, which provides the chemical reducing power in anabolic (biosynthetic) pathways. While prokaryotes typically encode a single NADK, eukaryotes encode multiple NADKs. How these different NADK genes are all related to each other and those of prokaryotes is not known. Here we conduct phylogenetic analysis of NADK genes and identify major clade-defining patterns of NADK evolution. First, almost all eukaryotic NADK genes belong to one of two ancient eukaryotic sister clades corresponding to cytosolic ("cyto") and mitochondrial ("mito") clades. Secondly, we find that the cyto-clade NADK gene is duplicated in connection with loss of the mito-clade NADK gene in several eukaryotic clades or with acquisition of plastids in Archaeplastida. Thirdly, we find that horizontal gene transfers from proteobacteria have replaced mitochondrial NADK genes in only a few rare cases. Last, we find that the eukaryotic cyto and mito paralogs are unrelated to independent duplications that occurred in sporulating bacteria, once in mycelial Actinobacteria and once in aerobic endospore-forming Firmicutes. Altogether these findings show that the eukaryotic NADK gene repertoire is ancient and evolves episodically with major evolutionary transitions.
烟酰胺腺嘌呤二核苷酸激酶（NADK）是唯一将烟酰胺腺嘌呤二核苷酸（NAD+/NADH）磷酸化为烟酰胺腺嘌呤二核苷酸磷酸（NADP+/NADPH）的酶，它为合成代谢（生物合成）途径提供了化学还原力。虽然原核生物通常编码单个 NADK，但真核生物编码多个 NADK。这些不同的 NADK 基因彼此之间以及与原核生物的关系尚不清楚。在这里，我们对 NADK 基因进行了系统发育分析，并确定了 NADK 进化的主要分支定义模式。首先，几乎所有真核生物的 NADK 基因都属于两个古老的真核生物姐妹群之一，对应于细胞质（“cyto”）和线粒体（“mito”）群。其次，我们发现，在几个真核生物类群中，细胞质 NADK 基因的复制与线粒体 NADK 基因的丢失有关，或者与古菌中的质体的获得有关。第三，我们发现，从变形菌中发生的水平基因转移仅在少数罕见情况下取代了线粒体 NADK 基因。最后，我们发现，真核生物的细胞质和线粒体等位基因与在孢子形成细菌中发生的独立复制无关，一次发生在放线菌的菌丝体中，一次发生在需氧芽孢形成的厚壁菌中。总之，这些发现表明，真核生物的 NADK 基因库是古老的，并随着主要进化转变而间歇性进化。
