Episodic evolution of a eukaryotic NADK repertoire of ancient provenance

Abstract

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.\n\nAuthor SummaryMetabolic enzymes are central to all living organisms and key to understanding the evolution of life on Earth. One important component of all metabolic pathways is the participation of chemically-reducing cofactors such as the redox system of NAD+ and NADH molecules. All living cells also possess a system for shifting their intracellular pool of NAD+ and NADH into NADP+ and NADPH via phosphorylation by the NAD kinase (NADK). Phosphorylation by NADK allows cells to regulate the use of their main chemical redox system for anabolic growth and the synthesis of basic cellular components. In our study we provide the first comprehensive analysis of the NAD kinase family. We find that eukaryotes possess two ancient NADK gene families of unknown provenance and also find unrelated bacterial families that also possess dual NADK genes. We also find that while NADK evolution has been mostly stable through the eons, this family has evolved substantially in association with the evolution of specific clades of organisms. Altogether these results provide a metabolic picture of the tree of life and its evolution.