Abstract
The NUDIX enzymes are involved in cellular metabolism and homeostasis, as well as mRNA processing. Although highly conserved throughout all organisms, their biological roles and biochemical redundancies remain largely unclear. To address this, we globally resolve their individual properties and inter-relationships. We purify 18 of the human NUDIX proteins and screen 52 substrates, providing a substrate redundancy map. Using crystal structures, we generate sequence alignment analyses revealing four major structural classes. To a certain extent, their substrate preference redundancies correlate with structural classes, thus linking structure and activity relationships. To elucidate interdependence among the NUDIX hydrolases, we pairwise deplete them generating an epistatic interaction map, evaluate cell cycle perturbations upon knockdown in normal and cancer cells, and analyse their protein and mRNA expression in normal and cancer tissues. Using a novel FUSION algorithm, we integrate all data creating a comprehensive NUDIX enzyme profile map, which will prove fundamental to understanding their biological functionality.
Highlights
The nucleoside diphosphates linked to moiety-X (NUDIX) enzymes are involved in cellular metabolism and homeostasis, as well as mRNA processing
The alignment and phylogenetic tree of the NUDIX fold domain sequences did have some significant differences compared with the full-length analysis (Fig. 1a and Supplementary Fig. 1b), multiple NUDIX protein structures in complex with relevant substrates have revealed that substrate binding is at times directed from residues outside the NUDIX fold domain[24,25] and, further analysis was carried out on the full-length sequence alignment and phylogenetic tree
There is no available structure for NUDT7 and NUDT8, as described earlier[29], our analysis suggests a high grade of sequence similarity between these two NUDIX enzymes given their posterior probability score, which is close to 1, and their percent pairwise identity of 36% (Fig. 1a)
Summary
The NUDIX enzymes are involved in cellular metabolism and homeostasis, as well as mRNA processing. The high diversity in substrate preferences of the NUDIX family members suggests that only a few, or potentially only MTH1, is involved in preventing mutations in DNA5. The NUDIX domain contains a NUDIX box (Gx5Ex5[UA] xREx2EExGU), which differs to a certain extent among the family members As their name suggests, the NUDIX hydrolases are enzymes that carry out hydrolysis reactions, substrates of which range from canonical (d)NTPs, oxidized (d)NTPs, nonnucleoside polyphosphates, and capped mRNAs6. Studying the NUDIX hydrolase family of enzymes individually may be hampered by their possible substrate and functional redundancies. We have undertaken a family-wide approach by building the largest collected set of information presented to date on all human NUDIX enzymes, including biochemical, structural, genetic, and biological properties, and using a novel algorithm, FUSION19, to interrogate their similarities
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