Substrate ambiguity among the nudix hydrolases: biologically significant, evolutionary remnant, or both?

Abstract

Many members of the nudix hydrolase family exhibit considerable substrate multispecificity and ambiguity, which raises significant issues when assessing their functions in vivo and gives rise to errors in database annotation. Several display low antimutator activity when expressed in bacterial tester strains as well as some degree of activity in vitro towards mutagenic, oxidized nucleotides such as 8-oxo-dGTP. However, many of these show greater activity towards other nucleotides such as ADP-ribose or diadenosine tetraphosphate (Ap(4)A). The antimutator activities have tended to gain prominence in the literature, whereas they may in fact represent the residual activity of an ancestral antimutator enzyme that has become secondary to the more recently evolved major activity after gene duplication. Whether any meaningful antimutagenic function has also been retained in vivo requires very careful assessment. Then again, other examples of substrate ambiguity may indicate as yet unexplored regulatory systems. For example, bacterial Ap(4)A hydrolases also efficiently remove pyrophosphate from the 5' termini of mRNAs, suggesting a potential role for Ap(4)A in the control of bacterial mRNA turnover, while the ability of some eukaryotic mRNA decapping enzymes to degrade IDP and dIDP or diphosphoinositol polyphosphates (DIPs) may also be indicative of new regulatory networks in RNA metabolism. DIP phosphohydrolases also degrade diadenosine polyphosphates and inorganic polyphosphates, suggesting further avenues for investigation. This article uses these and other examples to highlight the need for a greater awareness of the possible significance of substrate ambiguity among the nudix hydrolases as well as the need to exert caution when interpreting incomplete analyses.

Control of RNA Stability by NrrF, an Iron-Regulated Small RNA in Neisseria gonorrhoeae

“…We noted an increase in the half-life of NGO0224 (ntpA) mRNA in the mutant (Table 2). NGO0224 encodes a protein in the Nudix hydrolase superfamily of pyrophosphohydrolases, which typically targets intact and oxidatively damaged nucleoside triphosphates, dinucleotide polyphosphates, nucleotide sugars, and dinucleotide enzymes, removing potentially mutagenic nucleotide metabolites (38,39). Nudix hydrolases have also been implicated in the regulation of metabolism (40).…”

Diadenosine 5′, 5′′′-P1,P4-tetraphosphate (Ap4A) is synthesized in response to DNA damage and inhibits the initiation of DNA replication

“…Of these, it is generally accepted that the aminoacyl-tRNA synthetases are primarily responsible for the steady-state level of Ap4A in vivo [16]; however, the precise synthetic source of stress-induced increases may depend on the stimulus in question. In eukaryotes, the principal enzyme responsible for Ap4A degradation is the NUDT2 nudix hydrolase [17,18] although two HIT family proteins, the Fhit tumour suppressor [19] and aprataxin (APTX) [20], are also able to hydrolyse Ap4A to some extent.…”

Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway

“…FolQ is a member of the Nudix superfamily, whose members are notoriously difficult to annotate [40]. It is, therefore, difficult to propagate the annotation beyond genomes closely related to the ones where the function was experimentally validated; hence, the folQ gene is still missing in the majority of genomes (73%).…”