Regulatory roles of vertebrate Nocturnin: insights and remaining mysteries

Abstract

Post-transcriptional control of messenger RNA (mRNA) is an important layer of gene regulation that modulates mRNA decay, translation, and localization. Eukaryotic mRNA decay begins with the catalytic removal of the 3′ poly-adenosine tail by deadenylase enzymes. Multiple deadenylases have been identified in vertebrates and are known to have distinct biological roles; among these proteins is Nocturnin, which has been linked to circadian biology, adipogenesis, osteogenesis, and obesity. Multiple studies have investigated Nocturnin’s involvement in these processes; however, a full understanding of its molecular function remains elusive. Recent studies have provided new insights by identifying putative Nocturnin-regulated mRNAs in mice and by determining the structure and regulatory activities of human Nocturnin. This review seeks to integrate these new discoveries into our understanding of Nocturnin’s regulatory functions and highlight the important remaining unanswered questions surrounding its regulation, biochemical activities, protein partners, and target mRNAs.

Differential processing and localization of human Nocturnin controls metabolism of mRNA and nicotinamide dinucleotide metabolites

“…Mitochondrial targeting signals typically reside in the first 90 Nterminal residues, form amphipathic helices, have a high arginine content, and contain few negatively charged residues (27). Consistent with these features, amino acids 2-15 are predicted to be an amphipathic alpha-helix and the first 74 amino acids have an isoelectric point of 12.1, with 12 arginines and only one negatively charged residue (6). Deletion of amino acids 2-15 reduced the MitoFates probability score from 0.94 to 0.035.…”

“…Previously, over-expressed, epitope tagged NOCT was reported to be either cytoplasmic or peri-nuclear, whereas endogenous NOCT has been reported to localize to the nucleus or cytoplasm of cells in mouse embryos or to the cytoplasm in Xenopus retina (2,9,22,23). Intriguingly, sequence analysis of the unique Nterminus of mouse and human NOCT detected the presence of a putative mitochondrial targeting sequence (Figure 1a) (6). Moreover, we observed that the N-terminus of NOCT possesses two potential translation initiation sites, one of which would include the mitochondrial targeting sequence and one which would exclude it.…”

“…Analysis of the NOCT amino acid sequence detected a putative N-terminal mitochondrial targeting presequence and cleavage site for the mitochondrial processing peptidase (MPP) (Figure 1a), which are conserved in several vertebrates (6,27). The MitoFates and TPpred2 algorithms score the probability that the NOCT Nterminus has a mitochondrial presequence at 0.94 and 0.98, respectively (27)(28)(29).…”

“…Nocturnin (NOCT) is a eukaryotic protein that belongs to the Exonuclease-Endonuclease-Phosphatase (EEP) superfamily of enzymes and is conserved from insects to vertebrates (1)(2)(3)(4)(5)(6). While members of the EEP superfamily can act on diverse substrates, ranging from nucleic acids to phospholipids, NOCT is most similar to the CCR4 subclass of EEP enzymes, which is indicative of a role in RNA metabolism (1,2).…”

“…CCR4 and its orthologs are hydrolytic exoribonucleases that degrade the 3′ poly-adenosine tail of mRNA substrates (i.e., they are deadenylases) (7). Indeed, sequence and structural homology of the C-terminal EEP domain of NOCT revealed that it most closely resembles CCR4 class enzymes CNOT6 and PDE12 (1,6). Nonetheless, NOCT possesses unique features that distinguish it from other CCR4 type enzymes.…”