Expanding the Phenotype Associated with NAA10-Related N-Terminal Acetylation Deficiency

Abstract

N-terminal acetylation is a common protein modification in eukaryotes associated with numerous cellular processes. Inherited mutations in NAA10, encoding the catalytic subunit of the major N-terminal acetylation complex NatA have been associated with diverse, syndromic X-linked recessive disorders, whereas de novo missense mutations have been reported in one male and one female individual with severe intellectual disability but otherwise unspecific phenotypes. Thus, the full genetic and clinical spectrum of NAA10 deficiency is yet to be delineated. We identified three different novel and one known missense mutation in NAA10, de novo in 11 females, and due to maternal germ line mosaicism in another girl and her more severely affected and deceased brother. In vitro enzymatic assays for the novel, recurrent mutations p.(Arg83Cys) and p.(Phe128Leu) revealed reduced catalytic activity. X-inactivation was random in five females. The core phenotype of X-linked NAA10-related N-terminal-acetyltransferase deficiency in both males and females includes developmental delay, severe intellectual disability, postnatal growth failure with severe microcephaly, and skeletal or cardiac anomalies. Genotype-phenotype correlations within and between both genders are complex and may include various factors such as location and nature of mutations, enzymatic stability and activity, and X-inactivation in females.

Keywords: N-terminal acetylation; NAA10; X-linked; intellectual disability.

Figure 1

Mutations identified in NAA10. A: Schematic representation of the NAA10 protein, encoding exons (numbered after NM_003491.3), domains (based on NCBI reference NP_003482.1, UniProt P41227 and the crystal structure of the NatA complex [Liszczak et al., 2013]), and localization of mutations in affected males (blue circles) and females (red circles). #, previously published mutations [Rauch et al., 2012; Rope et al., 2011; Esmailpour et al., 2014; Popp et al., 2015]. One letter codes were used due to space constraint. For the mutation c.471+2T>A described by Esmailpour et al. (2014) and the deduced protein level changes (p.(Leu158Valfs*46), p.(Glu157_Leu158ins9)), the presumably expressed truncated transcript 1 was used for labelling. B: NAA10 homology model highlighting Arginine 83 and 116. These are localized in the Ac‐CoA binding pocket. C: NAA10 homology model showing the localization of Phe128, with its side chain pointing toward the hydrophobic core, similar to Val107. This amino acid was mutated in a previously published patient [Popp et al., 2015].

Figure 2

Facial phenotypes of females with NAA10‐related N‐terminal‐acetyltransferase deficiency. Note only minor dysmorphic aspects and a rather unspecific facial gestalt in most of the girls. Some have prominent or arched eyebrows.

Figure 3

Functional consequences of NAA10 mutations. A: Purified wild‐type (WT) or mutant NAA10 were each mixed with acetylation buffer, 500 μM peptide and 500 μM Ac‐CoA, and incubated at 37°C. Reactions were stopped in the linear phase of the reaction. The p.(Arg83Cys) mutation resulted in an approximately 60% reduction in catalytic activity of NAA10 for all tested oligopeptides, whereas the p.(Phe128Leu) mutation lead to a very low catalytic activity (more than 90% reduction). B–E: NAA10 stability in vivo, tested pairwise (mutant and control) by cyclohexamide chase experiments and monitored at different time points (between 0 and 6 hr post‐treatment) and by Western blotting. Figures show representative results from at least three independent experiments. B: Western blot for NAA10‐V5 WT or NAA10‐V5 carrying the mutation p.(Arg83C). Bands were quantified, and the relative amount of NAA10 present at each time point is showed in (C). D: Western blot for NAA10‐V5 WT or NAA10‐V5 carrying the mutation p.(Phe128Leu). Bands were quantified, and the relative amount of NAA10 present at each time point is showed in (E).