Biochemical analysis of novel NAA10 variants suggests distinct pathogenic mechanisms involving impaired protein N-terminal acetylation

Abstract

NAA10 is the catalytic subunit of the N-terminal acetyltransferase complex, NatA, which is responsible for N-terminal acetylation of nearly half the human proteome. Since 2011, at least 21 different NAA10 missense variants have been reported as pathogenic in humans. The clinical features associated with this X-linked condition vary, but commonly described features include developmental delay, intellectual disability, cardiac anomalies, brain abnormalities, facial dysmorphism and/or visual impairment. Here, we present eight individuals from five families with five different de novo or inherited NAA10 variants. In order to determine their pathogenicity, we have performed biochemical characterisation of the four novel variants c.16G>C p.(A6P), c.235C>T p.(R79C), c.386A>C p.(Q129P) and c.469G>A p.(E157K). Additionally, we clinically describe one new case with a previously identified pathogenic variant, c.384T>G p.(F128L). Our study provides important insight into how different NAA10 missense variants impact distinct biochemical functions of NAA10 involving the ability of NAA10 to perform N-terminal acetylation. These investigations may partially explain the phenotypic variability in affected individuals and emphasise the complexity of the cellular pathways downstream of NAA10.

Expanding the Phenotypic spectrum ofNAA10-related neurodevelopmental syndrome andNAA15-related neurodevelopmental syndrome

“…In regard to the biochemical analyses published to date, most variants have been primarily studied using either immunopurified overexpressed full-length NAA10 (235 residues) protein from yeast (Van Damme et al 2014) or mammalian culture (Myklebust et al 2015; McTiernan et al 2021, 2022; Støve et al 2018; Bader et al 2020), S. frugiperda ( Sf 9)-expressed recombinant NatA complex containing a C-terminally truncated NAA10 (1-160) (Cheng et al 2019), or an affinity-tagged full-length NAA10 expressed in E. coli (Rope et al 2011; Popp et al 2015; Saunier et al 2016; Myklebust et al 2015; McTiernan et al 2018; Rasmus Ree et al 2019; Casey et al 2015). Each of these methodologies have their limitations.…”

“…The structures were visually inspected using PyMol, which was also used in conjunction with Adobe Illustrator CC to prepare Figure 4 and Figure 5. The discussion was also informed by numerous biochemical and biophysical studies of NAA10 and NAA15 mutant proteins 13,16,[18][19][20][21]23,32,33 .…”

“…Most NAA10 variants identified to date in NAA10-related neurodevelopmental diseases reduce NAA10-and NatA-type activity 20 . Although novel variants clinically described here have not been characterized biochemically, it is possible to anticipate biochemical implications resulting from variants in the conserved region of NAA10 (residues 1-160) based on previous studies 13,16,[18][19][20][21]23,32,33 . However, variants and truncations occurring in the C-terminus of NAA10 require additional studies to understand the role of the NAA10 C-terminal domain.…”

“…The collection of presenting symptoms for families with NAA10 variants is currently referred to as, “Ogden syndrome” or “ NAA10 -related syndrome”, and “ NAA15 -related syndrome” for families with NAA15 variants. Although a prior review suggested that the name Ogden syndrome should be reserved only for the male neonatal lethal phenotype (Wu and Lyon 2018), this has been problematic, as there are some males that survive the neonatal period (Casey et al 2015; McTiernan et al 2022) and many families have reported that the name Ogden syndrome is more memorable. Additionally, some clinicians have also diagnosed females as having Ogden syndrome (Sidhu et al 2017).…”

Loss of N-terminal acetyltransferase A activity induces thermally unstable ribosomal proteins and increases their turnover

“…Unlike lysine acetylation, the most exhaustively studied acetylation type, Nt-acetylation has been regarded as an irreversible and static modification, as no deacetylase acting on N-termini has yet been identified ( 2, 4 ). Nevertheless, different reports suggested that Nt-acetylation may be regulated by cellular signaling and its cellular status can vary in different disease states and biological processes such as cancer( 10 ), developmental disorders( 11, 12 ), drought stress( 7, 13 ), calorie restriction and Ac-CoA availability( 14, 15 ) or apoptotic fate( 16, 17 ). Thus, Nt-acetylation has emerged as an important protein modification that is involved in the regulation of different biological pathways.…”