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1.
Cell ; 175(7): 1872-1886.e24, 2018 12 13.
Article in English | MEDLINE | ID: mdl-30449621

ABSTRACT

Generation of the "epitranscriptome" through post-transcriptional ribonucleoside modification embeds a layer of regulatory complexity into RNA structure and function. Here, we describe N4-acetylcytidine (ac4C) as an mRNA modification that is catalyzed by the acetyltransferase NAT10. Transcriptome-wide mapping of ac4C revealed discretely acetylated regions that were enriched within coding sequences. Ablation of NAT10 reduced ac4C detection at the mapped mRNA sites and was globally associated with target mRNA downregulation. Analysis of mRNA half-lives revealed a NAT10-dependent increase in stability in the cohort of acetylated mRNAs. mRNA acetylation was further demonstrated to enhance substrate translation in vitro and in vivo. Codon content analysis within ac4C peaks uncovered a biased representation of cytidine within wobble sites that was empirically determined to influence mRNA decoding efficiency. These findings expand the repertoire of mRNA modifications to include an acetylated residue and establish a role for ac4C in the regulation of mRNA translation.


Subject(s)
Cytidine/analogs & derivatives , N-Terminal Acetyltransferase E/metabolism , Protein Biosynthesis , RNA, Messenger/metabolism , Acetylation , Cytidine/genetics , Cytidine/metabolism , HeLa Cells , Humans , N-Terminal Acetyltransferase E/genetics , N-Terminal Acetyltransferases , RNA, Messenger/genetics
2.
Mol Cell ; 76(3): 500-515.e8, 2019 11 07.
Article in English | MEDLINE | ID: mdl-31422874

ABSTRACT

Diet-induced obesity can be caused by impaired thermogenesis of beige adipocytes, the brown-like adipocytes in white adipose tissue (WAT). Promoting brown-like features in WAT has been an attractive therapeutic approach for obesity. However, the mechanism underlying beige adipocyte formation is largely unknown. N-α-acetyltransferase 10 protein (Naa10p) catalyzes N-α-acetylation of nascent proteins, and overexpression of human Naa10p is linked to cancer development. Here, we report that both conventional and adipose-specific Naa10p deletions in mice result in increased energy expenditure, thermogenesis, and beige adipocyte differentiation. Mechanistically, Naa10p acetylates the N terminus of Pgc1α, which prevents Pgc1α from interacting with Pparγ to activate key genes, such as Ucp1, involved in beige adipocyte function. Consistently, fat tissues of obese human individuals show higher NAA10 expression. Thus, Naa10p-mediated N-terminal acetylation of Pgc1α downregulates thermogenic gene expression, making inhibition of Naa10p enzymatic activity a potential strategy for treating obesity.


Subject(s)
Adipocytes, Beige/enzymology , Adipose Tissue, Beige/enzymology , N-Terminal Acetyltransferase A/metabolism , N-Terminal Acetyltransferase E/metabolism , Obesity/enzymology , Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism , Protein Processing, Post-Translational , Thermogenesis , Acetylation , Adipose Tissue, Beige/physiopathology , Adiposity , Adolescent , Adult , Aged , Animals , Case-Control Studies , Diet, High-Fat , Disease Models, Animal , Energy Metabolism , Female , HEK293 Cells , Humans , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Middle Aged , N-Terminal Acetyltransferase A/deficiency , N-Terminal Acetyltransferase A/genetics , N-Terminal Acetyltransferase E/deficiency , N-Terminal Acetyltransferase E/genetics , NIH 3T3 Cells , Obesity/genetics , Obesity/physiopathology , Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/genetics , Phenotype , Signal Transduction , Young Adult
3.
Mol Cell ; 68(1): 89-103.e7, 2017 Oct 05.
Article in English | MEDLINE | ID: mdl-28943313

ABSTRACT

Genomic imprinting is an allelic gene expression phenomenon primarily controlled by allele-specific DNA methylation at the imprinting control region (ICR), but the underlying mechanism remains largely unclear. N-α-acetyltransferase 10 protein (Naa10p) catalyzes N-α-acetylation of nascent proteins, and mutation of human Naa10p is linked to severe developmental delays. Here we report that Naa10-null mice display partial embryonic lethality, growth retardation, brain disorders, and maternal effect lethality, phenotypes commonly observed in defective genomic imprinting. Genome-wide analyses further revealed global DNA hypomethylation and enriched dysregulation of imprinted genes in Naa10p-knockout embryos and embryonic stem cells. Mechanistically, Naa10p facilitates binding of DNA methyltransferase 1 (Dnmt1) to DNA substrates, including the ICRs of the imprinted allele during S phase. Moreover, the lethal Ogden syndrome-associated mutation of human Naa10p disrupts its binding to the ICR of H19 and Dnmt1 recruitment. Our study thus links Naa10p mutation-associated Ogden syndrome to defective DNA methylation and genomic imprinting.


Subject(s)
DNA (Cytosine-5-)-Methyltransferases/genetics , Developmental Disabilities/genetics , Epigenesis, Genetic , Genomic Imprinting , N-Terminal Acetyltransferase A/genetics , N-Terminal Acetyltransferase E/genetics , RNA, Long Noncoding/genetics , Animals , DNA/genetics , DNA/metabolism , DNA (Cytosine-5-)-Methyltransferase 1 , DNA (Cytosine-5-)-Methyltransferases/metabolism , DNA Methylation , Developmental Disabilities/metabolism , Developmental Disabilities/pathology , Disease Models, Animal , Embryo, Mammalian , Female , Gene Deletion , Genes, Lethal , Genome-Wide Association Study , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Mouse Embryonic Stem Cells/metabolism , Mouse Embryonic Stem Cells/pathology , N-Terminal Acetyltransferase A/deficiency , N-Terminal Acetyltransferase E/deficiency , Protein Binding , RNA, Long Noncoding/metabolism , S Phase/genetics
4.
Mol Cell ; 65(5): 917-931.e6, 2017 Mar 02.
Article in English | MEDLINE | ID: mdl-28238651

ABSTRACT

Autophagy is crucial for maintaining cell homeostasis. However, the precise mechanism underlying autophagy initiation remains to be defined. Here, we demonstrate that glutamine deprivation and hypoxia result in inhibition of mTOR-mediated acetyl-transferase ARD1 S228 phosphorylation, leading to ARD1-dependent phosphoglycerate kinase 1 (PGK1) K388 acetylation and subsequent PGK1-mediated Beclin1 S30 phosphorylation. This phosphorylation enhances ATG14L-associated class III phosphatidylinositol 3-kinase VPS34 activity by increasing the binding of phosphatidylinositol to VPS34. ARD1-dependent PGK1 acetylation and PGK1-mediated Beclin1 S30 phosphorylation are required for glutamine deprivation- and hypoxia-induced autophagy and brain tumorigenesis. Furthermore, PGK1 K388 acetylation levels correlate with Beclin1 S30 phosphorylation levels and poor prognosis in glioblastoma patients. Our study unearths an important mechanism underlying cellular-stress-induced autophagy initiation in which the protein kinase activity of the metabolic enzyme PGK1 plays an instrumental role and reveals the significance of the mutual regulation of autophagy and cell metabolism in maintaining cell homeostasis.


Subject(s)
Autophagosomes/enzymology , Autophagy , Beclin-1/metabolism , Brain Neoplasms/enzymology , Glioblastoma/enzymology , Phosphoglycerate Kinase/metabolism , Acetylation , Animals , Autophagosomes/pathology , Beclin-1/genetics , Brain Neoplasms/genetics , Brain Neoplasms/pathology , Cell Line, Tumor , Cell Proliferation , Class III Phosphatidylinositol 3-Kinases/genetics , Class III Phosphatidylinositol 3-Kinases/metabolism , Female , Glioblastoma/genetics , Glioblastoma/pathology , Glutamine/deficiency , HEK293 Cells , Humans , Mice, Nude , N-Terminal Acetyltransferase A/genetics , N-Terminal Acetyltransferase A/metabolism , N-Terminal Acetyltransferase E/genetics , N-Terminal Acetyltransferase E/metabolism , Phosphoglycerate Kinase/genetics , Phosphorylation , Protein Binding , RNA Interference , Signal Transduction , TOR Serine-Threonine Kinases/genetics , TOR Serine-Threonine Kinases/metabolism , Time Factors , Transfection , Tumor Burden , Tumor Hypoxia
6.
Hum Genet ; 141(8): 1355-1369, 2022 Aug.
Article in English | MEDLINE | ID: mdl-35039925

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.


Subject(s)
Intellectual Disability , N-Terminal Acetyltransferase A , N-Terminal Acetyltransferase E , Acetylation , Genes, X-Linked , Humans , Intellectual Disability/genetics , Intellectual Disability/pathology , N-Terminal Acetyltransferase A/genetics , N-Terminal Acetyltransferase A/metabolism , N-Terminal Acetyltransferase E/genetics , N-Terminal Acetyltransferase E/metabolism
7.
J Cell Mol Med ; 25(14): 6760-6772, 2021 07.
Article in English | MEDLINE | ID: mdl-34060226

ABSTRACT

Epithelial-mesenchymal transition (EMT) has been contributed to increase migration and invasion of cancer cells. However, the correlate of Naa10p and IKKα with EMT in oral squamous cell carcinoma (OSCC) is not yet fully understood. In our present study, we found N-α-acetyltransferase 10 protein (Naa10p) and IκB kinase α (IKKα) were abnormally abundant in oral squamous cell carcinoma (OSCC). Bioinformatic results indicate that the expression of Naa10p and IKKα is correlated with TGF-ß1/Smad and EMT-related molecules. The Transwell migration, invasion, qRT-PCR and Western blot assay indicated that Naa10p repressed OSCC cell migration, invasion and EMT, whereas IKKα promoted TGF-ß1-mediated OSCC cell migration, invasion and EMT. Mechanistically, Naa10p inhibited IKKα activation of Smad3 through the interaction with IKKα directly in OSCC cells after TGF-ß1 stimulation. Notably, knockdown of Naa10p reversed the IKKα-induced change in the migration, invasion and EMT-related molecules in OSCC cells after TGF-ß1 stimulation. These findings suggest that Naa10p interacted with IKKα mediates EMT in OSCC cells through TGF-ß1/Smad, a novel pathway for preventing OSCC.


Subject(s)
Carcinoma, Squamous Cell/metabolism , Epithelial-Mesenchymal Transition , I-kappa B Kinase/metabolism , Mouth Neoplasms/metabolism , N-Terminal Acetyltransferase A/metabolism , N-Terminal Acetyltransferase E/metabolism , Carcinoma, Squamous Cell/pathology , Cell Line, Tumor , Cell Movement , Female , Humans , I-kappa B Kinase/genetics , Male , Mouth Neoplasms/pathology , N-Terminal Acetyltransferase A/genetics , N-Terminal Acetyltransferase E/genetics , Protein Binding , Signal Transduction , Smad Proteins/metabolism , Transforming Growth Factor beta/metabolism
8.
Hum Mol Genet ; 28(17): 2900-2919, 2019 09 01.
Article in English | MEDLINE | ID: mdl-31127942

ABSTRACT

N-alpha-acetylation is one of the most common co-translational protein modifications in humans and is essential for normal cell function. NAA10 encodes for the enzyme NAA10, which is the catalytic subunit in the N-terminal acetyltransferase A (NatA) complex. The auxiliary and regulatory subunits of the NatA complex are NAA15 and Huntington-interacting protein (HYPK), respectively. Through a genotype-first approach with exome sequencing, we identified and phenotypically characterized 30 individuals from 30 unrelated families with 17 different de novo or inherited, dominantly acting missense variants in NAA10 or NAA15. Clinical features of affected individuals include variable levels of intellectual disability, delayed speech and motor milestones and autism spectrum disorder. Additionally, some subjects present with mild craniofacial dysmorphology, congenital cardiac anomalies and seizures. One of the individuals is an 11-year-old boy with a frameshift variant in exon 7 of NAA10, who presents most notably with microphthalmia, which confirms a prior finding with a single family with Lenz microphthalmia syndrome. Biochemical analyses of variants as part of the human NatA complex, as well as enzymatic analyses with and without the HYPK regulatory subunit, help to explain some of the phenotypic differences seen among the different variants.


Subject(s)
Biomarkers , Genetic Association Studies , Genetic Predisposition to Disease , Genetic Variation , N-Terminal Acetyltransferase A/genetics , N-Terminal Acetyltransferase E/genetics , Phenotype , Adolescent , Adult , Alleles , Child , Child, Preschool , Computational Biology/methods , Enzyme Activation , Enzyme Stability , Facies , Female , Genetic Loci , Genetic Testing , Genotype , Humans , Infant , Male , Models, Molecular , Mutation , N-Terminal Acetyltransferase A/chemistry , N-Terminal Acetyltransferase A/metabolism , N-Terminal Acetyltransferase E/chemistry , N-Terminal Acetyltransferase E/metabolism , Protein Conformation , Recombinant Proteins , Structure-Activity Relationship , Young Adult
9.
Am J Hum Genet ; 102(5): 985-994, 2018 05 03.
Article in English | MEDLINE | ID: mdl-29656860

ABSTRACT

N-alpha-acetylation is a common co-translational protein modification that is essential for normal cell function in humans. We previously identified the genetic basis of an X-linked infantile lethal Mendelian disorder involving a c.109T>C (p.Ser37Pro) missense variant in NAA10, which encodes the catalytic subunit of the N-terminal acetyltransferase A (NatA) complex. The auxiliary subunit of the NatA complex, NAA15, is the dimeric binding partner for NAA10. Through a genotype-first approach with whole-exome or genome sequencing (WES/WGS) and targeted sequencing analysis, we identified and phenotypically characterized 38 individuals from 33 unrelated families with 25 different de novo or inherited, dominantly acting likely gene disrupting (LGD) variants in NAA15. Clinical features of affected individuals with LGD variants in NAA15 include variable levels of intellectual disability, delayed speech and motor milestones, and autism spectrum disorder. Additionally, mild craniofacial dysmorphology, congenital cardiac anomalies, and seizures are present in some subjects. RNA analysis in cell lines from two individuals showed degradation of the transcripts with LGD variants, probably as a result of nonsense-mediated decay. Functional assays in yeast confirmed a deleterious effect for two of the LGD variants in NAA15. Further supporting a mechanism of haploinsufficiency, individuals with copy-number variant (CNV) deletions involving NAA15 and surrounding genes can present with mild intellectual disability, mild dysmorphic features, motor delays, and decreased growth. We propose that defects in NatA-mediated N-terminal acetylation (NTA) lead to variable levels of neurodevelopmental disorders in humans, supporting the importance of the NatA complex in normal human development.


Subject(s)
Abnormalities, Multiple/genetics , Autism Spectrum Disorder/genetics , Genetic Predisposition to Disease , Genetic Variation , Intellectual Disability/genetics , N-Terminal Acetyltransferase A/genetics , N-Terminal Acetyltransferase E/genetics , Adolescent , Adult , Cell Line , Child , Exons/genetics , Female , Gene Expression Regulation , Humans , Male , Middle Aged , Mutation/genetics , N-Terminal Acetyltransferase A/metabolism , N-Terminal Acetyltransferase E/metabolism , Pedigree , Phenotype , RNA, Messenger/genetics , RNA, Messenger/metabolism , Saccharomyces cerevisiae/metabolism
10.
BMC Cancer ; 21(1): 460, 2021 Apr 26.
Article in English | MEDLINE | ID: mdl-33902514

ABSTRACT

BACKGROUND: Gastric cancer is a fatal gastrointestinal cancer with high morbidity and poor prognosis. The dismal 5-year survival rate warrants reliable biomarkers to assess and improve the prognosis of gastric cancer. Distinguishing driver mutations that are required for the cancer phenotype from passenger mutations poses a formidable challenge for cancer genomics. METHODS: We integrated the multi-omics data of 293 primary gastric cancer patients from The Cancer Genome Atlas (TCGA) to identify key driver genes by establishing a prognostic model of the patients. Analyzing both copy number alteration and somatic mutation data helped us to comprehensively reveal molecular markers of genomic variation. Integrating the transcription level of genes provided a unique perspective for us to discover dysregulated factors in transcriptional regulation. RESULTS: We comprehensively identified 31 molecular markers of genomic variation. For instance, the copy number alteration of WASHC5 (also known as KIAA0196) frequently occurred in gastric cancer patients, which cannot be discovered using traditional methods based on significant mutations. Furthermore, we revealed that several dysregulation factors played a hub regulatory role in the process of biological metabolism based on dysregulation networks. Cancer hallmark and functional enrichment analysis showed that these key driver (KD) genes played a vital role in regulating programmed cell death. The drug response patterns and transcriptional signatures of KD genes reflected their clinical application value. CONCLUSIONS: These findings indicated that KD genes could serve as novel prognostic biomarkers for further research on the pathogenesis of gastric cancers. Our study elucidated a multidimensional and comprehensive genomic landscape and highlighted the molecular complexity of GC.


Subject(s)
Biomarkers, Tumor/genetics , Gene Expression Profiling/methods , Mutation , Proteins/genetics , Stomach Neoplasms/genetics , ATP-Binding Cassette Transporters/genetics , Antineoplastic Agents/pharmacology , Apoptosis/genetics , DNA Copy Number Variations , Databases, Genetic , Gene Dosage , Genetic Markers , Genomics , Humans , Membrane Proteins/genetics , N-Terminal Acetyltransferase A/genetics , N-Terminal Acetyltransferase E/genetics , Prognosis , Proteasome Endopeptidase Complex/genetics , Stomach Neoplasms/drug therapy , Transcriptome
11.
Am J Med Genet A ; 185(8): 2546-2560, 2021 08.
Article in English | MEDLINE | ID: mdl-34075687

ABSTRACT

Ogden syndrome is a rare lethal X-linked recessive disorder caused by a recurrent missense variant (Ser37Pro) in the NAA10 gene, encoding the catalytic subunit of the N-terminal acetyltransferase A complex (NatA). So far eight boys of two different families have been described in the literature, all presenting the distinctive and recognizable phenotype, which includes mostly postnatal growth retardation, global severe developmental delay, characteristic craniofacial features, and structural cardiac anomalies and/or arrhythmias. Here, we report the ninth case of Ogden syndrome with an independent recurrence of the Ser37Pro variant. We were able to follow the clinical course of the affected boy and delineate the evolving phenotype from his birth until his unfortunate death at 7 months. We could confirm the associated phenotype as well as the natural history of this severe disease. By describing new presenting features, we are further expanding the clinical spectrum associated with Ogden syndrome and review other phenotypes associated with NAA10 variants.


Subject(s)
Genetic Association Studies , Genetic Diseases, X-Linked/diagnosis , Genetic Diseases, X-Linked/genetics , Genetic Predisposition to Disease , Mutation , N-Terminal Acetyltransferase A/genetics , N-Terminal Acetyltransferase E/genetics , Adult , DNA Mutational Analysis , Electroencephalography , Female , Genotype , Humans , Infant, Newborn , Magnetic Resonance Imaging , Male , Phenotype , Pregnancy , Prenatal Diagnosis , Radiography , Syndrome
12.
Am J Med Genet A ; 185(1): 228-233, 2021 01.
Article in English | MEDLINE | ID: mdl-33103328

ABSTRACT

The NatA N-acetyltransferase complex is important for cotranslational protein modification and regulation of multiple cellular processes. The NatA complex includes the core components of NAA10, the catalytic subunit, and NAA15, the auxiliary component. Both NAA10 and NAA15 have been associated with neurodevelopmental disorders with overlapping clinical features, including variable intellectual disability, dysmorphic facial features, and, less commonly, congenital anomalies such as cleft lip or palate. Cardiac arrhythmias, including long QT syndrome, ventricular tachycardia, and ventricular fibrillation were among the first reported cardiac manifestations in patients with NAA10-related syndrome. Recently, three individuals with NAA10-related syndrome have been reported to also have hypertrophic cardiomyopathy (HCM). The general and cardiac phenotypes of NAA15-related syndrome are not as well described as NAA10-related syndrome. Congenital heart disease, including ventricular septal defects, and arrhythmias, such as ectopic atrial tachycardia, have been reported in a small proportion of patients with NAA15-related syndrome. Given the relationship between NAA10 and NAA15, we propose that HCM is also likely to occur in NAA15-related disorder. We present two patients with pediatric HCM found to have NAA15-related disorder via exome sequencing, providing the first evidence that variants in NAA15 can cause HCM.


Subject(s)
Cardiomyopathy, Hypertrophic/genetics , Intellectual Disability/genetics , N-Terminal Acetyltransferase A/genetics , N-Terminal Acetyltransferase E/genetics , Abnormalities, Multiple/genetics , Abnormalities, Multiple/pathology , Cardiomyopathy, Hypertrophic/complications , Cardiomyopathy, Hypertrophic/pathology , Child , Facies , Genetic Predisposition to Disease , Humans , Infant , Intellectual Disability/complications , Intellectual Disability/pathology , Male , Muscular Atrophy/complications , Muscular Atrophy/genetics , Muscular Atrophy/pathology , Neurodevelopmental Disorders/complications , Neurodevelopmental Disorders/genetics , Neurodevelopmental Disorders/pathology , Pediatrics , Exome Sequencing
13.
Nucleic Acids Res ; 47(16): 8502-8520, 2019 09 19.
Article in English | MEDLINE | ID: mdl-31616951

ABSTRACT

Microrchidia family CW-type zinc finger 2 (MORC2) is a newly identified chromatin remodeling enzyme with an emerging role in DNA damage response (DDR), but the underlying mechanism remains largely unknown. Here, we show that poly(ADP-ribose) polymerase 1 (PARP1), a key chromatin-associated enzyme responsible for the synthesis of poly(ADP-ribose) (PAR) polymers in mammalian cells, interacts with and PARylates MORC2 at two residues within its conserved CW-type zinc finger domain. Following DNA damage, PARP1 recruits MORC2 to DNA damage sites and catalyzes MORC2 PARylation, which stimulates its ATPase and chromatin remodeling activities. Mutation of PARylation residues in MORC2 results in reduced cell survival after DNA damage. MORC2, in turn, stabilizes PARP1 through enhancing acetyltransferase NAT10-mediated acetylation of PARP1 at lysine 949, which blocks its ubiquitination at the same residue and subsequent degradation by E3 ubiquitin ligase CHFR. Consequently, depletion of MORC2 or expression of an acetylation-defective PARP1 mutant impairs DNA damage-induced PAR production and PAR-dependent recruitment of DNA repair proteins to DNA lesions, leading to enhanced sensitivity to genotoxic stress. Collectively, these findings uncover a previously unrecognized mechanistic link between MORC2 and PARP1 in the regulation of cellular response to DNA damage.


Subject(s)
Cell Cycle Proteins/genetics , Chromatin/metabolism , DNA Repair , Neoplasm Proteins/genetics , Poly (ADP-Ribose) Polymerase-1/genetics , Poly-ADP-Ribose Binding Proteins/genetics , Protein Processing, Post-Translational , Transcription Factors/genetics , Ubiquitin-Protein Ligases/genetics , Acetylation/drug effects , Cell Cycle Proteins/metabolism , Cell Line, Tumor , Chromatin/chemistry , Chromatin/drug effects , Chromatin Assembly and Disassembly/drug effects , DNA Damage , HEK293 Cells , Humans , Mutation , N-Terminal Acetyltransferase E/genetics , N-Terminal Acetyltransferase E/metabolism , N-Terminal Acetyltransferases , Neoplasm Proteins/metabolism , Phthalazines/pharmacology , Piperazines/pharmacology , Poly (ADP-Ribose) Polymerase-1/antagonists & inhibitors , Poly (ADP-Ribose) Polymerase-1/metabolism , Poly Adenosine Diphosphate Ribose/metabolism , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology , Poly-ADP-Ribose Binding Proteins/metabolism , Proteolysis/drug effects , Signal Transduction , Transcription Factors/metabolism , Ubiquitin-Protein Ligases/metabolism , Ubiquitination/drug effects
14.
Int J Mol Sci ; 22(21)2021 Oct 30.
Article in English | MEDLINE | ID: mdl-34769235

ABSTRACT

NAA10 is a major N-terminal acetyltransferase (NAT) that catalyzes the cotranslational N-terminal (Nt-) acetylation of 40% of the human proteome. Several reports of lysine acetyltransferase (KAT) activity by NAA10 exist, but others have not been able to find any NAA10-derived KAT activity, the latter of which is supported by structural studies. The KAT activity of NAA10 towards hypoxia-inducible factor 1α (HIF-1α) was recently found to depend on the hydroxylation at Trp38 of NAA10 by factor inhibiting HIF-1α (FIH). In contrast, we could not detect hydroxylation of Trp38 of NAA10 in several human cell lines and found no evidence that NAA10 interacts with or is regulated by FIH. Our data suggest that NAA10 Trp38 hydroxylation is not a switch in human cells and that it alters its catalytic activity from a NAT to a KAT.


Subject(s)
Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , N-Terminal Acetyltransferase A/metabolism , N-Terminal Acetyltransferase E/metabolism , Protein Processing, Post-Translational , HEK293 Cells , HeLa Cells , Humans , Hydroxylation , Hypoxia-Inducible Factor 1, alpha Subunit/genetics , N-Terminal Acetyltransferase A/genetics , N-Terminal Acetyltransferase E/genetics , Tryptophan/genetics , Tryptophan/metabolism
15.
Cancer Sci ; 111(5): 1829-1839, 2020 May.
Article in English | MEDLINE | ID: mdl-32162442

ABSTRACT

Lysine acetyltransferases (KATs) are a highly diverse group of epigenetic enzymes that play important roles in various cellular processes including transcription, signal transduction, and cellular metabolism. However, our knowledge of the genomic and transcriptomic alterations of KAT genes and their clinical significance in human cancer remains incomplete. We undertook a metagenomic analysis of 37 KATs in more than 10 000 cancer samples across 33 tumor types, focusing on breast cancer. We identified associations among recurrent genetic alteration, gene expression, clinicopathologic features, and patient survival. Loss-of-function analysis was carried out to examine which KAT has important roles in growth and viability of breast cancer cells. We identified that a subset of KAT genes, including NAA10, KAT6A, and CREBBP, have high frequencies of genomic amplification or mutation in a spectrum of human cancers. Importantly, we found that 3 KATs, NAA10, ACAT2, and BRD4, were highly expressed in the aggressive basal-like subtype, and their expression was significantly associated with disease-free survival. Furthermore, we showed that depletion of NAA10 inhibits basal-like breast cancer growth in vitro. Our findings provide a strong foundation for further mechanistic research and for developing therapies that target NAA10 or other KATs in human cancer.


Subject(s)
Genome, Human/genetics , Lysine Acetyltransferases/genetics , Neoplasms/genetics , Neoplasms/pathology , Breast Neoplasms/classification , Breast Neoplasms/genetics , Breast Neoplasms/mortality , Breast Neoplasms/pathology , CREB-Binding Protein/genetics , Cell Line, Tumor , Cell Proliferation/genetics , Cell Survival/genetics , Disease-Free Survival , E1A-Associated p300 Protein/genetics , Gene Dosage , Gene Expression , Histone Acetyltransferases/genetics , Humans , Lysine Acetyltransferases/metabolism , Mutation , N-Terminal Acetyltransferase A/genetics , N-Terminal Acetyltransferase A/metabolism , N-Terminal Acetyltransferase E/genetics , N-Terminal Acetyltransferase E/metabolism , Neoplasms/mortality , Prognosis , TATA-Binding Protein Associated Factors/genetics , Transcription Factor TFIID/genetics , Transcription Factors/genetics
16.
BMC Med Genet ; 21(1): 153, 2020 07 22.
Article in English | MEDLINE | ID: mdl-32698785

ABSTRACT

BACKGROUND: NAA10 is the catalytic subunit of the major N-terminal acetyltransferase complex NatA which acetylates almost half the human proteome. Over the past decade, many NAA10 missense variants have been reported as causative of genetic disease in humans. Individuals harboring NAA10 variants often display variable degrees of intellectual disability (ID), developmental delay, and cardiac anomalies. Initially, carrier females appeared to be oligo- or asymptomatic with X-inactivation pattern skewed towards the wild type allele. However, recently it has been shown that NAA10 variants can cause syndromic or non-syndromic intellectual disability in females as well. The impact of specific NAA10 variants and the X-inactivation pattern on the individual phenotype in females remains to be elucidated. CASE PRESENTATION: Here we present a novel de novo NAA10 (NM_003491.3) c.[47A > C];[=] (p.[His16Pro];[=]) variant identified in a young female. The 10-year-old girl has severely delayed motor and language development, disturbed behavior with hyperactivity and restlessness, moderate dilatation of the ventricular system and extracerebral CSF spaces. Her blood leukocyte X-inactivation pattern was skewed (95/5) towards the maternally inherited X-chromosome. Our functional study indicates that NAA10 p.(H16P) impairs NatA complex formation and NatA catalytic activity, while monomeric NAA10 catalytic activity appears to be intact. Furthermore, cycloheximide experiments show that the NAA10 H16P variant does not affect the cellular stability of NAA10. DISCUSSION AND CONCLUSIONS: We demonstrate that NAA10 p.(His16Pro) causes a severe form of syndromic ID in a girl most likely through impaired NatA-mediated Nt-acetylation of cellular proteins. X-inactivation analyses showed a skewed X-inactivation pattern in DNA from blood of the patient with the maternally inherited allele being preferentially methylated/inactivated.


Subject(s)
Intellectual Disability/genetics , Mutation/genetics , N-Terminal Acetyltransferase A/genetics , N-Terminal Acetyltransferase E/genetics , X Chromosome Inactivation/genetics , Amino Acid Sequence , Biocatalysis , Child , Cycloheximide/metabolism , Female , HeLa Cells , Heterozygote , Humans , Male , N-Terminal Acetyltransferase A/chemistry , N-Terminal Acetyltransferase E/chemistry , Pedigree , Syndrome
17.
J Med Genet ; 56(7): 444-452, 2019 07.
Article in English | MEDLINE | ID: mdl-30842225

ABSTRACT

BACKGROUND: A single variant in NAA10 (c.471+2T>A), the gene encoding N-acetyltransferase 10, has been associated with Lenz microphthalmia syndrome. In this study, we aimed to identify causative variants in families with syndromic X-linked microphthalmia. METHODS: Three families, including 15 affected individuals with syndromic X-linked microphthalmia, underwent analyses including linkage analysis, exome sequencing and targeted gene sequencing. The consequences of two identified variants in NAA10 were evaluated using quantitative PCR and RNAseq. RESULTS: Genetic linkage analysis in family 1 supported a candidate region on Xq27-q28, which included NAA10. Exome sequencing identified a hemizygous NAA10 polyadenylation signal (PAS) variant, chrX:153,195,397T>C, c.*43A>G, which segregated with the disease. Targeted sequencing of affected males from families 2 and 3 identified distinct NAA10 PAS variants, chrX:g.153,195,401T>C, c.*39A>G and chrX:g.153,195,400T>C, c.*40A>G. All three variants were absent from gnomAD. Quantitative PCR and RNAseq showed reduced NAA10 mRNA levels and abnormal 3' UTRs in affected individuals. Targeted sequencing of NAA10 in 376 additional affected individuals failed to identify variants in the PAS. CONCLUSION: These data show that PAS variants are the most common variant type in NAA10-associated syndromic microphthalmia, suggesting reduced RNA is the molecular mechanism by which these alterations cause microphthalmia/anophthalmia. We reviewed recognised variants in PAS associated with Mendelian disorders and identified only 23 others, indicating that NAA10 harbours more than 10% of all known PAS variants. We hypothesise that PAS in other genes harbour unrecognised pathogenic variants associated with Mendelian disorders. The systematic interrogation of PAS could improve genetic testing yields.


Subject(s)
3' Untranslated Regions , Genetic Association Studies , Genetic Predisposition to Disease , Genetic Variation , N-Terminal Acetyltransferase A/genetics , N-Terminal Acetyltransferase E/genetics , Poly A , Alleles , Anophthalmos , Female , Genes, X-Linked , Genotype , Humans , Lod Score , Male , Microphthalmos , Pedigree , Sequence Analysis, DNA , X Chromosome Inactivation
18.
Nucleic Acids Res ; 46(18): 9601-9616, 2018 10 12.
Article in English | MEDLINE | ID: mdl-30165671

ABSTRACT

Anabolism and catabolism are tightly regulated according to the cellular energy supply. Upon energy stress, ribosomal RNA (rRNA) biogenesis is inhibited, and autophagy is induced. However, the mechanism linking rRNA biogenesis and autophagy is unclear. Here, we demonstrate that the nucleolar protein NAT10 plays a role in the transition between rRNA biogenesis and autophagy. Under normal conditions, NAT10 is acetylated to activate rRNA biogenesis and inhibit autophagy induction. Mechanistic studies demonstrate that NAT10 binds to and acetylates the autophagy regulator Che-1 at K228 to suppress the Che-1-mediated transcriptional activation of downstream genes Redd1 and Deptor under adequate energy supply conditions. Upon energy stress, NAT10 is deacetylated by Sirt1, leading to suppression of NAT10-activated rRNA biogenesis. In addition, deacetylation of NAT10 abolishes the NAT10-mediated transcriptional repression of Che-1, leading to the release of autophagy inhibition. Collectively, we demonstrate that the acetylation status of NAT10 is important for the anabolism-catabolism transition in response to energy stress, providing a novel mechanism by which nucleolar proteins control rRNA synthesis and autophagy in response to the cellular energy supply.


Subject(s)
Autophagy/genetics , N-Terminal Acetyltransferase E/genetics , RNA, Ribosomal/genetics , Stress, Physiological/genetics , Acetylation , Apoptosis Regulatory Proteins/genetics , Cell Nucleolus/metabolism , Humans , Intracellular Signaling Peptides and Proteins/genetics , Metabolism/genetics , N-Terminal Acetyltransferase E/metabolism , N-Terminal Acetyltransferases , RNA, Ribosomal/biosynthesis , RNA, Ribosomal/metabolism , Repressor Proteins/genetics , Sirtuin 1/genetics , Transcription Factors/genetics
19.
Int J Mol Sci ; 21(23)2020 Nov 26.
Article in English | MEDLINE | ID: mdl-33255974

ABSTRACT

The majority of the human proteome is subjected to N-terminal (Nt) acetylation catalysed by N-terminal acetyltransferases (NATs). The NatA complex is composed of two core subunits-the catalytic subunit NAA10 and the ribosomal anchor NAA15. Furthermore, NAA10 may also have catalytic and non-catalytic roles independent of NatA. Several inherited and de novo NAA10 variants have been associated with genetic disease in humans. In this study, we present a functional analysis of two de novo NAA10 variants, c.29A>G p.(D10G) and c.32T>G p.(L11R), previously identified in a male and a female, respectively. Both of these neighbouring amino acids are highly conserved in NAA10. Immunoprecipitation experiments revealed that both variants hamper complex formation with NAA15 and are thus likely to impair NatA-mediated Nt-acetylation in vivo. Despite their common impact on NatA formation, in vitro Nt-acetylation assays showed that the variants had opposing impacts on NAA10 catalytic activity. While NAA10 c.29A>G p.(D10G) exhibits normal intrinsic NatA activity and reduced monomeric NAA10 NAT activity, NAA10 c.32T>G p.(L11R) displays reduced NatA activity and normal NAA10 NAT activity. This study expands the scope of research into the functional consequences of NAA10 variants and underlines the importance of understanding the diverse cellular roles of NAA10 in disease mechanisms.


Subject(s)
Mutation/genetics , N-Terminal Acetyltransferase A/metabolism , N-Terminal Acetyltransferase E/genetics , Acetylation , Amino Acid Sequence , Biocatalysis , HeLa Cells , Humans , N-Terminal Acetyltransferase A/chemistry , N-Terminal Acetyltransferase A/genetics , N-Terminal Acetyltransferase E/chemistry
20.
Molecules ; 25(3)2020 Jan 29.
Article in English | MEDLINE | ID: mdl-32013195

ABSTRACT

Arrest defective 1 (ARD1), also known as N(alpha)-acetyltransferase 10 (NAA10) was originally identified as an N-terminal acetyltransferase (NAT) that catalyzes the acetylation of N-termini of newly synthesized peptides. After that, mammalian ARD1/NAA10 expanded its' role to lysine acetyltransferase (KAT) that post-translationally acetylates internal lysine residues of proteins. ARD1/NAA10 is the only enzyme with both NAT and KAT activities. However, recent studies on the role of human ARD1/NAA10 (hARD1/NAA10) in lysine acetylation are contradictory, as crystal structure and in vitro acetylation assay results revealed the lack of KAT activity. Thus, the role of hARD1/NAA10 in lysine acetylation is still debating. Here, we found a clue that possibly explains these complicated and controversial results on KAT activity of hARD1/NAA10. Recombinant hARD1/NAA10 exhibited KAT activity, which disappeared soon in vitro. Size-exclusion analysis revealed that most recombinant hARD1/NAA10 formed oligomers over time, resulting in the loss of KAT activity. While oligomeric recombinant hARD1/NAA10 lost its ability for lysine acetylation, its monomeric form clearly exhibited lysine acetylation activity in vitro. We also characterized the KAT activity of hARD1/NAA10 that was influenced by several experimental conditions, including concentration of reactants and reaction time. Taken together, our study proves that recombinant hARD1/NAA10 exhibits KAT activity in vitro but only under accurate conditions, including reactant concentrations and reaction duration.


Subject(s)
Lysine Acetyltransferases/metabolism , N-Terminal Acetyltransferase A/metabolism , N-Terminal Acetyltransferase E/metabolism , Acetylation , Dialysis , Escherichia coli , Humans , Lysine/metabolism , N-Terminal Acetyltransferase A/genetics , N-Terminal Acetyltransferase A/isolation & purification , N-Terminal Acetyltransferase E/genetics , N-Terminal Acetyltransferase E/isolation & purification , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism
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