51
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Protein N-Terminal Acetylation: Structural Basis, Mechanism, Versatility, and Regulation. Trends Biochem Sci 2020; 46:15-27. [PMID: 32912665 DOI: 10.1016/j.tibs.2020.08.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 12/15/2022]
Abstract
N-terminal acetylation (NTA) is one of the most widespread protein modifications, which occurs on most eukaryotic proteins, but is significantly less common on bacterial and archaea proteins. This modification is carried out by a family of enzymes called N-terminal acetyltransferases (NATs). To date, 12 NATs have been identified, harboring different composition, substrate specificity, and in some cases, modes of regulation. Recent structural and biochemical analysis of NAT proteins allows for a comparison of their molecular mechanisms and modes of regulation, which are described here. Although sharing an evolutionarily conserved fold and related catalytic mechanism, each catalytic subunit uses unique elements to mediate substrate-specific activity, and use NAT-type specific auxiliary and regulatory subunits, for their cellular functions.
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52
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Deng S, Pan B, Gottlieb L, Petersson EJ, Marmorstein R. Molecular basis for N-terminal alpha-synuclein acetylation by human NatB. eLife 2020; 9:57491. [PMID: 32885784 PMCID: PMC7494357 DOI: 10.7554/elife.57491] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/03/2020] [Indexed: 12/20/2022] Open
Abstract
NatB is one of three major N-terminal acetyltransferase (NAT) complexes (NatA-NatC), which co-translationally acetylate the N-termini of eukaryotic proteins. Its substrates account for about 21% of the human proteome, including well known proteins such as actin, tropomyosin, CDK2, and α-synuclein (αSyn). Human NatB (hNatB) mediated N-terminal acetylation of αSyn has been demonstrated to play key roles in the pathogenesis of Parkinson's disease and as a potential therapeutic target for hepatocellular carcinoma. Here we report the cryo-EM structure of hNatB bound to a CoA-αSyn conjugate, together with structure-guided analysis of mutational effects on catalysis. This analysis reveals functionally important differences with human NatA and Candida albicans NatB, resolves key hNatB protein determinants for αSyn N-terminal acetylation, and identifies important residues for substrate-specific recognition and acetylation by NatB enzymes. These studies have implications for developing small molecule NatB probes and for understanding the mode of substrate selection by NAT enzymes.
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Affiliation(s)
- Sunbin Deng
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Buyan Pan
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Leah Gottlieb
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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53
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Bienvenut WV, Brünje A, Boyer J, Mühlenbeck JS, Bernal G, Lassowskat I, Dian C, Linster E, Dinh TV, Koskela MM, Jung V, Seidel J, Schyrba LK, Ivanauskaite A, Eirich J, Hell R, Schwarzer D, Mulo P, Wirtz M, Meinnel T, Giglione C, Finkemeier I. Dual lysine and N-terminal acetyltransferases reveal the complexity underpinning protein acetylation. Mol Syst Biol 2020; 16:e9464. [PMID: 32633465 PMCID: PMC7339202 DOI: 10.15252/msb.20209464] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 01/02/2023] Open
Abstract
Protein acetylation is a highly frequent protein modification. However, comparatively little is known about its enzymatic machinery. N-α-acetylation (NTA) and ε-lysine acetylation (KA) are known to be catalyzed by distinct families of enzymes (NATs and KATs, respectively), although the possibility that the same GCN5-related N-acetyltransferase (GNAT) can perform both functions has been debated. Here, we discovered a new family of plastid-localized GNATs, which possess a dual specificity. All characterized GNAT family members display a number of unique features. Quantitative mass spectrometry analyses revealed that these enzymes exhibit both distinct KA and relaxed NTA specificities. Furthermore, inactivation of GNAT2 leads to significant NTA or KA decreases of several plastid proteins, while proteins of other compartments were unaffected. The data indicate that these enzymes have specific protein targets and likely display partly redundant selectivity, increasing the robustness of the acetylation process in vivo. In summary, this study revealed a new layer of complexity in the machinery controlling this prevalent modification and suggests that other eukaryotic GNATs may also possess these previously underappreciated broader enzymatic activities.
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Affiliation(s)
- Willy V Bienvenut
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
- Present address:
Génétique Quantitative et ÉvolutionGif‐sur‐YvetteFrance
| | - Annika Brünje
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Jean‐Baptiste Boyer
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Jens S Mühlenbeck
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Gautier Bernal
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
- Present address:
Institute of Plant Sciences Paris‐SaclayGif‐sur‐YvetteFrance
| | - Ines Lassowskat
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Cyril Dian
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Eric Linster
- Centre for Organismal Studies HeidelbergUniversity of HeidelbergHeidelbergGermany
| | - Trinh V Dinh
- Centre for Organismal Studies HeidelbergUniversity of HeidelbergHeidelbergGermany
| | - Minna M Koskela
- Department of BiochemistryMolecular Plant BiologyUniversity of TurkuTurkuFinland
- Present address:
Institute of MicrobiologyTřeboňCzech Republic
| | - Vincent Jung
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
- Present address:
Institute IMAGINEParisFrance
| | - Julian Seidel
- Interfaculty Institute of BiochemistryUniversity of TübingenTübingenGermany
| | - Laura K Schyrba
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Aiste Ivanauskaite
- Department of BiochemistryMolecular Plant BiologyUniversity of TurkuTurkuFinland
| | - Jürgen Eirich
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Rüdiger Hell
- Centre for Organismal Studies HeidelbergUniversity of HeidelbergHeidelbergGermany
| | - Dirk Schwarzer
- Interfaculty Institute of BiochemistryUniversity of TübingenTübingenGermany
| | - Paula Mulo
- Department of BiochemistryMolecular Plant BiologyUniversity of TurkuTurkuFinland
| | - Markus Wirtz
- Centre for Organismal Studies HeidelbergUniversity of HeidelbergHeidelbergGermany
| | - Thierry Meinnel
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Carmela Giglione
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Iris Finkemeier
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
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54
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Yamazawa K, Inoue T, Sakemi Y, Nakashima T, Yamashita H, Khono K, Fujita H, Enomoto K, Nakabayashi K, Hata K, Nakashima M, Matsunaga T, Nakamura A, Matsubara K, Ogata T, Kagami M. Loss of imprinting of the human-specific imprinted gene ZNF597 causes prenatal growth retardation and dysmorphic features: implications for phenotypic overlap with Silver-Russell syndrome. J Med Genet 2020; 58:427-432. [PMID: 32576657 PMCID: PMC8142457 DOI: 10.1136/jmedgenet-2020-107019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 11/04/2022]
Abstract
BACKGROUND ZNF597, encoding a zinc-finger protein, is the human-specific maternally expressed imprinted gene located on 16p13.3. The parent-of-origin expression of ZNF597 is regulated by the ZNF597:TSS-DMR, of which only the paternal allele acquires methylation during postimplantation period. Overexpression of ZNF597 may contribute to some of the phenotypes associated with maternal uniparental disomy of chromosome 16 (UPD(16)mat), and some patients with UPD(16)mat presenting with Silver-Russell syndrome (SRS) phenotype have recently been reported. METHODS A 6-year-old boy presented with prenatal growth restriction, macrocephaly at birth, forehead protrusion in infancy and clinodactyly of the fifth finger. Methylation, expression, microsatellite marker, single nucleotide polymorphism array and trio whole-exome sequencing analyses were conducted. RESULTS Isolated hypomethylation of the ZNF597:TSS-DMR and subsequent loss of imprinting and overexpression of ZNF597 were confirmed in the patient. Epigenetic alterations, such as UPD including UPD(16)mat and other methylation defects, were excluded. Pathogenic sequence or copy number variants affecting his phenotypes were not identified, indicating that primary epimutation occurred postzygotically. CONCLUSION We report the first case of isolated ZNF597 imprinting defect, showing phenotypic overlap with SRS despite not satisfying the clinical SRS criteria. A novel imprinting disorder entity involving the ZNF597 imprinted domain can be speculated.
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Affiliation(s)
- Kazuki Yamazawa
- Medical Genetics Center, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Takanobu Inoue
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, University of Tokyo, Tokyo, Japan
| | - Yoshihiro Sakemi
- Department of Pediatrics, National Hospital Organization Kokura Medical Center, Kitakyushu, Japan
| | - Toshinori Nakashima
- Department of Pediatrics, National Hospital Organization Kokura Medical Center, Kitakyushu, Japan
| | - Hironori Yamashita
- Department of Pediatrics, National Hospital Organization Kokura Medical Center, Kitakyushu, Japan
| | | | | | | | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Moeko Nakashima
- Medical Genetics Center, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Tatsuo Matsunaga
- Medical Genetics Center, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Akie Nakamura
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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55
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Deng S, McTiernan N, Wei X, Arnesen T, Marmorstein R. Molecular basis for N-terminal acetylation by human NatE and its modulation by HYPK. Nat Commun 2020; 11:818. [PMID: 32042062 PMCID: PMC7010799 DOI: 10.1038/s41467-020-14584-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/18/2020] [Indexed: 01/04/2023] Open
Abstract
The human N-terminal acetyltransferase E (NatE) contains NAA10 and NAA50 catalytic, and NAA15 auxiliary subunits and associates with HYPK, a protein with intrinsic NAA10 inhibitory activity. NatE co-translationally acetylates the N-terminus of half the proteome to mediate diverse biological processes, including protein half-life, localization, and interaction. The molecular basis for how NatE and HYPK cooperate is unknown. Here, we report the cryo-EM structures of human NatE and NatE/HYPK complexes and associated biochemistry. We reveal that NAA50 and HYPK exhibit negative cooperative binding to NAA15 in vitro and in human cells by inducing NAA15 shifts in opposing directions. NAA50 and HYPK each contribute to NAA10 activity inhibition through structural alteration of the NAA10 substrate-binding site. NAA50 activity is increased through NAA15 tethering, but is inhibited by HYPK through structural alteration of the NatE substrate-binding site. These studies reveal the molecular basis for coordinated N-terminal acetylation by NatE and HYPK.
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Affiliation(s)
- Sunbin Deng
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nina McTiernan
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Xuepeng Wei
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Biological Sciences, University of Bergen, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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56
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Lau MT, Ghazanfar S, Parkin A, Chou A, Rouaen JR, Littleboy JB, Nessem D, Khuong TM, Nevoltris D, Schofield P, Langley D, Christ D, Yang J, Pajic M, Neely GG. Systematic functional identification of cancer multi-drug resistance genes. Genome Biol 2020; 21:27. [PMID: 32028983 PMCID: PMC7006212 DOI: 10.1186/s13059-020-1940-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/20/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Drug resistance is a major obstacle in cancer therapy. To elucidate the genetic factors that regulate sensitivity to anti-cancer drugs, we performed CRISPR-Cas9 knockout screens for resistance to a spectrum of drugs. RESULTS In addition to known drug targets and resistance mechanisms, this study revealed novel insights into drug mechanisms of action, including cellular transporters, drug target effectors, and genes involved in target-relevant pathways. Importantly, we identified ten multi-drug resistance genes, including an uncharacterized gene C1orf115, which we named Required for Drug-induced Death 1 (RDD1). Loss of RDD1 resulted in resistance to five anti-cancer drugs. Finally, targeting RDD1 leads to chemotherapy resistance in mice and low RDD1 expression is associated with poor prognosis in multiple cancers. CONCLUSIONS Together, we provide a functional landscape of resistance mechanisms to a broad range of chemotherapeutic drugs and highlight RDD1 as a new factor controlling multi-drug resistance. This information can guide personalized therapies or instruct rational drug combinations to minimize acquisition of resistance.
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Affiliation(s)
- Man-Tat Lau
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
- Genome Editing Initiative, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Shila Ghazanfar
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
- The Judith and David Coffey Life Lab, Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Ashleigh Parkin
- The Kinghorn Cancer Centre, The Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW, 2010, Australia
| | - Angela Chou
- The Kinghorn Cancer Centre, The Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW, 2010, Australia
- The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jourdin R Rouaen
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jamie B Littleboy
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Danielle Nessem
- The Kinghorn Cancer Centre, The Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW, 2010, Australia
| | - Thang M Khuong
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Damien Nevoltris
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Kensington, Sydney, NSW, 2010, Australia
| | - David Langley
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Kensington, Sydney, NSW, 2010, Australia
| | - Jean Yang
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Marina Pajic
- The Kinghorn Cancer Centre, The Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW, 2010, Australia.
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Kensington, Sydney, NSW, 2010, Australia.
| | - G Gregory Neely
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
- Genome Editing Initiative, The University of Sydney, Sydney, NSW, 2006, Australia.
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57
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Huber M, Bienvenut WV, Linster E, Stephan I, Armbruster L, Sticht C, Layer D, Lapouge K, Meinnel T, Sinning I, Giglione C, Hell R, Wirtz M. NatB-Mediated N-Terminal Acetylation Affects Growth and Biotic Stress Responses. PLANT PHYSIOLOGY 2020; 182:792-806. [PMID: 31744933 PMCID: PMC6997699 DOI: 10.1104/pp.19.00792] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/07/2019] [Indexed: 05/22/2023]
Abstract
N∝-terminal acetylation (NTA) is one of the most abundant protein modifications in eukaryotes. In humans, NTA is catalyzed by seven Nα-acetyltransferases (NatA-F and NatH). Remarkably, the plant Nat machinery and its biological relevance remain poorly understood, although NTA has gained recognition as a key regulator of crucial processes such as protein turnover, protein-protein interaction, and protein targeting. In this study, we combined in vitro assays, reverse genetics, quantitative N-terminomics, transcriptomics, and physiological assays to characterize the Arabidopsis (Arabidopsis thaliana) NatB complex. We show that the plant NatB catalytic (NAA20) and auxiliary subunit (NAA25) form a stable heterodimeric complex that accepts canonical NatB-type substrates in vitro. In planta, NatB complex formation was essential for enzymatic activity. Depletion of NatB subunits to 30% of the wild-type level in three Arabidopsis T-DNA insertion mutants (naa20-1, naa20-2, and naa25-1) caused a 50% decrease in plant growth. A complementation approach revealed functional conservation between plant and human catalytic NatB subunits, whereas yeast NAA20 failed to complement naa20-1 Quantitative N-terminomics of approximately 1000 peptides identified 32 bona fide substrates of the plant NatB complex. In vivo, NatB was seen to preferentially acetylate N termini starting with the initiator Met followed by acidic amino acids and contributed 20% of the acetylation marks in the detected plant proteome. Global transcriptome and proteome analyses of NatB-depleted mutants suggested a function of NatB in multiple stress responses. Indeed, loss of NatB function, but not NatA, increased plant sensitivity toward osmotic and high-salt stress, indicating that NatB is required for tolerance of these abiotic stressors.
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Affiliation(s)
- Monika Huber
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Willy V Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Eric Linster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Iwona Stephan
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Laura Armbruster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | | | - Dominik Layer
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Ruediger Hell
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
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58
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Eldeeb MA, Fahlman RP, Ragheb MA, Esmaili M. Does N‐Terminal Protein Acetylation Lead to Protein Degradation? Bioessays 2019; 41:e1800167. [DOI: 10.1002/bies.201800167] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 08/12/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Mohamed A. Eldeeb
- Department of Chemistry (Biochemistry Division)Faculty of ScienceCairo University Giza 12613 Egypt
- Department of Neurology and NeurosurgeryMontreal Neurological InstituteMcGill University Montreal Quebec H3A 2B4 Canada
| | - Richard P. Fahlman
- Department of BiochemistryUniversity of Alberta Edmonton Alberta T6G 2R3 Canada
| | - Mohamed A. Ragheb
- Department of Chemistry (Biochemistry Division)Faculty of ScienceCairo University Giza 12613 Egypt
| | - Mansoore Esmaili
- Department of BiochemistryUniversity of Alberta Edmonton Alberta T6G 2R3 Canada
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59
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Deng S, Magin RS, Wei X, Pan B, Petersson EJ, Marmorstein R. Structure and Mechanism of Acetylation by the N-Terminal Dual Enzyme NatA/Naa50 Complex. Structure 2019; 27:1057-1070.e4. [PMID: 31155310 PMCID: PMC6610660 DOI: 10.1016/j.str.2019.04.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/03/2019] [Accepted: 04/23/2019] [Indexed: 01/07/2023]
Abstract
NatA co-translationally acetylates the N termini of over 40% of eukaryotic proteins and can associate with another catalytic subunit, Naa50, to form a ternary NatA/Naa50 dual enzyme complex (also called NatE). The molecular basis of association between Naa50 and NatA and the mechanism for how their association affects their catalytic activities in yeast and human are poorly understood. Here, we determined the X-ray crystal structure of yeast NatA/Naa50 as a scaffold to understand coregulation of NatA/Naa50 activity in both yeast and human. We find that Naa50 makes evolutionarily conserved contacts to both the Naa10 and Naa15 subunits of NatA. These interactions promote catalytic crosstalk within the human complex, but do so to a lesser extent in the yeast complex, where Naa50 activity is compromised. These studies have implications for understanding the role of the NatA/Naa50 complex in modulating the majority of the N-terminal acetylome in diverse species.
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Affiliation(s)
- Sunbin Deng
- Department of Chemistry, University of Pennsylvania, 231 South 34(th) Street, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert S Magin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Xuepeng Wei
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Buyan Pan
- Department of Chemistry, University of Pennsylvania, 231 South 34(th) Street, Philadelphia, PA 19104, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34(th) Street, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, 231 South 34(th) Street, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA.
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60
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Ree R, Geithus AS, Tørring PM, Sørensen KP, Damkjær M, Lynch SA, Arnesen T. A novel NAA10 p.(R83H) variant with impaired acetyltransferase activity identified in two boys with ID and microcephaly. BMC MEDICAL GENETICS 2019; 20:101. [PMID: 31174490 PMCID: PMC6554967 DOI: 10.1186/s12881-019-0803-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/08/2019] [Indexed: 12/21/2022]
Abstract
Background N-terminal acetylation is a common protein modification in human cells and is catalysed by N-terminal acetyltransferases (NATs), mostly cotranslationally. The NAA10-NAA15 (NatA) protein complex is the major NAT, responsible for acetylating ~ 40% of human proteins. Recently, NAA10 germline variants were found in patients with the X-linked lethal Ogden syndrome, and in other familial or de novo cases with variable degrees of developmental delay, intellectual disability (ID) and cardiac anomalies. Methods Here we report a novel NAA10 (NM_003491.3) c.248G > A, p.(R83H) missense variant in NAA10 which was detected by whole exome sequencing in two unrelated boys with intellectual disability, developmental delay, ADHD like behaviour, very limited speech and cardiac abnormalities. We employ in vitro acetylation assays to functionally test the impact of this variant on NAA10 enzyme activity. Results Functional characterization of NAA10-R83H by in vitro acetylation assays revealed a reduced enzymatic activity of monomeric NAA10-R83H. This variant is modelled to have an altered charge density in the acetyl-coenzyme A (Ac-CoA) binding region of NAA10. Conclusions We show that NAA10-R83H has a reduced monomeric catalytic activity, likely due to impaired enzyme-Ac-CoA binding. Our data support a model where reduced NAA10 and/or NatA activity cause the phenotypes observed in the two patients. Electronic supplementary material The online version of this article (10.1186/s12881-019-0803-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rasmus Ree
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, NO-5020, Bergen, Norway
| | - Anni Sofie Geithus
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, NO-5020, Bergen, Norway
| | | | | | - Mads Damkjær
- Hans Christian Andersen Children's Hospital, Odense University Hospital, DK-5000, Odense C, Denmark
| | | | - Sally Ann Lynch
- Temple Street Children's Hospital, Temple Street, Dublin, D01 X584, Ireland.
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, NO-5020, Bergen, Norway. .,Department of Biological Sciences, University of Bergen, NO-5020, Bergen, Norway. .,Department of Surgery, Haukeland University Hospital, NO-5021, Bergen, Norway.
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61
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Olzscha H. Posttranslational modifications and proteinopathies: how guardians of the proteome are defeated. Biol Chem 2019; 400:895-915. [DOI: 10.1515/hsz-2018-0458] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/13/2019] [Indexed: 01/15/2023]
Abstract
Abstract
Protein folding is one of the fundamental processes in life and therefore needs to be tightly regulated. Many cellular quality control systems are in place to ensure that proteostasis is optimally adjusted for a changing environment, facilitating protein folding, translocation and degradation. These systems include the molecular chaperones and the major protein degradation systems, namely the ubiquitin proteasome system and autophagy. However, the capacity of the quality control systems can be exhausted and protein misfolding and aggregation, including the formation of amyloids, can occur as a result of ageing, mutations or exogenous influences. There are many known diseases in which protein misfolding and aggregation can be the underlying cause of the pathological condition; these are referred to as proteinopathies. Over the last decade, it has become clear that posttranslational modifications can govern and modulate protein folding, and that aberrant posttranslational modifications can cause or contribute to proteinopathies. This review provides an overview of protein folding and misfolding and the role of the major protein quality control systems. It focusses on different posttranslational modifications and gives examples of how these posttranslational modifications can alter protein folding and cause or accompany proteinopathies.
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Affiliation(s)
- Heidi Olzscha
- Institut für Physiologische Chemie , Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg , Hollystr. 1 , D-06114 Halle/Saale , Germany
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62
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Characterization of Evolutionarily Conserved Trypanosoma cruzi NatC and NatA-N-Terminal Acetyltransferase Complexes. J Parasitol Res 2019; 2019:6594212. [PMID: 30956813 PMCID: PMC6431383 DOI: 10.1155/2019/6594212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/16/2019] [Accepted: 02/03/2019] [Indexed: 11/29/2022] Open
Abstract
Protein N-terminal acetylation is a co- and posttranslational modification, conserved among eukaryotes. It determines the functional fate of many proteins including their stability, complex formation, and subcellular localization. N-terminal acetyltransferases (NATs) transfer an acetyl group to the N-termini of proteins, and the major NATs in yeast and humans are NatA, NatB, and NatC. In this study, we characterized the Trypanosoma cruzi (T. cruzi) NatC and NatA protein complexes, each consisting of one catalytic subunit and predicted auxiliary subunits. The proteins were found to be expressed in the three main life cycle stages of the parasite, formed stable complexes in vivo, and partially cosedimented with the ribosome in agreement with a cotranslational function. An in vitro acetylation assay clearly demonstrated that the acetylated substrates of the NatC catalytic subunit from T. cruzi were similar to those of yeast and human NatC, suggesting evolutionary conservation of function. An RNAi knockdown of the Trypanosoma brucei (T. brucei) NatC catalytic subunit indicated that reduced NatC-mediated N-terminal acetylation of target proteins reduces parasite growth.
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63
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Aksnes H, Ree R, Arnesen T. Co-translational, Post-translational, and Non-catalytic Roles of N-Terminal Acetyltransferases. Mol Cell 2019; 73:1097-1114. [PMID: 30878283 DOI: 10.1016/j.molcel.2019.02.007] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/23/2019] [Accepted: 02/04/2019] [Indexed: 02/07/2023]
Abstract
Recent studies of N-terminal acetylation have identified new N-terminal acetyltransferases (NATs) and expanded the known functions of these enzymes beyond their roles as ribosome-associated co-translational modifiers. For instance, the identification of Golgi- and chloroplast-associated NATs shows that acetylation of N termini also happens post-translationally. In addition, we now appreciate that some NATs are highly specific; for example, a dedicated NAT responsible for post-translational N-terminal acetylation of actin was recently revealed. Other studies have extended NAT function beyond Nt acetylation, including functions as lysine acetyltransferases (KATs) and non-catalytic roles. Finally, emerging studies emphasize the physiological relevance of N-terminal acetylation, including roles in calorie-restriction-induced longevity and pathological α-synuclein aggregation in Parkinson's disease. Combined, the NATs rise as multifunctional proteins, and N-terminal acetylation is gaining recognition as a major cellular regulator.
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Affiliation(s)
- Henriette Aksnes
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.
| | - Rasmus Ree
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; Department of Biological Sciences, University of Bergen, 5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, 5021 Bergen, Norway.
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64
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Zhang J, Wang G, He WW, Losh M, Berry-Kravis E, Funk WE. Expression and Characterization of Human Fragile X Mental Retardation Protein Isoforms and Interacting Proteins in Human Cells. PROTEOMICS INSIGHTS 2019; 10:1178641818825268. [PMID: 30853789 PMCID: PMC6399764 DOI: 10.1177/1178641818825268] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 12/21/2018] [Indexed: 11/16/2022]
Abstract
Fragile X mental retardation protein is an mRNA-binding protein associated with phenotypic manifestations of fragile X syndrome, an X-linked disorder caused by mutation in the FMR1 gene that is the most common inherited cause of intellectual disability. Despite the well-studied genetic mechanism of the disease, the proteoforms of fragile X mental retardation protein have not been thoroughly characterized. Here, we report the expression and mass spectrometric characterization of human fragile X mental retardation protein. FMR1 cDNA clone was transfected into human HEK293 cells to express the full-length human fragile X mental retardation protein. Purified fragile X mental retardation protein was subjected to trypsin digestion and characterized by mass spectrometry. Results show 80.5% protein sequence coverage of fragile X mental retardation protein (Q06787, FMR1_HUMAN) including both the N- and C-terminal peptides, indicating successful expression of the full-length protein. Identified post-translational modifications include N-terminal acetylation, phosphorylation (Ser600), and methylation (Arg290, 471, and 474). In addition to the full-length fragile X mental retardation protein isoform (isoform 6), two endogenous fragile X mental retardation protein alternative splicing isoforms (isoforms 4 and 7), as well as fragile X mental retardation protein interacting proteins, were also identified in the co-purified samples, suggesting the interaction network of the human fragile X mental retardation protein. Quantification was performed at the peptide level, and this information provides important reference for the future development of a targeted assay for quantifying fragile X mental retardation protein in clinical samples. Collectively, this study provides the first comprehensive report of human fragile X mental retardation protein proteoforms and may help advance the mechanistic understanding of fragile X syndrome and related phenotypes associated with the FMR1 mutation.
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Affiliation(s)
- Jiang Zhang
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Wei-Wu He
- OriGene Technology, Inc., Rockville, MD, USA
| | - Molly Losh
- Department of Communication Sciences and Disorders, Northwestern University, Evanston, IL, USA
| | - Elizabeth Berry-Kravis
- Departments of Biochemistry, Neurological Sciences and Pediatrics, Rush University, Chicago, IL, USA
| | - William E Funk
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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65
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Chen H, Li S, Li L, Wu W, Ke X, Zou W, Zhao J. Nα-Acetyltransferases 10 and 15 are Required for the Correct Initiation of Endosperm Cellularization in Arabidopsis. PLANT & CELL PHYSIOLOGY 2018; 59:2113-2128. [PMID: 30020502 DOI: 10.1093/pcp/pcy135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
The endosperm and embryo originate from the fertilized central cell and egg cell through a programmed series of cell division and differentiation events. Characterization of more vital genes involved in endosperm and embryo development can help us to understand the regulatory mechanism in more depth. In this study, we found that loss of NAA10 and NAA15, the catalytic and auxiliary subunits of Arabidopsis thaliana N-terminal acetyltransferase A (AtNatA), respectively, led to severely delayed and incomplete endosperm cellularization, accompanied by disordered cell division in the early embryo. Studies on the marker genes/lines of the endosperm (AGL62-GFP, pDD19::GFP, pDD22::NLS-GFP and N9185) and embryo (STM, FIL, SCR and WOX5) in naa10/naa15 mutants showed that expression patterns of these markers were significantly affected, which were tightly associated with the defective feature of endosperm cellularization and embryo cell differentiation. Subsequently, embryonic complementation rescued the abortive embryos, but failed to initiate endosperm cellularization properly, further confirming the essential role of AtNatA in both endosperm and embryo development. Moreover, repression of AGL62 in naa10 and naa15 restored the endosperm cellularization, suggesting that NAA10/NAA15 functions in initiation of endosperm cellularization by inhibiting the expression of AGL62 in Arabidopsis. Therefore, NAA10 and NAA15 could be considered as crucial factors involved in promoting endosperm cellularization in Arabidopsis.
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Affiliation(s)
- Hongyu Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shuqin Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lu Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Weiying Wu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaolong Ke
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wenxuan Zou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
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66
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Varland S, Aksnes H, Kryuchkov F, Impens F, Van Haver D, Jonckheere V, Ziegler M, Gevaert K, Van Damme P, Arnesen T. N-terminal Acetylation Levels Are Maintained During Acetyl-CoA Deficiency in Saccharomyces cerevisiae. Mol Cell Proteomics 2018; 17:2309-2323. [PMID: 30150368 PMCID: PMC6283290 DOI: 10.1074/mcp.ra118.000982] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/22/2018] [Indexed: 12/17/2022] Open
Abstract
Nt-acetylation is a prevalent protein modification catalyzed by N-terminal acetyltransferases using acetyl-CoA as acetyl donor. Here, we performed a global analysis of Nt-acetylation in yeast following nutrient starvation. Contrary to histone acetylation, which is sensitive to acetyl-CoA levels, we demonstrate that Nt-acetylation remains largely unaffected to changes in cellular metabolism. We did, however, identify two protein groups that were differentially Nt-acetylated, one showing the same sensitivity to acetyl-CoA as histones. We propose that specific, rather than global, Nt-acetylation events are subject to metabolic regulation. N-terminal acetylation (Nt-acetylation) is a highly abundant protein modification in eukaryotes and impacts a wide range of cellular processes, including protein quality control and stress tolerance. Despite its prevalence, the mechanisms regulating Nt-acetylation are still nebulous. Here, we present the first global study of Nt-acetylation in yeast cells as they progress to stationary phase in response to nutrient starvation. Surprisingly, we found that yeast cells maintain their global Nt-acetylation levels upon nutrient depletion, despite a marked decrease in acetyl-CoA levels. We further observed two distinct sets of protein N termini that display differential and opposing Nt-acetylation behavior upon nutrient starvation, indicating a dynamic process. The first protein cluster was enriched for annotated N termini showing increased Nt-acetylation in stationary phase compared with exponential growth phase. The second protein cluster was conversely enriched for alternative nonannotated N termini (i.e. N termini indicative of shorter N-terminal proteoforms) and, like histones, showed reduced acetylation levels in stationary phase when acetyl-CoA levels were low. Notably, the degree of Nt-acetylation of Pcl8, a negative regulator of glycogen biosynthesis and two components of the pre-ribosome complex (Rsa3 and Rpl7a) increased during starvation. Moreover, the steady-state levels of these proteins were regulated both by starvation and NatA activity. In summary, this study represents the first comprehensive analysis of metabolic regulation of Nt-acetylation and reveals that specific, rather than global, Nt-acetylation events are subject to metabolic regulation.
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Affiliation(s)
- Sylvia Varland
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway; Donnelly Center for Cellular and Bio‡molecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
| | - Henriette Aksnes
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway
| | - Fedor Kryuchkov
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium; VIB Proteomics Core, B-9000 Ghent, Belgium
| | - Delphi Van Haver
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium; VIB Proteomics Core, B-9000 Ghent, Belgium
| | - Veronique Jonckheere
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium
| | - Mathias Ziegler
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium
| | - Petra Van Damme
- Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, N-5020 Bergen, Norway; Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
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67
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Arnesen T, Marmorstein R, Dominguez R. Actin's N-terminal acetyltransferase uncovered. Cytoskeleton (Hoboken) 2018; 75:318-322. [PMID: 30084538 DOI: 10.1002/cm.21455] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/16/2018] [Accepted: 05/22/2018] [Indexed: 12/18/2022]
Abstract
Humans express six highly conserved actin isoforms, which differ the most at their N-termini. Actin's N-terminus undergoes co- and post-translational processing unique among eukaryotic proteins. During translation, the initiator methionine of the two cytoplasmic isoforms is N-terminally acetylated (Nt-acetylated) and that of the four muscle isoforms is removed and the exposed cysteine is Nt-acetylated. Then, an unidentified acetylaminopeptidase post-translationally removes the Ac-Met (or Ac-Cys), and all six isoforms are re-acetylated at the N-terminus. Despite the vital importance of actin for cellular processes ranging from cell motility to organelle trafficking and cell division, the mechanism and functional consequences of Nt-acetylation remained unresolved. Two recent studies significantly advance our understanding of actin Nt-acetylation. Drazic et al. (2018, Proc Natl Acad Sci U S A, 115, 4399-4404) identify actin's dedicated N-terminal acetyltransferase (NAA80/NatH), and demonstrate that Nt-acetylation critically impacts actin assembly in vitro and in cells. NAA80 knockout cells display increased filopodia and lamellipodia formation and accelerated cell motility. In vitro, the absence of Nt-acetylation leads to a decrease in the rates of filament depolymerization and elongation, including formin-induced elongation. Goris et al. (2018, Proc Natl Acad Sci U S A, 115, 4405-4410] describe the structure of Drosophila NAA80 in complex with a peptide-CoA bi-substrate analog mimicking the N-terminus of β-actin. The structure reveals the source of NAA80's specificity for actin's negatively-charged N-terminus. Nt-acetylation neutralizes a positive charge, thus enhancing the overall negative charge of actin's unique N-terminus. Actin's N-terminus is exposed in the filament and influences the interactions of many actin-binding proteins. These advances open the way to understanding the many likely consequences and functional roles of actin Nt-acetylation.
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Affiliation(s)
- Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Biological Sciences, University of Bergen, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Roberto Dominguez
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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68
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Wiame E, Tahay G, Tyteca D, Vertommen D, Stroobant V, Bommer GT, Van Schaftingen E. NAT6 acetylates the N-terminus of different forms of actin. FEBS J 2018; 285:3299-3316. [PMID: 30028079 DOI: 10.1111/febs.14605] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 06/01/2018] [Accepted: 07/17/2018] [Indexed: 01/11/2023]
Abstract
All forms of mammalian actin comprise at their N-terminus a negatively charged region consisting of an N-acetylated aspartate or glutamate followed by two or three acidic residues. This structural feature is unique to actins and important for their interaction with other proteins. The enzyme catalyzing the acetylation of the N-terminal acidic residue is thought to be NAA10, an enzyme that acetylates multiple intracellular proteins. We report here that this acetylation is essentially carried out by NAT6 (Fus2), a protein of unknown function. Tests of the activity of human recombinant NAT6 on a series of purified proteins showed that the best substrate had several acidic residues near its N-terminus. Accordingly NAT6 was particularly active on highly acidic peptides with sequences corresponding to the N-terminus of different forms of mammalian actins. Knocking out of NAT6 in two human cell lines led to absence of acetylation of the first residue of mature beta-actin (Asp2) and gamma-actin-1 (Glu2). Complete acetylation of these two actins was restored by re-expression of NAT6, or by incubation of extracts of NAT6-deficient cells with low concentrations of recombinant NAT6, while NAA10 showed much less or no activity in such assays. Alpha-actin-1 expressed in NAT6-knockout cells was not acetylated at its N-terminus, indicating that the requirement of NAT6 for acetylation of actin N-termini also applies to the skeletal muscle actin isoform. Taken together, our findings reveal that NAT6 plays a critical role in the maturation of actins by carrying out the acetylation of their N-terminal acidic residue.
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Affiliation(s)
- Elsa Wiame
- Walloon Excellence in Lifesciences and Biotechnology (WELBIO), Brussels, Belgium.,Laboratory of Biochemistry, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Gaëlle Tahay
- Laboratory of Biochemistry, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Donatienne Tyteca
- CELL Unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Didier Vertommen
- Mass Spectrometry Platform, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Vincent Stroobant
- Ludwig Institute for Cancer Research, Université Catholique de Louvain, Brussels, Belgium
| | - Guido T Bommer
- Walloon Excellence in Lifesciences and Biotechnology (WELBIO), Brussels, Belgium.,Laboratory of Biochemistry, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Emile Van Schaftingen
- Walloon Excellence in Lifesciences and Biotechnology (WELBIO), Brussels, Belgium.,Laboratory of Biochemistry, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
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69
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Nguyen KT, Mun SH, Lee CS, Hwang CS. Control of protein degradation by N-terminal acetylation and the N-end rule pathway. Exp Mol Med 2018; 50:1-8. [PMID: 30054456 PMCID: PMC6063864 DOI: 10.1038/s12276-018-0097-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 04/11/2018] [Indexed: 11/10/2022] Open
Abstract
Nα-terminal acetylation (Nt-acetylation) occurs very frequently and is found in most proteins in eukaryotes. Despite the pervasiveness and universality of Nt-acetylation, its general functions in terms of physiological outcomes remain largely elusive. However, several recent studies have revealed that Nt-acetylation has a significant impact on protein stability, activity, folding patterns, cellular localization, etc. In addition, Nt-acetylation marks specific proteins for degradation by a branch of the N-end rule pathway, a subset of the ubiquitin-mediated proteolytic system. The N-end rule associates a protein's in vivo half-life with its N-terminal residue or modifications on its N-terminus. This review provides a current understanding of intracellular proteolysis control by Nt-acetylation and the N-end rule pathway.
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Affiliation(s)
- Kha The Nguyen
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Sang-Hyeon Mun
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Chang-Seok Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea.
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70
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Ree R, Varland S, Arnesen T. Spotlight on protein N-terminal acetylation. Exp Mol Med 2018; 50:1-13. [PMID: 30054468 PMCID: PMC6063853 DOI: 10.1038/s12276-018-0116-z] [Citation(s) in RCA: 261] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 01/11/2023] Open
Abstract
N-terminal acetylation (Nt-acetylation) is a widespread protein modification among eukaryotes and prokaryotes alike. By appending an acetyl group to the N-terminal amino group, the charge, hydrophobicity, and size of the N-terminus is altered in an irreversible manner. This alteration has implications for the lifespan, folding characteristics and binding properties of the acetylated protein. The enzymatic machinery responsible for Nt-acetylation has been largely described, but significant knowledge gaps remain. In this review, we provide an overview of eukaryotic N-terminal acetyltransferases (NATs) and the impact of Nt-acetylation. We also discuss other functions of known NATs and outline methods for studying Nt-acetylation.
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Affiliation(s)
- Rasmus Ree
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 55, N-5020, Bergen, Norway
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5020, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, N-5021, Bergen, Norway
| | - Sylvia Varland
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 55, N-5020, Bergen, Norway
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5020, Bergen, Norway
- Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Thomas Arnesen
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 55, N-5020, Bergen, Norway.
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5020, Bergen, Norway.
- Department of Surgery, Haukeland University Hospital, N-5021, Bergen, Norway.
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71
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Varland S, Arnesen T. Investigating the functionality of a ribosome-binding mutant of NAA15 using Saccharomyces cerevisiae. BMC Res Notes 2018; 11:404. [PMID: 29929531 PMCID: PMC6013942 DOI: 10.1186/s13104-018-3513-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/18/2018] [Indexed: 11/29/2022] Open
Abstract
Objective N-terminal acetylation is a common protein modification that occurs preferentially co-translationally as the substrate N-terminus is emerging from the ribosome. The major N-terminal acetyltransferase complex A (NatA) is estimated to N-terminally acetylate more than 40% of the human proteome. To form a functional NatA complex the catalytic subunit NAA10 must bind the auxiliary subunit NAA15, which properly folds NAA10 for correct substrate acetylation as well as anchors the entire complex to the ribosome. Mutations in these two genes are associated with various neurodevelopmental disorders in humans. The aim of this study was to investigate the in vivo functionality of a Schizosaccharomyces pombe NAA15 mutant that is known to prevent NatA from associating with ribosomes, but retains NatA-specific activity in vitro. Results Here, we show that Schizosaccharomyces pombe NatA can functionally replace Saccharomyces cerevisiae NatA. We further demonstrate that the NatA ribosome-binding mutant Naa15 ΔN K6E is unable to rescue the temperature-sensitive growth phenotype of budding yeast lacking NatA. This finding indicates the in vivo importance of the co-translational nature of NatA-mediated N-terminal acetylation.
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Affiliation(s)
- Sylvia Varland
- Department of Biological Sciences, University of Bergen, 5006, Bergen, Norway. .,Department of Biomedicine, University of Bergen, 5009, Bergen, Norway. .,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
| | - Thomas Arnesen
- Department of Biological Sciences, University of Bergen, 5006, Bergen, Norway.,Department of Biomedicine, University of Bergen, 5009, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, 5021, Bergen, Norway
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72
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Gottlieb L, Marmorstein R. Structure of Human NatA and Its Regulation by the Huntingtin Interacting Protein HYPK. Structure 2018; 26:925-935.e8. [PMID: 29754825 DOI: 10.1016/j.str.2018.04.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/22/2018] [Accepted: 04/05/2018] [Indexed: 12/31/2022]
Abstract
Co-translational N-terminal protein acetylation regulates many protein functions including degradation, folding, interprotein interactions, and targeting. Human NatA (hNatA), one of six conserved metazoan N-terminal acetyltransferases, contains Naa10 catalytic and Naa15 auxiliary subunits, and associates with the intrinsically disordered Huntingtin yeast two-hybrid protein K (HYPK). We report on the crystal structures of hNatA and hNatA/HYPK, and associated biochemical and enzymatic analyses. We demonstrate that hNatA contains unique features: a stabilizing inositol hexaphosphate (IP6) molecule and a metazoan-specific Naa15 domain that mediates high-affinity HYPK binding. We find that HYPK harbors intrinsic hNatA-specific inhibitory activity through a bipartite structure: a ubiquitin-associated domain that binds a hNaa15 metazoan-specific region and an N-terminal loop-helix region that distorts the hNaa10 active site. We show that HYPK binding blocks hNaa50 targeting to hNatA, likely limiting Naa50 ribosome localization in vivo. These studies provide a model for metazoan NAT activity and HYPK regulation of N-terminal acetylation.
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Affiliation(s)
- Leah Gottlieb
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA.
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73
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Drazic A, Arnesen T. [ 14C]-Acetyl-Coenzyme A-Based In Vitro N-Terminal Acetylation Assay. Methods Mol Biol 2018; 1574:1-8. [PMID: 28315239 DOI: 10.1007/978-1-4939-6850-3_1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
N-terminal acetylation is one of the most abundant co- and posttranslational protein modifications, conserved from prokaryotes to eukaryotes. The functional consequences of this modification are manifold, ranging from protein folding, stability, and interaction to subcellular localization. We describe here an isotope-labeled [14C]-acetyl-Coenzyme A-based acetylation assay, allowing the determination of weak catalytic activities of NATs in vitro. It allows the use of purified recombinant enzymes from Escherichia coli, or co-immunoprecipitated enzymes from various organisms, as well as the determination of the in vitro activity of various cell lysates. Although marked as an old-fashioned biochemical approach, it is the ideal method to hunt for catalytic activities and defining peptide specificities of new potential N-terminal acetyltransferase candidates.
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Affiliation(s)
- Adrian Drazic
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5020, Bergen, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5020, Bergen, Norway. .,Department of Surgery, Haukeland University Hospital, N-5021, Bergen, Norway.
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74
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DTNB-Based Quantification of In Vitro Enzymatic N-Terminal Acetyltransferase Activity. Methods Mol Biol 2018; 1574:9-15. [PMID: 28315240 DOI: 10.1007/978-1-4939-6850-3_2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
We here describe a quick and easy method to quantitatively measure in vitro acetylation activity of not only N-terminal acetyltransferase (NAT) enzymes, but acetyltransferases using acetyl-coenzyme A as an acetyl donor in general.
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75
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Jonckheere V, Fijałkowska D, Van Damme P. Omics Assisted N-terminal Proteoform and Protein Expression Profiling On Methionine Aminopeptidase 1 (MetAP1) Deletion. Mol Cell Proteomics 2018; 17:694-708. [PMID: 29317475 DOI: 10.1074/mcp.ra117.000360] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/12/2017] [Indexed: 12/14/2022] Open
Abstract
Excision of the N-terminal initiator methionine (iMet) residue from nascent peptide chains is an essential and omnipresent protein modification carried out by methionine aminopeptidases (MetAPs) that accounts for a major source of N-terminal proteoform diversity. Although MetAP2 is known to be implicated in processes such as angiogenesis and proliferation in mammals, the physiological role of MetAP1 is much less clear. In this report we studied the omics-wide effects of human MetAP1 deletion and general MetAP inhibition. The levels of iMet retention are inversely correlated with cellular proliferation rates. Further, despite the increased MetAP2 expression on MetAP1 deletion, MetAP2 was unable to restore processing of Met-Ser-, Met-Pro-, and Met-Ala- starting N termini as inferred from the iMet retention profiles observed, indicating a higher activity of MetAP1 over these N termini. Proteome and transcriptome expression profiling point to differential expression of proteins implicated in lipid metabolism, cytoskeleton organization, cell proliferation and protein synthesis upon perturbation of MetAP activity.
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Affiliation(s)
- Veronique Jonckheere
- From the ‡VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium.,§Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Daria Fijałkowska
- From the ‡VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium.,§Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Petra Van Damme
- From the ‡VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium; .,§Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
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76
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Varland S, Myklebust LM, Goksøyr SØ, Glomnes N, Torsvik J, Varhaug JE, Arnesen T. Identification of an alternatively spliced nuclear isoform of human N-terminal acetyltransferase Naa30. Gene 2017; 644:27-37. [PMID: 29247799 DOI: 10.1016/j.gene.2017.12.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/08/2017] [Accepted: 12/11/2017] [Indexed: 12/20/2022]
Abstract
N-terminal acetylation is a highly abundant and important protein modification in eukaryotes catalyzed by N-terminal acetyltransferases (NATs). In humans, six different NATs have been identified (NatA-NatF), each composed of individual subunits and acetylating a distinct set of substrates. Along with most NATs, NatC acts co-translationally at the ribosome. The NatC complex consists of the catalytic subunit Naa30 and the auxiliary subunits Naa35 and Naa38, and can potentially Nt-acetylate cytoplasmic proteins when the initiator methionine is followed by a bulky hydrophobic/amphipathic residue at position 2. Here, we have identified a splice variant of human NAA30, which encodes a truncated protein named Naa30288. The splice variant was abundantly present in thyroid cancer tissues and in several different human cancer cell lines. Surprisingly, Naa30288 localized predominantly to the nucleus, as opposed to annotated Naa30 which has a cytoplasmic localization. Full-length Naa30 acetylated a classical NatC substrate peptide in vitro, whereas no significant NAT activity was detected for Naa30288. Due to the nuclear localization, we also examined acetyltransferase activity towards lysine residues. Neither full-length Naa30 nor Naa30288 displayed any lysine acetyltransferase activity. Overexpression of full-length Naa30 increased cell viability via inhibition of apoptosis. In contrast, Naa30288 did not exert an anti-apoptotic effect. In sum, we identified a novel and widely expressed Naa30 isoform with a potential non-catalytic role in the nucleus.
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Affiliation(s)
- Sylvia Varland
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway
| | - Line M Myklebust
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway
| | - Siri Øfsthus Goksøyr
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway
| | - Nina Glomnes
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway; Department of Clinical Science, University of Bergen, Jonas Lies vei 87, 5021 Bergen, Norway
| | - Janniche Torsvik
- Department of Neurology, Haukeland University Hospital, Jonas Lies vei 87, 5021 Bergen, Norway
| | - Jan Erik Varhaug
- Department of Surgery, Haukeland University Hospital, Jonas Lies vei 87, 5021 Bergen, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, 5006 Bergen, Norway; Department of Surgery, Haukeland University Hospital, Jonas Lies vei 87, 5021 Bergen, Norway.
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77
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N-terminal acetylation modulates Bax targeting to mitochondria. Int J Biochem Cell Biol 2017; 95:35-42. [PMID: 29233735 DOI: 10.1016/j.biocel.2017.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/28/2017] [Accepted: 12/06/2017] [Indexed: 01/13/2023]
Abstract
The pro-apoptotic Bax protein is the main effector of mitochondrial permeabilization during apoptosis. Bax is controlled at several levels, including post-translational modifications such as phosphorylation and S-palmitoylation. However, little is known about the contribution of other protein modifications to Bax activity. Here, we used heterologous expression of human Bax in yeast to study the involvement of N-terminal acetylation by yNaa20p (yNatB) on Bax function. We found that human Bax is N-terminal (Nt-)acetylated by yNaa20p and that Nt-acetylation of Bax is essential to maintain Bax in an inactive conformation in the cytosol of yeast and Mouse Embryonic Fibroblast (MEF) cells. Bax accumulates in the mitochondria of yeast naa20Δ and Naa25-/- MEF cells, but does not promote cytochrome c release, suggesting that an additional step is required for full activation of Bax. Altogether, our results show that Bax N-terminal acetylation by NatB is involved in its mitochondrial targeting.
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78
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Ndah E, Jonckheere V, Giess A, Valen E, Menschaert G, Van Damme P. REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes. Nucleic Acids Res 2017; 45:e168. [PMID: 28977509 PMCID: PMC5714196 DOI: 10.1093/nar/gkx758] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 08/17/2017] [Indexed: 12/13/2022] Open
Abstract
Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated methods depend heavily on sequence composition and often underestimate the complexity of the proteome. We developed RibosomeE Profiling Assisted (re-)AnnotaTION (REPARATION), a de novo machine learning algorithm that takes advantage of experimental protein synthesis evidence from ribosome profiling (Ribo-seq) to delineate translated open reading frames (ORFs) in bacteria, independent of genome annotation (https://github.com/Biobix/REPARATION). REPARATION evaluates all possible ORFs in the genome and estimates minimum thresholds based on a growth curve model to screen for spurious ORFs. We applied REPARATION to three annotated bacterial species to obtain a more comprehensive mapping of their translation landscape in support of experimental data. In all cases, we identified hundreds of novel (small) ORFs including variants of previously annotated ORFs and >70% of all (variants of) annotated protein coding ORFs were predicted by REPARATION to be translated. Our predictions are supported by matching mass spectrometry proteomics data, sequence composition and conservation analysis. REPARATION is unique in that it makes use of experimental translation evidence to intrinsically perform a de novo ORF delineation in bacterial genomes irrespective of the sequence features linked to open reading frames.
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Affiliation(s)
- Elvis Ndah
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium.,Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - Veronique Jonckheere
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Adam Giess
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway.,Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
| | - Gerben Menschaert
- Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - Petra Van Damme
- VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
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79
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Comprehensive analysis of human protein N-termini enables assessment of various protein forms. Sci Rep 2017; 7:6599. [PMID: 28747677 PMCID: PMC5529458 DOI: 10.1038/s41598-017-06314-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/09/2017] [Indexed: 01/10/2023] Open
Abstract
Various forms of protein (proteoforms) are generated by genetic variations, alternative splicing, alternative translation initiation, co- or post-translational modification and proteolysis. Different proteoforms are in part discovered by characterizing their N-terminal sequences. Here, we introduce an N-terminal-peptide-enrichment method, Nrich. Filter-aided negative selection formed the basis for the use of two N-blocking reagents and two endoproteases in this method. We identified 6,525 acetylated (or partially acetylated) and 6,570 free protein N-termini arising from 5,727 proteins in HEK293T human cells. The protein N-termini included translation initiation sites annotated in the UniProtKB database, putative alternative translational initiation sites, and N-terminal sites exposed after signal/transit/pro-peptide removal or unknown processing, revealing various proteoforms in cells. In addition, 46 novel protein N-termini were identified in 5′ untranslated region (UTR) sequence with pseudo start codons. Our data showing the observation of N-terminal sequences of mature proteins constitutes a useful resource that may provide information for a better understanding of various proteoforms in cells.
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80
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Starheim KK, Kalvik TV, Bjørkøy G, Arnesen T. Depletion of the human N-terminal acetyltransferase hNaa30 disrupts Golgi integrity and ARFRP1 localization. Biosci Rep 2017; 37:BSR20170066. [PMID: 28356483 PMCID: PMC5408665 DOI: 10.1042/bsr20170066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/16/2017] [Accepted: 03/28/2017] [Indexed: 01/01/2023] Open
Abstract
The organization of the Golgi apparatus (GA) is tightly regulated. Golgi stack scattering is observed in cellular processes such as apoptosis and mitosis, and has also been associated with disruption of cellular lipid metabolism and neurodegenerative diseases. Our studies show that depletion of the human N-α-acetyltransferase 30 (hNaa30) induces fragmentation of the Golgi stack in HeLa and CAL-62 cell lines. The GA associated GTPase ADP ribosylation factor related protein 1 (ARFRP1) was previously shown to require N-terminal acetylation for membrane association and based on its N-terminal sequence, it is likely to be a substrate of hNaa30. ARFRP1 is involved in endosome-to-trans-Golgi network (TGN) traffic. We observed that ARFRP1 shifted from a predominantly cis-Golgi and TGN localization to localizing both Golgi and non-Golgi vesicular structures in hNaa30-depleted cells. However, we did not observe loss of membrane association of ARFRP1. We conclude that hNaa30 depletion induces Golgi scattering and induces aberrant ARFRP1 Golgi localization.
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Affiliation(s)
- Kristian K Starheim
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
- Department of Molecular Medicine and Cancer Research, Center of Molecular Inflammation Research, Norwegian University of Technology and Natural Sciences, N-7006 Trondheim, Norway
| | - Thomas V Kalvik
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Geir Bjørkøy
- Department of Molecular Medicine and Cancer Research, Center of Molecular Inflammation Research, Norwegian University of Technology and Natural Sciences, N-7006 Trondheim, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
- Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
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81
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Chen BJ, Lam TC, Liu LQ, To CH. Post-translational modifications and their applications in eye research (Review). Mol Med Rep 2017; 15:3923-3935. [PMID: 28487982 DOI: 10.3892/mmr.2017.6529] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 02/22/2017] [Indexed: 02/05/2023] Open
Abstract
Gene expression is the process by which genetic information is used for the synthesis of a functional gene product, and ultimately regulates cell function. The increase of biological complexity from genome to proteome is vast, and the post-translational modification (PTM) of proteins contribute to this complexity. The study of protein expression and PTMs has attracted attention in the post‑genomic era. Due to the limited capability of conventional biochemical techniques in the past, large‑scale PTM studies were technically challenging. The introduction of effective protein separation methods, specific PTM purification strategies and advanced mass spectrometers has enabled the global profiling of PTMs and the identification of a targeted PTM within the proteome. The present review provides an overview of current proteomic technologies being applied in eye research, with a particular focus on studies of PTMs in ocular tissues and ocular diseases.
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Affiliation(s)
- Bing-Jie Chen
- Department of Optometry and Visual Science, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Thomas Chuen Lam
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, P.R. China
| | - Long-Qian Liu
- Department of Optometry and Visual Science, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Chi-Ho To
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, P.R. China
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82
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Willems P, Ndah E, Jonckheere V, Stael S, Sticker A, Martens L, Van Breusegem F, Gevaert K, Van Damme P. N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana. Mol Cell Proteomics 2017; 16:1064-1080. [PMID: 28432195 PMCID: PMC5461538 DOI: 10.1074/mcp.m116.066662] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/11/2017] [Indexed: 01/05/2023] Open
Abstract
Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N termini encoded in the Arabidopsis thaliana genome. After a stringent false discovery rate filtering, 117 protein N termini compliant with N-terminal methionine excision specificity and indicative of translation initiation were found. These include N-terminal protein extensions and translation from transposable elements and pseudogenes. Gene prediction provided supporting protein-coding models for approximately half of the protein N termini. Besides the prediction of functional domains (partially) contained within the newly predicted ORFs, further supporting evidence of translation was found in the recently released Araport11 genome re-annotation of Arabidopsis and computational translations of sequences stored in public repositories. Most interestingly, complementary evidence by ribosome profiling was found for 23 protein N termini. Finally, by analyzing protein N-terminal peptides, an in silico analysis demonstrates the applicability of our N-terminal proteogenomics strategy in revealing protein-coding potential in species with well- and poorly-annotated genomes.
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Affiliation(s)
- Patrick Willems
- From the ‡VIB/UGent Center for Plant Systems Biology, 9052 Ghent, Belgium.,§Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent.,¶VIB/UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‖Ghent University, Department of Biochemistry, 9000 Ghent, Belgium
| | - Elvis Ndah
- ¶VIB/UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‖Ghent University, Department of Biochemistry, 9000 Ghent, Belgium.,**Ghent University, Department of Mathematical Modeling, Statistics and Bioinformatics, 9000 Ghent, Belgium
| | - Veronique Jonckheere
- ¶VIB/UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‖Ghent University, Department of Biochemistry, 9000 Ghent, Belgium
| | - Simon Stael
- From the ‡VIB/UGent Center for Plant Systems Biology, 9052 Ghent, Belgium.,§Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent.,¶VIB/UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‖Ghent University, Department of Biochemistry, 9000 Ghent, Belgium
| | - Adriaan Sticker
- ¶VIB/UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‖Ghent University, Department of Biochemistry, 9000 Ghent, Belgium.,**Ghent University, Department of Mathematical Modeling, Statistics and Bioinformatics, 9000 Ghent, Belgium
| | - Lennart Martens
- ¶VIB/UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‖Ghent University, Department of Biochemistry, 9000 Ghent, Belgium.,**Ghent University, Department of Mathematical Modeling, Statistics and Bioinformatics, 9000 Ghent, Belgium
| | - Frank Van Breusegem
- From the ‡VIB/UGent Center for Plant Systems Biology, 9052 Ghent, Belgium.,§Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent
| | - Kris Gevaert
- ¶VIB/UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‖Ghent University, Department of Biochemistry, 9000 Ghent, Belgium
| | - Petra Van Damme
- ¶VIB/UGent Center for Medical Biotechnology, 9000 Ghent, Belgium; .,‖Ghent University, Department of Biochemistry, 9000 Ghent, Belgium
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83
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Aksnes H, Goris M, Strømland Ø, Drazic A, Waheed Q, Reuter N, Arnesen T. Molecular determinants of the N-terminal acetyltransferase Naa60 anchoring to the Golgi membrane. J Biol Chem 2017; 292:6821-6837. [PMID: 28196861 DOI: 10.1074/jbc.m116.770362] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/29/2017] [Indexed: 11/06/2022] Open
Abstract
Nα-Acetyltransferase 60 (Naa60 or NatF) was recently identified as an unconventional N-terminal acetyltransferase (NAT) because it localizes to organelles, in particular the Golgi apparatus, and has a preference for acetylating N termini of the transmembrane proteins. This knowledge challenged the prevailing view of N-terminal acetylation as a co-translational ribosome-associated process and suggested a new mechanistic functioning for the enzymes responsible for this increasingly recognized protein modification. Crystallography studies on Naa60 were unable to resolve the C-terminal tail of Naa60, which is responsible for the organellar localization. Here, we combined modeling, in vitro assays, and cellular localization studies to investigate the secondary structure and membrane interacting capacity of Naa60. The results show that Naa60 is a peripheral membrane protein. Two amphipathic helices within the Naa60 C terminus bind the membrane directly in a parallel position relative to the lipid bilayer via hydrophobic and electrostatic interactions. A peptide corresponding to the C terminus was unstructured in solution and only folded into an α-helical conformation in the presence of liposomes. Computational modeling and cellular mutational analysis revealed the hydrophobic face of two α-helices to be critical for membranous localization. Furthermore, we found a strong and specific binding preference of Naa60 toward membranes containing the phosphatidylinositol PI(4)P, thus possibly explaining the primary residency of Naa60 at the PI(4)P-rich Golgi. In conclusion, we have defined the mode of cytosolic Naa60 anchoring to the Golgi apparatus, most likely occurring post-translationally and specifically facilitating post-translational N-terminal acetylation of many transmembrane proteins.
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Affiliation(s)
- Henriette Aksnes
- From the Department of Molecular Biology, University of Bergen, N-5020 Bergen
| | - Marianne Goris
- From the Department of Molecular Biology, University of Bergen, N-5020 Bergen
| | - Øyvind Strømland
- From the Department of Molecular Biology, University of Bergen, N-5020 Bergen
| | - Adrian Drazic
- From the Department of Molecular Biology, University of Bergen, N-5020 Bergen
| | - Qaiser Waheed
- From the Department of Molecular Biology, University of Bergen, N-5020 Bergen.,the Computational Biology Unit, Department of Informatics, University of Bergen, N-5020 Bergen, and
| | - Nathalie Reuter
- From the Department of Molecular Biology, University of Bergen, N-5020 Bergen.,the Computational Biology Unit, Department of Informatics, University of Bergen, N-5020 Bergen, and
| | - Thomas Arnesen
- From the Department of Molecular Biology, University of Bergen, N-5020 Bergen, .,the Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
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84
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Dörfel MJ, Fang H, Crain J, Klingener M, Weiser J, Lyon GJ. Proteomic and genomic characterization of a yeast model for Ogden syndrome. Yeast 2017; 34:19-37. [PMID: 27668839 PMCID: PMC5248646 DOI: 10.1002/yea.3211] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/12/2016] [Accepted: 09/16/2016] [Indexed: 11/10/2022] Open
Abstract
Naa10 is an Nα -terminal acetyltransferase that, in a complex with its auxiliary subunit Naa15, co-translationally acetylates the α-amino group of newly synthetized proteins as they emerge from the ribosome. Roughly 40-50% of the human proteome is acetylated by Naa10, rendering this an enzyme one of the most broad substrate ranges known. Recently, we reported an X-linked disorder of infancy, Ogden syndrome, in two families harbouring a c.109 T > C (p.Ser37Pro) variant in NAA10. In the present study we performed in-depth characterization of a yeast model of Ogden syndrome. Stress tests and proteomic analyses suggest that the S37P mutation disrupts Naa10 function and reduces cellular fitness during heat shock, possibly owing to dysregulation of chaperone expression and accumulation. Microarray and RNA-seq revealed a pseudo-diploid gene expression profile in ΔNaa10 cells, probably responsible for a mating defect. In conclusion, the data presented here further support the disruptive nature of the S37P/Ogden mutation and identify affected cellular processes potentially contributing to the severe phenotype seen in Ogden syndrome. Data are available via GEO under identifier GSE86482 or with ProteomeXchange under identifier PXD004923. © 2016 The Authors. Yeast published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Max J. Dörfel
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - Han Fang
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - Jonathan Crain
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - Michael Klingener
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - Jake Weiser
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - Gholson J. Lyon
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
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85
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Ribeiro AL, Silva RD, Foyn H, Tiago MN, Rathore OS, Arnesen T, Martinho RG. Naa50/San-dependent N-terminal acetylation of Scc1 is potentially important for sister chromatid cohesion. Sci Rep 2016; 6:39118. [PMID: 27996020 PMCID: PMC5171793 DOI: 10.1038/srep39118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/17/2016] [Indexed: 12/17/2022] Open
Abstract
The gene separation anxiety (san) encodes Naa50/San, a N-terminal acetyltransferase required for chromosome segregation during mitosis. Although highly conserved among higher eukaryotes, the mitotic function of this enzyme is still poorly understood. Naa50/San was originally proposed to be required for centromeric sister chromatid cohesion in Drosophila and human cells, yet, more recently, it was also suggested to be a negative regulator of microtubule polymerization through internal acetylation of beta Tubulin. We used genetic and biochemical approaches to clarify the function of Naa50/San during development. Our work suggests that Naa50/San is required during tissue proliferation for the correct interaction between the cohesin subunits Scc1 and Smc3. Our results also suggest a working model where Naa50/San N-terminally acetylates the nascent Scc1 polypeptide, and that this co-translational modification is subsequently required for the establishment and/or maintenance of sister chromatid cohesion.
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Affiliation(s)
- Ana Luisa Ribeiro
- Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.,Center for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
| | - Rui D Silva
- Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.,Center for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
| | - Håvard Foyn
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Margarida N Tiago
- Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.,Center for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
| | - Om Singh Rathore
- Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.,Center for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway.,Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Rui Gonçalo Martinho
- Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.,Center for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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86
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Gao J, Barroso C, Zhang P, Kim HM, Li S, Labrador L, Lightfoot J, Gerashchenko MV, Labunskyy VM, Dong MQ, Martinez-Perez E, Colaiácovo MP. N-terminal acetylation promotes synaptonemal complex assembly in C. elegans. Genes Dev 2016; 30:2404-2416. [PMID: 27881602 PMCID: PMC5131780 DOI: 10.1101/gad.277350.116] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 10/20/2016] [Indexed: 12/16/2022]
Abstract
N-terminal acetylation of the first two amino acids on proteins is a prevalent cotranslational modification. Despite its abundance, the biological processes associated with this modification are not well understood. Here, we mapped the pattern of protein N-terminal acetylation in Caenorhabditis elegans, uncovering a conserved set of rules for this protein modification and identifying substrates for the N-terminal acetyltransferase B (NatB) complex. We observed an enrichment for global protein N-terminal acetylation and also specifically for NatB substrates in the nucleus, supporting the importance of this modification for regulating biological functions within this cellular compartment. Peptide profiling analysis provides evidence of cross-talk between N-terminal acetylation and internal modifications in a NAT substrate-specific manner. In vivo studies indicate that N-terminal acetylation is critical for meiosis, as it regulates the assembly of the synaptonemal complex (SC), a proteinaceous structure ubiquitously present during meiosis from yeast to humans. Specifically, N-terminal acetylation of NatB substrate SYP-1, an SC structural component, is critical for SC assembly. These findings provide novel insights into the biological functions of N-terminal acetylation and its essential role during meiosis.
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Affiliation(s)
- Jinmin Gao
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Consuelo Barroso
- Medical Research Council Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom
| | - Pan Zhang
- College of Life Science, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Hyun-Min Kim
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Shangtong Li
- College of Life Science, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Leticia Labrador
- Medical Research Council Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom
| | - James Lightfoot
- Medical Research Council Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom
| | - Maxim V. Gerashchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Vyacheslav M. Labunskyy
- Department of Dermatology, Boston University School of Medicine, Boston, Massachusetts 02218, USA
| | - Meng-Qiu Dong
- College of Life Science, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Enrique Martinez-Perez
- Medical Research Council Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom
| | - Monica P. Colaiácovo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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87
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Müller SA, Scilabra SD, Lichtenthaler SF. Proteomic Substrate Identification for Membrane Proteases in the Brain. Front Mol Neurosci 2016; 9:96. [PMID: 27790089 PMCID: PMC5062031 DOI: 10.3389/fnmol.2016.00096] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 09/21/2016] [Indexed: 12/26/2022] Open
Abstract
Cell-cell communication in the brain is controlled by multiple mechanisms, including proteolysis. Membrane-bound proteases generate signaling molecules from membrane-bound precursor proteins and control the length and function of cell surface membrane proteins. These proteases belong to different families, including members of the “a disintegrin and metalloprotease” (ADAM), the beta-site amyloid precursor protein cleaving enzymes (BACE), membrane-type matrix metalloproteases (MT-MMP) and rhomboids. Some of these proteases, in particular ADAM10 and BACE1 have been shown to be essential not only for the correct development of the mammalian brain, but also for myelination and maintaining neuronal connections in the adult nervous system. Additionally, these proteases are considered as drug targets for brain diseases, including Alzheimer’s disease (AD), schizophrenia and cancer. Despite their biomedical relevance, the molecular functions of these proteases in the brain have not been explored in much detail, as little was known about their substrates. This has changed with the recent development of novel proteomic methods which allow to identify substrates of membrane-bound proteases from cultured cells, primary neurons and other primary brain cells and even in vivo from minute amounts of mouse cerebrospinal fluid (CSF). This review summarizes the recent advances and highlights the strengths of the individual proteomic methods. Finally, using the example of the Alzheimer-related proteases BACE1, ADAM10 and γ-secretase, as well as ADAM17 and signal peptide peptidase like 3 (SPPL3), we illustrate how substrate identification with novel methods is instrumental in elucidating broad physiological functions of these proteases in the brain and other organs.
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Affiliation(s)
- Stephan A Müller
- German Center for Neurodegenerative Diseases (DZNE)Munich, Germany; Neuroproteomics, Klinikum rechts der Isar, Technische Universität MünchenMunich, Germany
| | - Simone D Scilabra
- German Center for Neurodegenerative Diseases (DZNE)Munich, Germany; Neuroproteomics, Klinikum rechts der Isar, Technische Universität MünchenMunich, Germany
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE)Munich, Germany; Neuroproteomics, Klinikum rechts der Isar, Technische Universität MünchenMunich, Germany; Institute for Advanced Study, Technische Universität MunichGarching, Germany; Munich Cluster for Systems Neurology (SyNergy)Munich, Germany
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88
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Harper JW, Bennett EJ. Proteome complexity and the forces that drive proteome imbalance. Nature 2016; 537:328-38. [PMID: 27629639 DOI: 10.1038/nature19947] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 07/29/2016] [Indexed: 12/28/2022]
Abstract
The cellular proteome is a complex microcosm of structural and regulatory networks that requires continuous surveillance and modification to meet the dynamic needs of the cell. It is therefore crucial that the protein flux of the cell remains in balance to ensure proper cell function. Genetic alterations that range from chromosome imbalance to oncogene activation can affect the speed, fidelity and capacity of protein biogenesis and degradation systems, which often results in proteome imbalance. An improved understanding of the causes and consequences of proteome imbalance is helping to reveal how these systems can be targeted to treat diseases such as cancer.
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Affiliation(s)
- J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Eric J Bennett
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, USA
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89
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Van Damme P, Kalvik TV, Starheim KK, Jonckheere V, Myklebust LM, Menschaert G, Varhaug JE, Gevaert K, Arnesen T. A Role for Human N-alpha Acetyltransferase 30 (Naa30) in Maintaining Mitochondrial Integrity. Mol Cell Proteomics 2016; 15:3361-3372. [PMID: 27694331 DOI: 10.1074/mcp.m116.061010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Indexed: 12/26/2022] Open
Abstract
N-terminal acetylation (Nt-acetylation) by N-terminal acetyltransferases (NATs) is one of the most common protein modifications in eukaryotes. The NatC complex represents one of three major NATs of which the substrate profile remains largely unexplored. Here, we defined the in vivo human NatC Nt-acetylome on a proteome-wide scale by combining knockdown of its catalytic subunit Naa30 with positional proteomics. We identified 46 human NatC substrates, expanding our current knowledge on the substrate repertoire of NatC which now includes proteins harboring Met-Leu, Met-Ile, Met-Phe, Met-Trp, Met-Val, Met-Met, Met-His and Met-Lys N termini. Upon Naa30 depletion the expression levels of several organellar proteins were found reduced, in particular mitochondrial proteins, some of which were found to be NatC substrates. Interestingly, knockdown of Naa30 induced the loss of mitochondrial membrane potential and fragmentation of mitochondria. In conclusion, NatC Nt-acetylates a large variety of proteins and is essential for mitochondrial integrity and function.
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Affiliation(s)
- Petra Van Damme
- From the ‡Medical Biotechnology Center, VIB, B-9000 Ghent, Belgium; .,§Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Thomas V Kalvik
- ¶Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Kristian K Starheim
- ¶Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway.,‖Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway.,**Center of Molecular Inflammation Research, Department of Molecular Medicine and Cancer Research, Norwegian University of Technology and Natural Sciences, N-7006 Trondheim, Norway
| | - Veronique Jonckheere
- From the ‡Medical Biotechnology Center, VIB, B-9000 Ghent, Belgium.,§Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Line M Myklebust
- ¶Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Gerben Menschaert
- ‡‡Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, B-9000 Ghent, Belgium
| | - Jan Erik Varhaug
- ‖Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway.,§§Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Kris Gevaert
- From the ‡Medical Biotechnology Center, VIB, B-9000 Ghent, Belgium.,§Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Thomas Arnesen
- ¶Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway.,§§Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
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90
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Physiological functions and clinical implications of the N-end rule pathway. Front Med 2016; 10:258-70. [PMID: 27492620 DOI: 10.1007/s11684-016-0458-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/06/2016] [Indexed: 01/19/2023]
Abstract
The N-end rule pathway is a unique branch of the ubiquitin-proteasome system in which the determination of a protein's half-life is dependent on its N-terminal residue. The N-terminal residue serves as the degradation signal of a protein and thus called N-degron. N-degron can be recognized and modifed by several steps of post-translational modifications, such as oxidation, deamination, arginylation or acetylation, it then polyubiquitinated by the N-recognin for degradation. The molecular basis of the N-end rule pathway has been elucidated and its physiological functions have been revealed in the past 30 years. This pathway is involved in several biological aspects, including transcription, differentiation, chromosomal segregation, genome stability, apoptosis, mitochondrial quality control, cardiovascular development, neurogenesis, carcinogenesis, and spermatogenesis. Disturbance of this pathway often causes the failure of these processes, resulting in some human diseases. This review summarized the physiological functions of the N-end rule pathway, introduced the related biological processes and diseases, with an emphasis on the inner link between this pathway and certain symptoms.
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91
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Microscopy-based Saccharomyces cerevisiae complementation model reveals functional conservation and redundancy of N-terminal acetyltransferases. Sci Rep 2016; 6:31627. [PMID: 27555049 PMCID: PMC4995432 DOI: 10.1038/srep31627] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/10/2016] [Indexed: 01/05/2023] Open
Abstract
N-terminal acetylation is a highly abundant protein modification catalyzed by N-terminal acetyltransferases (NATs) NatA-NatG. The Saccharomyces cerevisiae protein Arl3 depends on interaction with Sys1 for its localization to the Golgi and this targeting strictly requires NatC-mediated N-terminal acetylation of Arl3. We utilized the Arl3 acetylation-dependent localization phenotype as a model system for assessing the functional conservation and in vivo redundancy of several human NATs. The catalytic subunit of human NatC, hNaa30 (Mak3), restored Arl3 localization in the absence of yNaa30, but only in the presence of either yeast or human Naa35 subunit (Mak10). In contrast, hNaa35 was not able to replace its yeast orthologue without the co-expression of hNaa30, suggesting co-evolution of the two NatC subunits. The most recently discovered and organellar human NAT, NatF/Naa60, restored the Golgi localization of Arl3 in the absence of yNaa30. Interestingly, this was also true for hNaa60 lacking its membrane-binding domain whereas hNaa50 did not complement NatC function. This in vivo redundancy reflects NatC and NatF´s overlapping in vitro substrate specificities. The yeast model presented here provides a robust and rapid readout of NatC and NatF activity in vivo, and revealed evolutionary conservation of the NatC complex and redundancy between NatC and NatF.
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92
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Structure and function of human Naa60 (NatF), a Golgi-localized bi-functional acetyltransferase. Sci Rep 2016; 6:31425. [PMID: 27550639 PMCID: PMC4993997 DOI: 10.1038/srep31425] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 07/20/2016] [Indexed: 11/08/2022] Open
Abstract
N-terminal acetylation (Nt-acetylation), carried out by N-terminal acetyltransferases (NATs), is a conserved and primary modification of nascent peptide chains. Naa60 (also named NatF) is a recently identified NAT found only in multicellular eukaryotes. This protein was shown to locate on the Golgi apparatus and mainly catalyze the Nt-acetylation of transmembrane proteins, and it also harbors lysine Nε-acetyltransferase (KAT) activity to catalyze the acetylation of lysine ε-amine. Here, we report the crystal structures of human Naa60 (hNaa60) in complex with Acetyl-Coenzyme A (Ac-CoA) or Coenzyme A (CoA). The hNaa60 protein contains an amphipathic helix following its GNAT domain that may contribute to Golgi localization of hNaa60, and the β7-β8 hairpin adopted different conformations in the hNaa60(1-242) and hNaa60(1-199) crystal structures. Remarkably, we found that the side-chain of Phe 34 can influence the position of the coenzyme, indicating a new regulatory mechanism involving enzyme, co-factor and substrates interactions. Moreover, structural comparison and biochemical studies indicated that Tyr 97 and His 138 are key residues for catalytic reaction and that a non-conserved β3-β4 long loop participates in the regulation of hNaa60 activity.
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93
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Aksnes H, Drazic A, Marie M, Arnesen T. First Things First: Vital Protein Marks by N-Terminal Acetyltransferases. Trends Biochem Sci 2016; 41:746-760. [PMID: 27498224 DOI: 10.1016/j.tibs.2016.07.005] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/01/2016] [Accepted: 07/08/2016] [Indexed: 11/28/2022]
Abstract
N-terminal (Nt) acetylation is known to be a highly abundant co-translational protein modification, but the recent discovery of Golgi- and chloroplast-resident N-terminal acetyltransferases (NATs) revealed that it can also be added post-translationally. Nt-acetylation may act as a degradation signal in a novel branch of the N-end rule pathway, whose functions include the regulation of human blood pressure. Nt-acetylation also modulates protein interactions, targeting, and folding. In plants, Nt-acetylation plays a role in the control of resistance to drought and in regulation of immune responses. Mutations of specific human NATs that decrease their activity can cause either the lethal Ogden syndrome or severe intellectual disability and cardiovascular defects. In sum, recent advances highlight Nt-acetylation as a key factor in many biological pathways.
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Affiliation(s)
- Henriette Aksnes
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | - Adrian Drazic
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | - Michaël Marie
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, 5021 Bergen, Norway.
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94
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Reddi R, Saddanapu V, Chinthapalli DK, Sankoju P, Sripadi P, Addlagatta A. Human Naa50 Protein Displays Broad Substrate Specificity for Amino-terminal Acetylation: DETAILED STRUCTURAL AND BIOCHEMICAL ANALYSIS USING TETRAPEPTIDE LIBRARY. J Biol Chem 2016; 291:20530-8. [PMID: 27484799 DOI: 10.1074/jbc.m116.730432] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Indexed: 11/06/2022] Open
Abstract
Amino-terminal acetylation is a critical co-translational modification of the newly synthesized proteins in a eukaryotic cell carried out by six amino-terminal acetyltransferases (NATs). All NATs contain at least one catalytic subunit, and some contain one or two additional auxiliary subunits. For example, NatE is a complex of Naa10, Naa50, and Naa15 (auxiliary). In the present study, the crystal structure of human Naa50 suggested the presence of CoA and acetylated tetrapeptide (AcMMXX) that have co-purified with the protein. Biochemical and thermal stability studies on the tetrapeptide library with variations in the first and second positions confirm our results from the crystal structure that a peptide with Met-Met in the first two positions is the best substrate for this enzyme. In addition, Naa50 acetylated all MXAA peptides except for MPAA. Transcriptome analysis of 10 genes that make up six NATs in humans from eight different cell lines suggests that components of NatE are transcribed in all cell lines, whereas others are variable. Because Naa10 is reported to acetylate all amino termini that are devoid of methionine and Naa50 acetylates all other peptides that are followed by methionine, we believe that NatE complex can be a major contributor for amino-terminal acetylation at the ribosome exit tunnel.
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Affiliation(s)
| | | | - Dinesh Kumar Chinthapalli
- National Centre for Mass Spectrometry, Council of Scientific and Industrial Research-Indian Institute of Chemical Technology, Hyderabad, Telangana 500 607, India
| | | | - Prabhakar Sripadi
- National Centre for Mass Spectrometry, Council of Scientific and Industrial Research-Indian Institute of Chemical Technology, Hyderabad, Telangana 500 607, India
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95
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Støve SI, Magin RS, Foyn H, Haug BE, Marmorstein R, Arnesen T. Crystal Structure of the Golgi-Associated Human Nα-Acetyltransferase 60 Reveals the Molecular Determinants for Substrate-Specific Acetylation. Structure 2016; 24:1044-56. [PMID: 27320834 DOI: 10.1016/j.str.2016.04.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/22/2016] [Accepted: 04/26/2016] [Indexed: 01/17/2023]
Abstract
N-Terminal acetylation is a common and important protein modification catalyzed by N-terminal acetyltransferases (NATs). Six human NATs (NatA-NatF) contain one catalytic subunit each, Naa10 to Naa60, respectively. In contrast to the ribosome-associated NatA to NatE, NatF/Naa60 specifically associates with Golgi membranes and acetylates transmembrane proteins. To gain insight into the molecular basis for the function of Naa60, we developed an Naa60 bisubstrate CoA-peptide conjugate inhibitor, determined its X-ray structure when bound to CoA and inhibitor, and carried out biochemical experiments. We show that Naa60 adapts an overall fold similar to that of the catalytic subunits of ribosome-associated NATs, but with the addition of two novel elongated loops that play important roles in substrate-specific binding. One of these loops mediates a dimer to monomer transition upon substrate-specific binding. Naa60 employs a catalytic mechanism most similar to Naa50. Collectively, these data reveal the molecular basis for Naa60-specific acetyltransferase activity with implications for its Golgi-specific functions.
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Affiliation(s)
- Svein Isungset Støve
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, 5021 Bergen, Norway
| | - Robert S Magin
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Program in Gene Expression and Regulation, Wistar Institute, Philadelphia, PA 19104, USA
| | - Håvard Foyn
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | - Bengt Erik Haug
- Department of Chemistry, University of Bergen, 5020 Bergen, Norway
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Program in Gene Expression and Regulation, Wistar Institute, Philadelphia, PA 19104, USA.
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, 5021 Bergen, Norway.
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96
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Drazic A, Myklebust LM, Ree R, Arnesen T. The world of protein acetylation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1372-401. [PMID: 27296530 DOI: 10.1016/j.bbapap.2016.06.007] [Citation(s) in RCA: 518] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/04/2016] [Accepted: 06/08/2016] [Indexed: 12/30/2022]
Abstract
Acetylation is one of the major post-translational protein modifications in the cell, with manifold effects on the protein level as well as on the metabolome level. The acetyl group, donated by the metabolite acetyl-coenzyme A, can be co- or post-translationally attached to either the α-amino group of the N-terminus of proteins or to the ε-amino group of lysine residues. These reactions are catalyzed by various N-terminal and lysine acetyltransferases. In case of lysine acetylation, the reaction is enzymatically reversible via tightly regulated and metabolism-dependent mechanisms. The interplay between acetylation and deacetylation is crucial for many important cellular processes. In recent years, our understanding of protein acetylation has increased significantly by global proteomics analyses and in depth functional studies. This review gives a general overview of protein acetylation and the respective acetyltransferases, and focuses on the regulation of metabolic processes and physiological consequences that come along with protein acetylation.
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Affiliation(s)
- Adrian Drazic
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Line M Myklebust
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Rasmus Ree
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway.
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97
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Affiliation(s)
- Henriette Aksnes
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - Michaël Marie
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, Bergen, Norway.,Department of Surgery, Haukeland University Hospital, Bergen, Norway
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98
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Lee KE, Heo JE, Kim JM, Hwang CS. N-Terminal Acetylation-Targeted N-End Rule Proteolytic System: The Ac/N-End Rule Pathway. Mol Cells 2016; 39:169-78. [PMID: 26883906 PMCID: PMC4794598 DOI: 10.14348/molcells.2016.2329] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/11/2016] [Accepted: 01/14/2016] [Indexed: 12/12/2022] Open
Abstract
Although Nα-terminal acetylation (Nt-acetylation) is a pervasive protein modification in eukaryotes, its general functions in a majority of proteins are poorly understood. In 2010, it was discovered that Nt-acetylation creates a specific protein degradation signal that is targeted by a new class of the N-end rule proteolytic system, called the Ac/N-end rule pathway. Here, we review recent advances in our understanding of the mechanism and biological functions of the Ac/N-end rule pathway, and its crosstalk with the Arg/N-end rule pathway (the classical N-end rule pathway).
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Affiliation(s)
- Kang-Eun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790–784,
Korea
| | - Ji-Eun Heo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790–784,
Korea
| | - Jeong-Mok Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790–784,
Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790–784,
Korea
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99
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Gawron D, Ndah E, Gevaert K, Van Damme P. Positional proteomics reveals differences in N-terminal proteoform stability. Mol Syst Biol 2016; 12:858. [PMID: 26893308 PMCID: PMC4770386 DOI: 10.15252/msb.20156662] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
To understand the impact of alternative translation initiation on a proteome, we performed a proteome‐wide study on protein turnover using positional proteomics and ribosome profiling to distinguish between N‐terminal proteoforms of individual genes. By combining pulsed SILAC with N‐terminal COFRADIC, we monitored the stability of 1,941 human N‐terminal proteoforms, including 147 N‐terminal proteoform pairs that originate from alternative translation initiation, alternative splicing or incomplete processing of the initiator methionine. N‐terminally truncated proteoforms were less abundant than canonical proteoforms and often displayed altered stabilities, likely attributed to individual protein characteristics, including intrinsic disorder, but independent of N‐terminal amino acid identity or truncation length. We discovered that the removal of initiator methionine by methionine aminopeptidases reduced the stability of processed proteoforms, while susceptibility for N‐terminal acetylation did not seem to influence protein turnover rates. Taken together, our findings reveal differences in protein stability between N‐terminal proteoforms and point to a role for alternative translation initiation and co‐translational initiator methionine removal, next to alternative splicing, in the overall regulation of proteome homeostasis.
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Affiliation(s)
- Daria Gawron
- Department of Medical Protein Research, VIB, Ghent, Belgium Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Elvis Ndah
- Department of Medical Protein Research, VIB, Ghent, Belgium Department of Biochemistry, Ghent University, Ghent, Belgium Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Petra Van Damme
- Department of Medical Protein Research, VIB, Ghent, Belgium Department of Biochemistry, Ghent University, Ghent, Belgium
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100
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Rathore OS, Faustino A, Prudêncio P, Van Damme P, Cox CJ, Martinho RG. Absence of N-terminal acetyltransferase diversification during evolution of eukaryotic organisms. Sci Rep 2016; 6:21304. [PMID: 26861501 PMCID: PMC4748286 DOI: 10.1038/srep21304] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/18/2016] [Indexed: 11/09/2022] Open
Abstract
Protein N-terminal acetylation is an ancient and ubiquitous co-translational modification catalyzed by a highly conserved family of N-terminal acetyltransferases (NATs). Prokaryotes have at least 3 NATs, whereas humans have six distinct but highly conserved NATs, suggesting an increase in regulatory complexity of this modification during eukaryotic evolution. Despite this, and against our initial expectations, we determined that NAT diversification did not occur in the eukaryotes, as all six major human NATs were most likely present in the Last Eukaryotic Common Ancestor (LECA). Furthermore, we also observed that some NATs were actually secondarily lost during evolution of major eukaryotic lineages; therefore, the increased complexity of the higher eukaryotic proteome occurred without a concomitant diversification of NAT complexes.
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Affiliation(s)
- Om Singh Rathore
- Department of Biomedical Sciences and Medicine, Faro, Portugal.,Center for Biomedical Research (CBMR), Faro, Portugal.,ProRegeM-PhD Program in Mechanisms of Disease and Regenerative Medicine, Faro, Portugal
| | - Alexandra Faustino
- Department of Biomedical Sciences and Medicine, Faro, Portugal.,Center for Biomedical Research (CBMR), Faro, Portugal
| | - Pedro Prudêncio
- Department of Biomedical Sciences and Medicine, Faro, Portugal.,Center for Biomedical Research (CBMR), Faro, Portugal.,Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2781-901, Portugal
| | - Petra Van Damme
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Cymon J Cox
- Center of Marine Sciences, University of Algarve, Faro, Portugal
| | - Rui Gonçalo Martinho
- Department of Biomedical Sciences and Medicine, Faro, Portugal.,Center for Biomedical Research (CBMR), Faro, Portugal.,Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2781-901, Portugal
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