151
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Scalable production in human cells and biochemical characterization of full-length normal and mutant huntingtin. PLoS One 2015; 10:e0121055. [PMID: 25799558 PMCID: PMC4370734 DOI: 10.1371/journal.pone.0121055] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/29/2015] [Indexed: 11/21/2022] Open
Abstract
Huntingtin (Htt) is a 350 kD intracellular protein, ubiquitously expressed and mainly localized in the cytoplasm. Huntington’s disease (HD) is caused by a CAG triplet amplification in exon 1 of the corresponding gene resulting in a polyglutamine (polyQ) expansion at the N-terminus of Htt. Production of full-length Htt has been difficult in the past and so far a scalable system or process has not been established for recombinant production of Htt in human cells. The ability to produce Htt in milligram quantities would be a prerequisite for many biochemical and biophysical studies aiming in a better understanding of Htt function under physiological conditions and in case of mutation and disease. For scalable production of full-length normal (17Q) and mutant (46Q and 128Q) Htt we have established two different systems, the first based on doxycycline-inducible Htt expression in stable cell lines, the second on “gutless” adenovirus mediated gene transfer. Purified material has then been used for biochemical characterization of full-length Htt. Posttranslational modifications (PTMs) were determined and several new phosphorylation sites were identified. Nearly all PTMs in full-length Htt localized to areas outside of predicted alpha-solenoid protein regions. In all detected N-terminal peptides methionine as the first amino acid was missing and the second, alanine, was found to be acetylated. Differences in secondary structure between normal and mutant Htt, a helix-rich protein, were not observed in our study. Purified Htt tends to form dimers and higher order oligomers, thus resembling the situation observed with N-terminal fragments, although the mechanism of oligomer formation may be different.
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152
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Messana I, Cabras T, Iavarone F, Manconi B, Huang L, Martelli C, Olianas A, Sanna MT, Pisano E, Sanna M, Arba M, D'Alessandro A, Desiderio C, Vitali A, Pirolli D, Tirone C, Lio A, Vento G, Romagnoli C, Cordaro M, Manni A, Gallenzi P, Fiorita A, Scarano E, Calò L, Passali GC, Picciotti PM, Paludetti G, Fanos V, Faa G, Castagnola M. Chrono-proteomics of human saliva: variations of the salivary proteome during human development. J Proteome Res 2015; 14:1666-77. [PMID: 25761918 DOI: 10.1021/pr501270x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An important contribution to the variability of any proteome is given by the time dimension that should be carefully considered to define physiological modifications. To this purpose, whole saliva proteome was investigated in a wide age range. Whole saliva was collected from 17 preterm newborns with a postconceptional age at birth of 178-217 days. In these subjects sample collection was performed serially starting immediately after birth and within about 1 year follow-up, gathering a total of 111 specimens. Furthermore, whole saliva was collected from 182 subjects aged between 0 and 17 years and from 23 adults aged between 27 and 57 years. The naturally occurring intact salivary proteome of the 316 samples was analyzed by low- and high-resolution HPLC-ESI-MS platforms. Proteins peculiar of the adults appeared in saliva with different time courses during human development. Acidic proline-rich proteins encoded by PRH2 locus and glycosylated basic proline-rich proteins encoded by PRB3 locus appeared following 180 days of postconceptional age, followed at 7 months (±2 weeks) by histatin 1, statherin, and P-B peptide. The other histatins and acidic proline-rich proteins encoded by PRH1 locus appeared in whole saliva of babies from 1 to 3 weeks after the normal term of delivery, S-type cystatins appeared at 1 year (±3 months), and basic proline-rich proteins appeared at 4 years (±1 year) of age. All of the proteinases involved in the maturation of salivary proteins were more active in preterm than in at-term newborns, on the basis of the truncated forms detected. The activity of the Fam20C kinase, involved in the phosphorylation of various proteins, started around 180 days of postconceptional age, slowly increased reaching values comparable to adults at about 2 years (±6 months) of age. Instead, MAPK14 involved in the phosphorylation of S100A9 was fully active since birth also in preterm newborns.
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Affiliation(s)
- Irene Messana
- †Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Tiziana Cabras
- †Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Federica Iavarone
- ‡Istituto di Biochimica e Biochimica Clinica, Università Cattolica, Largo Francesco Vito 1, Roma 00168, Italy
| | - Barbara Manconi
- †Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Liling Huang
- ‡Istituto di Biochimica e Biochimica Clinica, Università Cattolica, Largo Francesco Vito 1, Roma 00168, Italy
| | - Claudia Martelli
- ‡Istituto di Biochimica e Biochimica Clinica, Università Cattolica, Largo Francesco Vito 1, Roma 00168, Italy
| | - Alessandra Olianas
- †Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Maria Teresa Sanna
- †Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Elisabetta Pisano
- §Dipartimento di Scienze Chirurgiche, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Monica Sanna
- †Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Morena Arba
- †Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Alfredo D'Alessandro
- †Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Claudia Desiderio
- ∥Istituto di Chimica del Riconoscimento Molecolare, CNR, Largo Francesco Vito 1, Roma 00168, Italy
| | - Alberto Vitali
- ∥Istituto di Chimica del Riconoscimento Molecolare, CNR, Largo Francesco Vito 1, Roma 00168, Italy
| | - Davide Pirolli
- ‡Istituto di Biochimica e Biochimica Clinica, Università Cattolica, Largo Francesco Vito 1, Roma 00168, Italy
| | - Chiara Tirone
- ⊥Istituto di Clinica Pediatrica, Università Cattolica, Roma 00168, Italy
| | - Alessandra Lio
- ⊥Istituto di Clinica Pediatrica, Università Cattolica, Roma 00168, Italy
| | - Giovanni Vento
- ⊥Istituto di Clinica Pediatrica, Università Cattolica, Roma 00168, Italy
| | | | - Massimo Cordaro
- #Istituto di Clinica Odontostomatologica, Università Cattolica, Roma 00168, Italy
| | - Armando Manni
- #Istituto di Clinica Odontostomatologica, Università Cattolica, Roma 00168, Italy
| | - Patrizia Gallenzi
- #Istituto di Clinica Odontostomatologica, Università Cattolica, Roma 00168, Italy
| | - Antonella Fiorita
- ▽Istituto di Clinica Otorinolaringoiatrica, Università Cattolica, Roma 00168, Italy
| | - Emanuele Scarano
- ▽Istituto di Clinica Otorinolaringoiatrica, Università Cattolica, Roma 00168, Italy
| | - Lea Calò
- ▽Istituto di Clinica Otorinolaringoiatrica, Università Cattolica, Roma 00168, Italy
| | | | | | - Gaetano Paludetti
- ▽Istituto di Clinica Otorinolaringoiatrica, Università Cattolica, Roma 00168, Italy
| | - Vassilios Fanos
- §Dipartimento di Scienze Chirurgiche, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Gavino Faa
- §Dipartimento di Scienze Chirurgiche, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy
| | - Massimo Castagnola
- ‡Istituto di Biochimica e Biochimica Clinica, Università Cattolica, Largo Francesco Vito 1, Roma 00168, Italy.,∥Istituto di Chimica del Riconoscimento Molecolare, CNR, Largo Francesco Vito 1, Roma 00168, Italy
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153
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Richardson SL, Hanjra P, Zhang G, Mackie BD, Peterson DL, Huang R. A direct, ratiometric, and quantitative MALDI-MS assay for protein methyltransferases and acetyltransferases. Anal Biochem 2015; 478:59-64. [PMID: 25778392 DOI: 10.1016/j.ab.2015.03.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/18/2015] [Accepted: 03/04/2015] [Indexed: 01/22/2023]
Abstract
Protein methylation and acetylation play important roles in biological processes, and misregulation of these modifications is involved in various diseases. Therefore, it is critical to understand the activities of the enzymes responsible for these modifications. Herein we describe a sensitive method for ratiometric quantification of methylated and acetylated peptides via MALDI-MS by direct spotting of enzymatic methylation and acetylation reaction mixtures without tedious purification procedures. The quantifiable detection limit for peptides with our method is approximately 10 fmol. This is achieved by increasing the signal-to-noise ratio through the addition of NH4H2PO4 to the matrix solution and reduction of the matrix α-cyanohydroxycinnamic acid concentration to 2 mg/ml. We have demonstrated the application of this method in enzyme kinetic analysis and inhibition studies. The unique feature of this method is the simultaneous quantification of multiple peptide species for investigation of processivity mechanisms. Its wide buffer compatibility makes it possible to be adapted to investigate the activity of any protein methyltransferase or acetyltransferase.
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Affiliation(s)
- Stacie L Richardson
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Pahul Hanjra
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Gang Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Brianna D Mackie
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Darrell L Peterson
- Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA; Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Rong Huang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, USA.
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154
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Park SE, Kim JM, Seok OH, Cho H, Wadas B, Kim SY, Varshavsky A, Hwang CS. Control of mammalian G protein signaling by N-terminal acetylation and the N-end rule pathway. Science 2015; 347:1249-1252. [PMID: 25766235 PMCID: PMC4748709 DOI: 10.1126/science.aaa3844] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Rgs2, a regulator of G proteins, lowers blood pressure by decreasing signaling through Gαq. Human patients expressing Met-Leu-Rgs2 (ML-Rgs2) or Met-Arg-Rgs2 (MR-Rgs2) are hypertensive relative to people expressing wild-type Met-Gln-Rgs2 (MQ-Rgs2). We found that wild-type MQ-Rgs2 and its mutant, MR-Rgs2, were destroyed by the Ac/N-end rule pathway, which recognizes N(α)-terminally acetylated (Nt-acetylated) proteins. The shortest-lived mutant, ML-Rgs2, was targeted by both the Ac/N-end rule and Arg/N-end rule pathways. The latter pathway recognizes unacetylated N-terminal residues. Thus, the Nt-acetylated Ac-MX-Rgs2 (X = Arg, Gln, Leu) proteins are specific substrates of the mammalian Ac/N-end rule pathway. Furthermore, the Ac/N-degron of Ac-MQ-Rgs2 was conditional, and Teb4, an endoplasmic reticulum (ER) membrane-embedded ubiquitin ligase, was able to regulate G protein signaling by targeting Ac-MX-Rgs2 proteins for degradation through their N(α)-terminal acetyl group.
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Affiliation(s)
- Sang-Eun Park
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Jeong-Mok Kim
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Ok-Hee Seok
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Hanna Cho
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Brandon Wadas
- Division of Biology and Biological Engineering, California Institute
of Technology, Pasadena, CA 91125, USA
| | - Seon-Young Kim
- Medical Genomics Research Center, KRIBB, Daejeon, South Korea
- Department of Functional Genomics, University of Science and
Technology, Daejeon, South Korea
| | - Alexander Varshavsky
- Division of Biology and Biological Engineering, California Institute
of Technology, Pasadena, CA 91125, USA
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang, Gyeongbuk 790-784, South Korea
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155
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Aksnes H, Van Damme P, Goris M, Starheim KK, Marie M, Støve SI, Hoel C, Kalvik TV, Hole K, Glomnes N, Furnes C, Ljostveit S, Ziegler M, Niere M, Gevaert K, Arnesen T. An organellar nα-acetyltransferase, naa60, acetylates cytosolic N termini of transmembrane proteins and maintains Golgi integrity. Cell Rep 2015; 10:1362-74. [PMID: 25732826 DOI: 10.1016/j.celrep.2015.01.053] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 12/23/2014] [Accepted: 01/20/2015] [Indexed: 01/28/2023] Open
Abstract
N-terminal acetylation is a major and vital protein modification catalyzed by N-terminal acetyltransferases (NATs). NatF, or Nα-acetyltransferase 60 (Naa60), was recently identified as a NAT in multicellular eukaryotes. Here, we find that Naa60 differs from all other known NATs by its Golgi localization. A new membrane topology assay named PROMPT and a selective membrane permeabilization assay established that Naa60 faces the cytosolic side of intracellular membranes. An Nt-acetylome analysis of NAA60-knockdown cells revealed that Naa60, as opposed to other NATs, specifically acetylates transmembrane proteins and has a preference for N termini facing the cytosol. Moreover, NAA60 knockdown causes Golgi fragmentation, indicating an important role in the maintenance of the Golgi's structural integrity. This work identifies a NAT associated with membranous compartments and establishes N-terminal acetylation as a common modification among transmembrane proteins, a thus-far poorly characterized part of the N-terminal acetylome.
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Affiliation(s)
- Henriette Aksnes
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | - Petra Van Damme
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Marianne Goris
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | | | - Michaël Marie
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | | | - Camilla Hoel
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | | | - Kristine Hole
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway; Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Nina Glomnes
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway; Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Clemens Furnes
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | - Sonja Ljostveit
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | - Mathias Ziegler
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | - Marc Niere
- Department of Molecular Biology, University of Bergen, 5020 Bergen, Norway
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - 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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156
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Magin RS, Liszczak GP, Marmorstein R. The molecular basis for histone H4- and H2A-specific amino-terminal acetylation by NatD. Structure 2015; 23:332-41. [PMID: 25619998 DOI: 10.1016/j.str.2014.10.025] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 10/22/2014] [Accepted: 10/24/2014] [Indexed: 11/18/2022]
Abstract
N-terminal acetylation is among the most common protein modifications in eukaryotes and is mediated by evolutionarily conserved N-terminal acetyltransferases (NATs). NatD is among the most selective NATs; its only known substrates are histones H4 and H2A, containing the N-terminal sequence SGRGK in humans. Here we characterize the molecular basis for substrate-specific acetylation by NatD by reporting its crystal structure bound to cognate substrates and performing related biochemical studies. A novel N-terminal segment wraps around the catalytic core domain to make stabilizing interactions, and the α1-α2 and β6-β7 loops adopt novel conformations to properly orient the histone N termini in the binding site. Ser1 and Arg3 of the histone make extensive contacts to highly conserved NatD residues in the substrate binding pocket, and flanking glycine residues also appear to contribute to substrate-specific binding by NatD, together defining a Ser-Gly-Arg-Gly recognition sequence. These studies have implications for understanding substrate-specific acetylation by NAT enzymes.
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Affiliation(s)
- 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; Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Glen P Liszczak
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - 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; Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA; Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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157
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van Deventer S, Menendez-Benito V, van Leeuwen F, Neefjes J. N-terminal acetylation and replicative age affect proteasome localization and cell fitness during aging. J Cell Sci 2015; 128:109-17. [PMID: 25413350 PMCID: PMC4282048 DOI: 10.1242/jcs.157354] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 11/05/2014] [Indexed: 01/05/2023] Open
Abstract
Specific degradation of proteins is essential for virtually all cellular processes and is carried out predominantly by the proteasome. The proteasome is important for clearance of damaged cellular proteins. Damaged proteins accumulate over time and excess damaged proteins can aggregate and induce the death of old cells. In yeast, the localization of the proteasome changes dramatically during aging, possibly in response to altered proteasome activity requirements. We followed two key parameters of this process: the distribution of proteasomes in nuclear and cytosolic compartments, and the formation of cytoplasmic aggregate-like structures called proteasome storage granules (PSGs). Whereas replicative young cells efficiently relocalized proteasomes from the nucleus to the cytoplasm and formed PSGs, replicative old cells were less efficient in relocalizing the proteasome and had less PSGs. By using a microscopy-based genome-wide screen, we identified genetic factors involved in these processes. Both relocalization of the proteasome and PSG formation were affected by two of the three N-acetylation complexes. These N-acetylation complexes also had different effects on the longevity of cells, indicating that each N-acetylation complex has different roles in proteasome location and aging.
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Affiliation(s)
- Sjoerd van Deventer
- Division of Cell Biology, Netherlands Cancer Institute and Netherlands Proteomics Center, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Victoria Menendez-Benito
- Division of Cell Biology, Netherlands Cancer Institute and Netherlands Proteomics Center, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute and Netherlands Proteomics Center, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Jacques Neefjes
- Division of Cell Biology, Netherlands Cancer Institute and Netherlands Proteomics Center, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
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158
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Kapos P, Xu F, Meinnel T, Giglione C, Li X. N-terminal modifications contribute to flowering time and immune response regulations. PLANT SIGNALING & BEHAVIOR 2015; 10:e1073874. [PMID: 26361095 PMCID: PMC4883885 DOI: 10.1080/15592324.2015.1073874] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 07/13/2015] [Indexed: 05/26/2023]
Abstract
A variety of N-terminal co-translational modifications play crucial roles in many cellular processes across eukaryotic organisms. Recently, N-terminal acetylation has been proposed as a regulatory mechanism for the control of plant immunity. Analysis of an N-terminal acetyltransferase complex A (NatA) mutant, naa15-1, revealed that NatA controls the stability of immune receptor Suppressor of NPR1, Constitutive 1 (SNC1) in an antagonistic fashion with NatB. Here, we further report on an antagonistic regulation of flowering time by NatA and NatB, where naa15-1 plants exhibit late flowering, opposite of the early flowering phenotype previously observed in natB mutants. In addition, we provide evidence for the involvement of another N-terminal modification, N-myristoylation, in controlling pathogen-associated molecular pattern (PAMP) triggered immunity (PTI) through the characterization of N-myristoyltransferase 1 (NMT1) defective mutants, which express a low level of NMT1 protein. The mutant line lacks induced production of reactive oxygen species and MAP kinase phosphorylation in response to treatment with the known immune elicitor flg22. NMT1 deficient plants also exhibit increased susceptibility to Pst hrcC, a non-pathogenic Pseudomonas syringae tomato strain lacking a functional type-III secretion system. The potential for the NatA-NatB antagonistic relationship to exist outside of the regulation of SNC1 as well as the disclosing of NMT1s role in PTI further supports the significant contribution of N-terminal co-translational modifications in the regulation of biological processes in plants, and present interesting areas for further exploration.
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Affiliation(s)
- Paul Kapos
- Michael Smith Laboratories; University of British Columbia; British Columbia, Canada
- Department of Botany; University of British Columbia; British Columbia, Canada
| | - Fang Xu
- Michael Smith Laboratories; University of British Columbia; British Columbia, Canada
- Department of Botany; University of British Columbia; British Columbia, Canada
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC); CEA, CNRS, University Paris-Sud; Gif sur Yvette, France
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC); CEA, CNRS, University Paris-Sud; Gif sur Yvette, France
| | - Xin Li
- Michael Smith Laboratories; University of British Columbia; British Columbia, Canada
- Department of Botany; University of British Columbia; British Columbia, Canada
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159
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Molecular, Cellular, and Physiological Significance of N-Terminal Acetylation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 316:267-305. [DOI: 10.1016/bs.ircmb.2015.01.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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160
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Myklebust LM, Van Damme P, Støve SI, Dörfel MJ, Abboud A, Kalvik TV, Grauffel C, Jonckheere V, Wu Y, Swensen J, Kaasa H, Liszczak G, Marmorstein R, Reuter N, Lyon GJ, Gevaert K, Arnesen T. Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects. Hum Mol Genet 2014; 24:1956-76. [PMID: 25489052 PMCID: PMC4355026 DOI: 10.1093/hmg/ddu611] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The X-linked lethal Ogden syndrome was the first reported human genetic disorder associated with a mutation in an N-terminal acetyltransferase (NAT) gene. The affected males harbor an Ser37Pro (S37P) mutation in the gene encoding Naa10, the catalytic subunit of NatA, the major human NAT involved in the co-translational acetylation of proteins. Structural models and molecular dynamics simulations of the human NatA and its S37P mutant highlight differences in regions involved in catalysis and at the interface between Naa10 and the auxiliary subunit hNaa15. Biochemical data further demonstrate a reduced catalytic capacity and an impaired interaction between hNaa10 S37P and Naa15 as well as Naa50 (NatE), another interactor of the NatA complex. N-Terminal acetylome analyses revealed a decreased acetylation of a subset of NatA and NatE substrates in Ogden syndrome cells, supporting the genetic findings and our hypothesis regarding reduced Nt-acetylation of a subset of NatA/NatE-type substrates as one etiology for Ogden syndrome. Furthermore, Ogden syndrome fibroblasts display abnormal cell migration and proliferation capacity, possibly linked to a perturbed retinoblastoma pathway. N-Terminal acetylation clearly plays a role in Ogden syndrome, thus revealing the in vivo importance of N-terminal acetylation in human physiology and disease.
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Affiliation(s)
- Line M Myklebust
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway
| | - Petra Van Damme
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium, Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium,
| | - Svein I Støve
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway, Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Max J Dörfel
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, NY 11797, USA
| | - Angèle Abboud
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
| | - Thomas V Kalvik
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway
| | - Cedric Grauffel
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
| | - Veronique Jonckheere
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium, Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Yiyang Wu
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, NY 11797, USA, Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Hanna Kaasa
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway
| | - Glen Liszczak
- Program in Gene Expression and Regulation, Wistar Institute, PA 19104, USA, Department of Chemistry, and Department of Biochemistry and Biophysics and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Program in Gene Expression and Regulation, Wistar Institute, PA 19104, USA, Department of Chemistry, and Department of Biochemistry and Biophysics and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathalie Reuter
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway, Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, NY 11797, USA, Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA,
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium, Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, Bergen N-5020, Norway, Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway,
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161
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Johnson EA, Lecomte JTJ. Characterization of the truncated hemoglobin THB1 from protein extracts of Chlamydomonas reinhardtii. F1000Res 2014; 3:294. [PMID: 25653846 PMCID: PMC4304232 DOI: 10.12688/f1000research.5873.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/01/2014] [Indexed: 11/20/2022] Open
Abstract
Truncated hemoglobins (TrHbs) belong to the hemoglobin superfamily, but unlike their distant vertebrate relatives, little is known about their principal physiologic functions. Several TrHbs have been studied in vitro using engineered recombinant peptides. These efforts have resulted in a wealth of knowledge about the chemical properties of TrHbs and have generated interesting functional leads. However, questions persist as to how closely these engineered proteins mimic their counterparts within the native cell. In this report, we examined THB1, one of several TrHbs from the model organism Chlamydomonas reinhardtii. The recombinant THB1 (rTHB1) has favorable solubility and stability properties and is an excellent candidate for in vitro characterization. Linking rTHB1 to the in vivo protein is a critical step in understanding the physiologic function of this protein. Using a simplified three-step purification protocol, 3.5-L batches of algal culture were processed to isolate 50-60 μL fractions enriched in THB1. These fractions of C. reinhardtii proteins were then subjected to physical examination. Using gel mobility, optical absorbance and immunoreactivity, THB1 was identified in these enriched fractions and its presence correlated with that of a heme molecule. Mass spectrometry confirmed this cofactor to be a type b heme and revealed that the native protein contains a co-translational modification consistent with amino-terminal acetylation following initial methionine cleavage.
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Affiliation(s)
- Eric A Johnson
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
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162
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Renuse S, Madugundu AK, Kumar P, Nair BG, Gowda H, Prasad TSK, Pandey A. Proteomic analysis and genome annotation ofPichia pastoris, a recombinant protein expression host. Proteomics 2014; 14:2769-79. [DOI: 10.1002/pmic.201400267] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 10/01/2014] [Accepted: 10/20/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Santosh Renuse
- Institute of Bioinformatics; International Technology Park; Bangalore India
- Amrita School of Biotechnology; Amrita Vishwa Vidyapeetham; Kollam India
| | - Anil K. Madugundu
- Institute of Bioinformatics; International Technology Park; Bangalore India
- Centre of Excellence in Bioinformatics, School of Life Sciences; Pondicherry University; Puducherry India
| | - Praveen Kumar
- Institute of Bioinformatics; International Technology Park; Bangalore India
| | - Bipin G. Nair
- Amrita School of Biotechnology; Amrita Vishwa Vidyapeetham; Kollam India
| | - Harsha Gowda
- Institute of Bioinformatics; International Technology Park; Bangalore India
| | - T. S. Keshava Prasad
- Institute of Bioinformatics; International Technology Park; Bangalore India
- Amrita School of Biotechnology; Amrita Vishwa Vidyapeetham; Kollam India
- Centre of Excellence in Bioinformatics, School of Life Sciences; Pondicherry University; Puducherry India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Oncology and Pathology; Johns Hopkins University School of Medicine; Baltimore MD USA
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163
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Liat1, an arginyltransferase-binding protein whose evolution among primates involved changes in the numbers of its 10-residue repeats. Proc Natl Acad Sci U S A 2014; 111:E4936-45. [PMID: 25369936 DOI: 10.1073/pnas.1419587111] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The arginyltransferase Ate1 is a component of the N-end rule pathway, which recognizes proteins containing N-terminal degradation signals called N-degrons, polyubiquitylates these proteins, and thereby causes their degradation by the proteasome. At least six isoforms of mouse Ate1 are produced through alternative splicing of Ate1 pre-mRNA. We identified a previously uncharacterized mouse protein, termed Liat1 (ligand of Ate1), that interacts with Ate1 but does not appear to be its arginylation substrate. Liat1 has a higher affinity for the isoforms Ate1(1A7A) and Ate1(1B7A). Liat1 stimulated the in vitro N-terminal arginylation of a model substrate by Ate1. All examined vertebrate and some invertebrate genomes encode proteins sequelogous (similar in sequence) to mouse Liat1. Sequelogs of Liat1 share a highly conserved ∼30-residue region that is shown here to be required for the binding of Liat1 to Ate1. We also identified non-Ate1 proteins that interact with Liat1. In contrast to Liat1 genes of nonprimate mammals, Liat1 genes of primates are subtelomeric, a location that tends to confer evolutionary instability on a gene. Remarkably, Liat1 proteins of some primates, from macaques to humans, contain tandem repeats of a 10-residue sequence, whereas Liat1 proteins of other mammals contain a single copy of this motif. Quantities of these repeats are, in general, different in Liat1 of different primates. For example, there are 1, 4, 13, 13, 17, and 17 repeats in the gibbon, gorilla, orangutan, bonobo, neanderthal, and human Liat1, respectively, suggesting that repeat number changes in this previously uncharacterized protein may contribute to evolution of primates.
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164
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Warnhoff K, Murphy JT, Kumar S, Schneider DL, Peterson M, Hsu S, Guthrie J, Robertson JD, Kornfeld K. The DAF-16 FOXO transcription factor regulates natc-1 to modulate stress resistance in Caenorhabditis elegans, linking insulin/IGF-1 signaling to protein N-terminal acetylation. PLoS Genet 2014; 10:e1004703. [PMID: 25330323 PMCID: PMC4199503 DOI: 10.1371/journal.pgen.1004703] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 08/26/2014] [Indexed: 12/24/2022] Open
Abstract
The insulin/IGF-1 signaling pathway plays a critical role in stress resistance and longevity, but the mechanisms are not fully characterized. To identify genes that mediate stress resistance, we screened for C. elegans mutants that can tolerate high levels of dietary zinc. We identified natc-1, which encodes an evolutionarily conserved subunit of the N-terminal acetyltransferase C (NAT) complex. N-terminal acetylation is a widespread modification of eukaryotic proteins; however, relatively little is known about the biological functions of NATs. We demonstrated that loss-of-function mutations in natc-1 cause resistance to a broad-spectrum of physiologic stressors, including multiple metals, heat, and oxidation. The C. elegans FOXO transcription factor DAF-16 is a critical target of the insulin/IGF-1 signaling pathway that mediates stress resistance, and DAF-16 is predicted to directly bind the natc-1 promoter. To characterize the regulation of natc-1 by DAF-16 and the function of natc-1 in insulin/IGF-1 signaling, we analyzed molecular and genetic interactions with key components of the insulin/IGF-1 pathway. natc-1 mRNA levels were repressed by DAF-16 activity, indicating natc-1 is a physiological target of DAF-16. Genetic studies suggested that natc-1 functions downstream of daf-16 to mediate stress resistance and dauer formation. Based on these findings, we hypothesize that natc-1 is directly regulated by the DAF-16 transcription factor, and natc-1 is a physiologically significant effector of the insulin/IGF-1 signaling pathway that mediates stress resistance and dauer formation. These studies identify a novel biological function for natc-1 as a modulator of stress resistance and dauer formation and define a functionally significant downstream effector of the insulin/IGF-1 signaling pathway. Protein N-terminal acetylation mediated by the NatC complex may play an evolutionarily conserved role in regulating stress resistance.
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Affiliation(s)
- Kurt Warnhoff
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - John T. Murphy
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sandeep Kumar
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Daniel L. Schneider
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michelle Peterson
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Simon Hsu
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - James Guthrie
- Research Reactor Center, University of Missouri, Columbia, Missouri, United States of America
| | - J. David Robertson
- Research Reactor Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Chemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Kerry Kornfeld
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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165
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Top-down analytical platforms for the characterization of the human salivary proteome. Bioanalysis 2014; 6:563-81. [PMID: 24568357 DOI: 10.4155/bio.13.349] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Comprehensive analysis and characterization of the human salivary proteome is an important step towards the possible use of saliva for diagnostic and prognostic purposes. The contribution of the different sources to whole saliva, and the evaluation of individual variability and physiological modifications have been investigated by top-down proteomic approaches, disclosing the faceted and complex profile of the human salivary proteome. All this information is essential to develop saliva protein biomarkers. In this Review the major results obtained in the field by top-down platforms, and the improvements required to allow a more complete picture, will be discussed.
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166
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Gibbs DJ, Bacardit J, Bachmair A, Holdsworth MJ. The eukaryotic N-end rule pathway: conserved mechanisms and diverse functions. Trends Cell Biol 2014; 24:603-11. [DOI: 10.1016/j.tcb.2014.05.001] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 04/30/2014] [Accepted: 05/01/2014] [Indexed: 12/30/2022]
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167
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Tooley JG, Schaner Tooley CE. New roles for old modifications: emerging roles of N-terminal post-translational modifications in development and disease. Protein Sci 2014; 23:1641-9. [PMID: 25209108 DOI: 10.1002/pro.2547] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 09/08/2014] [Indexed: 01/07/2023]
Abstract
The importance of internal post-translational modification (PTM) in protein signaling and function has long been known and appreciated. However, the significance of the same PTMs on the alpha amino group of N-terminal amino acids has been comparatively understudied. Historically considered static regulators of protein stability, additional functional roles for N-terminal PTMs are now beginning to be elucidated. New findings show that N-terminal methylation, along with N-terminal acetylation, is an important regulatory modification with significant roles in development and disease progression. There are also emerging studies on the enzymology and functional roles of N-terminal ubiquitylation and N-terminal propionylation. Here, will discuss the recent advances in the functional studies of N-terminal PTMs, recount the new N-terminal PTMs being identified, and briefly examine the possibility of dynamic N-terminal PTM exchange.
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Affiliation(s)
- John G Tooley
- Department of Biochemistry and Molecular Biology, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, Kentucky
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168
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Pan Y, Karagiannis K, Zhang H, Dingerdissen H, Shamsaddini A, Wan Q, Simonyan V, Mazumder R. Human germline and pan-cancer variomes and their distinct functional profiles. Nucleic Acids Res 2014; 42:11570-88. [PMID: 25232094 PMCID: PMC4191387 DOI: 10.1093/nar/gku772] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Identification of non-synonymous single nucleotide variations (nsSNVs) has exponentially increased due to advances in Next-Generation Sequencing technologies. The functional impacts of these variations have been difficult to ascertain because the corresponding knowledge about sequence functional sites is quite fragmented. It is clear that mapping of variations to sequence functional features can help us better understand the pathophysiological role of variations. In this study, we investigated the effect of nsSNVs on more than 17 common types of post-translational modification (PTM) sites, active sites and binding sites. Out of 1 705 285 distinct nsSNVs on 259 216 functional sites we identified 38 549 variations that significantly affect 10 major functional sites. Furthermore, we found distinct patterns of site disruptions due to germline and somatic nsSNVs. Pan-cancer analysis across 12 different cancer types led to the identification of 51 genes with 106 nsSNV affected functional sites found in 3 or more cancer types. 13 of the 51 genes overlap with previously identified Significantly Mutated Genes (Nature. 2013 Oct 17;502(7471)). 62 mutations in these 13 genes affecting functional sites such as DNA, ATP binding and various PTM sites occur across several cancers and can be prioritized for additional validation and investigations.
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Affiliation(s)
- Yang Pan
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Konstantinos Karagiannis
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Haichen Zhang
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Hayley Dingerdissen
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Amirhossein Shamsaddini
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Quan Wan
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA
| | - Vahan Simonyan
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Raja Mazumder
- The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA McCormick Genomic and Proteomic Center, George Washington University, Washington, DC 20037, USA
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169
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Lee KE, Ahn JY, Kim JM, Hwang CS. Synthetic lethal screen of NAA20, a catalytic subunit gene of NatB N-terminal acetylase in Saccharomyces cerevisiae. J Microbiol 2014; 52:842-8. [PMID: 25163837 DOI: 10.1007/s12275-014-3694-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 06/30/2014] [Accepted: 07/24/2014] [Indexed: 01/08/2023]
Abstract
The Saccharomyces cerevisiae NatB N-terminal acetylase contains a catalytic subunit Naa20 and an auxiliary subunit Naa25. To elucidate the cellular functions of the NatB, we utilized the Synthetic Genetic Array to screen for genes that are essential for cell growth in the absence of NAA20. The genome-wide synthetic lethal screen of NAA20 identified genes encoding for serine/threonine protein kinase Vps15, 1,3-beta-glucanosyltransferase Gas5, and a catabolic repression regulator Mig3. The present study suggests that the catalytic activity of the NatB N-terminal aceytase is involved in vacuolar protein sorting and cell wall maintenance.
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Affiliation(s)
- Kang-Eun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Gyeongbuk, 790-784, Republic of Korea
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170
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Beltran-Alvarez P, Tarradas A, Chiva C, Pérez-Serra A, Batlle M, Pérez-Villa F, Schulte U, Sabidó E, Brugada R, Pagans S. Identification of N-terminal protein acetylation and arginine methylation of the voltage-gated sodium channel in end-stage heart failure human heart. J Mol Cell Cardiol 2014; 76:126-9. [PMID: 25172307 DOI: 10.1016/j.yjmcc.2014.08.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 07/25/2014] [Accepted: 08/15/2014] [Indexed: 11/30/2022]
Abstract
The α subunit of the cardiac voltage-gated sodium channel, NaV1.5, provides the rapid sodium inward current that initiates cardiomyocyte action potentials. Here, we analyzed for the first time the post-translational modifications of NaV1.5 purified from end-stage heart failure human cardiac tissue. We identified R526 methylation as the major post-translational modification of any NaV1.5 arginine or lysine residue. Unexpectedly, we found that the N terminus of NaV1.5 was: 1) devoid of the initiation methionine, and 2) acetylated at the resulting initial alanine residue. This is the first evidence for N-terminal acetylation in any member of the voltage-gated ion channel superfamily. Our results open the door to explore NaV1.5 N-terminal acetylation and arginine methylation levels as drivers or markers of end-stage heart failure.
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Affiliation(s)
- Pedro Beltran-Alvarez
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, 17003 Girona, Spain.
| | - Anna Tarradas
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, 17003 Girona, Spain; Department of Medical Sciences, School of Medicine, University of Girona, 17003 Girona, Spain
| | - Cristina Chiva
- Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Alexandra Pérez-Serra
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, 17003 Girona, Spain; Department of Medical Sciences, School of Medicine, University of Girona, 17003 Girona, Spain
| | - Montserrat Batlle
- Thorax Institute, Cardiology Department, Hospital Clínic, University of Barcelona, Institute of Biomedical Research August Pi i Sunyer, 08036 Barcelona, Spain
| | - Félix Pérez-Villa
- Thorax Institute, Cardiology Department, Hospital Clínic, University of Barcelona, Institute of Biomedical Research August Pi i Sunyer, 08036 Barcelona, Spain
| | - Uwe Schulte
- Logopharm GmbH, 79232 March-Buchheim, Germany
| | - Eduard Sabidó
- Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Ramon Brugada
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, 17003 Girona, Spain; Department of Medical Sciences, School of Medicine, University of Girona, 17003 Girona, Spain.
| | - Sara Pagans
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, 17003 Girona, Spain; Department of Medical Sciences, School of Medicine, University of Girona, 17003 Girona, Spain.
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171
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Homeostasis of N-α-terminal acetylation of EsxA correlates with virulence in Mycobacterium marinum. Infect Immun 2014; 82:4572-86. [PMID: 25135684 DOI: 10.1128/iai.02153-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The mycobacterial Esx-1 (ESAT-6 system 1) exporter translocates virulence factors across the cytoplasmic membrane to the cell wall, cell surface, and the bacteriological medium in vitro. The mechanisms underlying substrate targeting to distinct locations are unknown. Several Esx-1 substrates are N-α-terminally acetylated. The role of this rare modification in bacteria is unclear. We sought to identify genes required for Esx-1 substrate modification, transport, and localization. Pathogenic mycobacteria lyse Acanthamoeba castellanii in an Esx-1-dependent manner. We conducted a genetic screen to identify Mycobacterium marinum strains which failed to lyse amoebae. We identified a noncytotoxic M. marinum strain with a transposon insertion in a predicted N-α-terminal acetyltransferase not previously linked to mycobacterial pathogenesis. Disruption of this gene led to attenuation of virulence, failure to induce a type I interferon response during macrophage infection, and loss of hemolytic activity. The major Esx-1 substrates, EsxA and EsxB, were exported to the cell surface, but only low levels were released into the bacteriological medium. The balance of EsxA N-α-terminal acetylation was disrupted, resulting in a mycobacterial strain in which surface-associated EsxA was hyperacetylated. Genetic complementation completely restored Esx-1 function and the levels of N-α-terminally acetylated EsxA on the surface but restored only low levels of Esx-1 substrates in the bacteriological medium. Our results reveal a novel gene required for mycobacterial Esx-1 export. Our findings indicate that maintaining the homeostasis of Esx-1 substrate N-α-terminal acetylation is essential for Esx-1-mediated virulence. We propose an inverse correlation between EsxA acetylation and virulence.
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172
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De novo missense mutations in the NAA10 gene cause severe non-syndromic developmental delay in males and females. Eur J Hum Genet 2014; 23:602-9. [PMID: 25099252 PMCID: PMC4402627 DOI: 10.1038/ejhg.2014.150] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 06/13/2014] [Accepted: 06/20/2014] [Indexed: 12/30/2022] Open
Abstract
Recent studies revealed the power of whole-exome sequencing to identify mutations in sporadic cases with non-syndromic intellectual disability. We now identified de novo missense variants in NAA10 in two unrelated individuals, a boy and a girl, with severe global developmental delay but without any major dysmorphism by trio whole-exome sequencing. Both de novo variants were predicted to be deleterious, and we excluded other variants in this gene. This X-linked gene encodes N-alpha-acetyltransferase 10, the catalytic subunit of the NatA complex involved in multiple cellular processes. A single hypomorphic missense variant p.(Ser37Pro) was previously associated with Ogden syndrome in eight affected males from two different families. This rare disorder is characterized by a highly recognizable phenotype, global developmental delay and results in death during infancy. In an attempt to explain the discrepant phenotype, we used in vitro N-terminal acetylation assays which suggested that the severity of the phenotype correlates with the remaining catalytic activity. The variant in the Ogden syndrome patients exhibited a lower activity than the one seen in the boy with intellectual disability, while the variant in the girl was the most severe exhibiting only residual activity in the acetylation assays used. We propose that N-terminal acetyltransferase deficiency is clinically heterogeneous with the overall catalytic activity determining the phenotypic severity.
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173
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Holmes WM, Mannakee BK, Gutenkunst RN, Serio TR. Loss of amino-terminal acetylation suppresses a prion phenotype by modulating global protein folding. Nat Commun 2014; 5:4383. [PMID: 25023910 PMCID: PMC4140192 DOI: 10.1038/ncomms5383] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/13/2014] [Indexed: 01/08/2023] Open
Abstract
N-terminal acetylation is among the most ubiquitous of protein modifications in eukaryotes. While loss of N-terminal acetylation is associated with many abnormalities, the molecular basis of these effects is known for only a few cases, where acetylation of single factors has been linked to binding avidity or metabolic stability. In contrast, the impact of N-terminal acetylation for the majority of the proteome, and its combinatorial contributions to phenotypes, are unknown. Here, by studying the yeast prion [PSI+], an amyloid of the Sup35 protein, we show that loss of N-terminal acetylation promotes general protein misfolding, a redeployment of chaperones to these substrates, and a corresponding stress response. These proteostasis changes, combined with the decreased stability of unacetylated Sup35 amyloid, reduce the size of prion aggregates and reverse their phenotypic consequences. Thus, loss of N-terminal acetylation, and its previously unanticipated role in protein biogenesis, globally resculpts the proteome to create a unique phenotype.
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Affiliation(s)
- William M Holmes
- 1] Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, Rhode Island 02912, USA [2]
| | - Brian K Mannakee
- Graduate Interdisciplinary Program in Statistics, University of Arizona, 1548 East Drachman Street, Tucson, Arizona 85721, USA
| | - Ryan N Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, 1007 East Lowell Street, Tucson, Arizona 85721, USA
| | - Tricia R Serio
- 1] Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, Rhode Island 02912, USA [2]
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174
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Theillet FX, Binolfi A, Frembgen-Kesner T, Hingorani K, Sarkar M, Kyne C, Li C, Crowley PB, Gierasch L, Pielak GJ, Elcock AH, Gershenson A, Selenko P. Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs). Chem Rev 2014; 114:6661-714. [PMID: 24901537 PMCID: PMC4095937 DOI: 10.1021/cr400695p] [Citation(s) in RCA: 326] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Francois-Xavier Theillet
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Andres Binolfi
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Tamara Frembgen-Kesner
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Karan Hingorani
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Mohona Sarkar
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Ciara Kyne
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Conggang Li
- Key Laboratory
of Magnetic Resonance in Biological Systems, State Key Laboratory
of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center
for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P.R. China
| | - Peter B. Crowley
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Lila Gierasch
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Gary J. Pielak
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Adrian H. Elcock
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Anne Gershenson
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Philipp Selenko
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
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175
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Nα-Acetyltransferase NatA Is Involved in Ribosome Synthesis inSaccharomyces cerevisiae. Biosci Biotechnol Biochem 2014; 77:631-8. [DOI: 10.1271/bbb.120860] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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176
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Affiliation(s)
- Jeong-Mok Kim
- Department of Life Sciences; Pohang University of Science and Technology; Pohang, Gyeongbuk, South Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences; Pohang University of Science and Technology; Pohang, Gyeongbuk, South Korea
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177
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Van Damme P, Gawron D, Van Criekinge W, Menschaert G. N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men. Mol Cell Proteomics 2014; 13:1245-61. [PMID: 24623590 DOI: 10.1074/mcp.m113.036442] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Usage of presumed 5'UTR or downstream in-frame AUG codons, next to non-AUG codons as translation start codons contributes to the diversity of a proteome as protein isoforms harboring different N-terminal extensions or truncations can serve different functions. Recent ribosome profiling data revealed a highly underestimated occurrence of database nonannotated, and thus alternative translation initiation sites (aTIS), at the mRNA level. N-terminomics data in addition showed that in higher eukaryotes around 20% of all identified protein N termini point to such aTIS, to incorrect assignments of the translation start codon, translation initiation at near-cognate start codons, or to alternative splicing. We here report on more than 1700 unique alternative protein N termini identified at the proteome level in human and murine cellular proteomes. Customized databases, created using the translation initiation mapping obtained from ribosome profiling data, additionally demonstrate the use of initiator methionine decoded near-cognate start codons besides the existence of N-terminal extended protein variants at the level of the proteome. Various newly identified aTIS were confirmed by mutagenesis, and meta-analyses demonstrated that aTIS reside in strong Kozak-like motifs and are conserved among eukaryotes, hinting to a possible biological impact. Finally, TargetP analysis predicted that the usage of aTIS often results in altered subcellular localization patterns, providing a mechanism for functional diversification.
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Affiliation(s)
- Petra Van Damme
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
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178
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Calpain-generated natural protein fragments as short-lived substrates of the N-end rule pathway. Proc Natl Acad Sci U S A 2014; 111:E817-26. [PMID: 24550490 DOI: 10.1073/pnas.1401639111] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Calpains are Ca(2+)-dependent intracellular proteases. We show here that calpain-generated natural C-terminal fragments of proteins that include G protein-coupled receptors, transmembrane ion channels, transcriptional regulators, apoptosis controllers, kinases, and phosphatases (Phe-GluN2a, Lys-Ica512, Arg-Ankrd2, Tyr-Grm1, Arg-Atp2b2, Glu-Bak, Arg-Igfbp2, Glu-IκBα, and Arg-c-Fos), are short-lived substrates of the Arg/N-end rule pathway, which targets destabilizing N-terminal residues. We also found that the identity of a fragment's N-terminal residue can change during evolution, but the residue's destabilizing activity is virtually always retained, suggesting selection pressures that favor a short half-life of the calpain-generated fragment. It is also shown that a self-cleavage of a calpain can result in an N-end rule substrate. Thus, the autoprocessing of calpains can control them by making active calpains short-lived. These and related results indicate that the Arg/N-end rule pathway mediates the remodeling of oligomeric complexes by eliminating protein fragments that are produced in these complexes through cleavages by calpains or other nonprocessive proteases. We suggest that this capability of the Arg/N-end rule pathway underlies a multitude of its previously known but mechanistically unclear functions.
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179
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Moccand C, Boycheva S, Surriabre P, Tambasco-Studart M, Raschke M, Kaufmann M, Fitzpatrick TB. The pseudoenzyme PDX1.2 boosts vitamin B6 biosynthesis under heat and oxidative stress in Arabidopsis. J Biol Chem 2014; 289:8203-16. [PMID: 24505140 DOI: 10.1074/jbc.m113.540526] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Vitamin B6 is an indispensable compound for survival, well known as a cofactor for numerous central metabolic enzymes and more recently for playing a role in several stress responses, particularly in association with oxidative stress. Regulatory aspects for the use of the vitamin in these roles are not known. Here we show that certain plants carry a pseudoenzyme (PDX1.2), which is involved in regulating vitamin B6 biosynthesis de novo under stress conditions. Specifically, we demonstrate that Arabidopsis PDX1.2 enhances the activity of its catalytic paralogs by forming a heterododecameric complex. PDX1.2 is strongly induced by heat as well as singlet oxygen stress, concomitant with an enhancement of vitamin B6 production. Analysis of pdx1.2 knockdown lines demonstrates that boosting vitamin B6 content is dependent on PDX1.2, revealing that this pseudoenzyme acts as a positive regulator of vitamin B6 biosynthesis during such stress conditions in plants.
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Affiliation(s)
- Cyril Moccand
- From the Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland and
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180
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Zhu HY, Li CM, Wang LF, Bai H, Li YP, Yu WX, Xia DA, Liu CC. In silico identification and characterization of N-Terminal acetyltransferase genes of poplar (Populus trichocarpa). Int J Mol Sci 2014; 15:1852-64. [PMID: 24473137 PMCID: PMC3958825 DOI: 10.3390/ijms15021852] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 01/17/2014] [Accepted: 01/18/2014] [Indexed: 11/24/2022] Open
Abstract
N-terminal acetyltransferase (Nats) complex is responsible for protein N-terminal acetylation (Nα-acetylation), which is one of the most common covalent modifications of eukaryotic proteins. Although genome-wide investigation and characterization of Nat catalytic subunits (CS) and auxiliary subunits (AS) have been conducted in yeast and humans they remain unexplored in plants. Here we report on the identification of eleven genes encoding eleven putative Nat CS polypeptides, and five genes encoding five putative Nat AS polypeptides in Populus. We document that the expansion of Nat CS genes occurs as duplicated blocks distributed across 10 of the 19 poplar chromosomes, likely only as a result of segmental duplication events. Based on phylogenetic analysis, poplar Nat CS were assigned to six subgroups, which corresponded well to the Nat CS types (CS of Nat A–F), being consistent with previous reports in humans and yeast. In silico analysis of microarray data showed that in the process of normal development of the poplar, their Nat CS and AS genes are commonly expressed at one relatively low level but share distinct tissue-specific expression patterns. This exhaustive survey of Nat genes in poplar provides important information to assist future studies on their functional role in poplar.
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Affiliation(s)
- Hang-Yong Zhu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
| | - Chun-Ming Li
- Forestry Research Institution of Heilongjiang Province, Harbin 150081, China.
| | - Li-Feng Wang
- Faculty of life Science and Technology, Mudanjiang Normal University, 191 Wenhua Street, Mudanjiang 157012, China.
| | - Hui Bai
- Forestry Research Institution of Heilongjiang Province, Harbin 150081, China.
| | - Yan-Ping Li
- Faculty of life Science and Technology, Mudanjiang Normal University, 191 Wenhua Street, Mudanjiang 157012, China.
| | - Wen-Xi Yu
- Forestry Research Institution of Heilongjiang Province, Harbin 150081, China.
| | - De-An Xia
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
| | - Chang-Cai Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
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181
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Van Damme P, Støve SI, Glomnes N, Gevaert K, Arnesen T. A Saccharomyces cerevisiae model reveals in vivo functional impairment of the Ogden syndrome N-terminal acetyltransferase NAA10 Ser37Pro mutant. Mol Cell Proteomics 2014; 13:2031-41. [PMID: 24408909 DOI: 10.1074/mcp.m113.035402] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
N-terminal acetylation (Nt-acetylation) occurs on the majority of eukaryotic proteins and is catalyzed by N-terminal acetyltransferases (NATs). Nt-acetylation is increasingly recognized as a vital modification with functional implications ranging from protein degradation to protein localization. Although early genetic studies in yeast demonstrated that NAT-deletion strains displayed a variety of phenotypes, only recently, the first human genetic disorder caused by a mutation in a NAT gene was reported; boys diagnosed with the X-linked Ogden syndrome harbor a p.Ser37Pro (S37P) mutation in the gene encoding Naa10, the catalytic subunit of the NatA complex, and suffer from global developmental delays and lethality during infancy. Here, we describe a Saccharomyces cerevisiae model developed by introducing the human wild-type or mutant NatA complex into yeast lacking NatA (NatA-Δ). The wild-type human NatA complex phenotypically complemented the NatA-Δ strain, whereas only a partial rescue was observed for the Ogden mutant NatA complex suggesting that hNaa10 S37P is only partially functional in vivo. Immunoprecipitation experiments revealed a reduced subunit complexation for the mutant hNatA S37P next to a reduced in vitro catalytic activity. We performed quantitative Nt-acetylome analyses on a control yeast strain (yNatA), a yeast NatA deletion strain (yNatA-Δ), a yeast NatA deletion strain expressing wild-type human NatA (hNatA), and a yeast NatA deletion strain expressing mutant human NatA (hNatA S37P). Interestingly, a generally reduced degree of Nt-acetylation was observed among a large group of NatA substrates in the yeast expressing mutant hNatA as compared with yeast expressing wild-type hNatA. Combined, these data provide strong support for the functional impairment of hNaa10 S37P in vivo and suggest that reduced Nt-acetylation of one or more target substrates contributes to the pathogenesis of the Ogden syndrome. Comparative analysis between human and yeast NatA also provided new insights into the co-evolution of the NatA complexes and their substrates. For instance, (Met-)Ala- N termini are more prevalent in the human proteome as compared with the yeast proteome, and hNatA displays a preference toward these N termini as compared with yNatA.
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Affiliation(s)
- Petra Van Damme
- From the ‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium;
| | - Svein I Støve
- ¶Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; **Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Nina Glomnes
- ¶Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; ‖Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway; and
| | - Kris Gevaert
- From the ‡Department of Medical Protein Research, 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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182
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Kim HK, Kim RR, Oh JH, Cho H, Varshavsky A, Hwang CS. The N-terminal methionine of cellular proteins as a degradation signal. Cell 2013; 156:158-69. [PMID: 24361105 DOI: 10.1016/j.cell.2013.11.031] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 09/26/2013] [Accepted: 11/20/2013] [Indexed: 11/28/2022]
Abstract
The Arg/N-end rule pathway targets for degradation proteins that bear specific unacetylated N-terminal residues while the Ac/N-end rule pathway targets proteins through their N(α)-terminally acetylated (Nt-acetylated) residues. Here, we show that Ubr1, the ubiquitin ligase of the Arg/N-end rule pathway, recognizes unacetylated N-terminal methionine if it is followed by a hydrophobic residue. This capability of Ubr1 expands the range of substrates that can be targeted for degradation by the Arg/N-end rule pathway because virtually all nascent cellular proteins bear N-terminal methionine. We identified Msn4, Sry1, Arl3, and Pre5 as examples of normal or misfolded proteins that can be destroyed through the recognition of their unacetylated N-terminal methionine. Inasmuch as proteins bearing the Nt-acetylated N-terminal methionine residue are substrates of the Ac/N-end rule pathway, the resulting complementarity of the Arg/N-end rule and Ac/N-end rule pathways enables the elimination of protein substrates regardless of acetylation state of N-terminal methionine in these substrates.
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Affiliation(s)
- Heon-Ki Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Ryu-Ryun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Jang-Hyun Oh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hanna Cho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Alexander Varshavsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, South Korea.
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183
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Low TY, van Heesch S, van den Toorn H, Giansanti P, Cristobal A, Toonen P, Schafer S, Hübner N, van Breukelen B, Mohammed S, Cuppen E, Heck AJR, Guryev V. Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis. Cell Rep 2013; 5:1469-78. [PMID: 24290761 DOI: 10.1016/j.celrep.2013.10.041] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/28/2013] [Accepted: 10/24/2013] [Indexed: 02/07/2023] Open
Abstract
Quantitative and qualitative protein characteristics are regulated at genomic, transcriptomic, and posttranscriptional levels. Here, we integrated in-depth transcriptome and proteome analyses of liver tissues from two rat strains to unravel the interactions within and between these layers. We obtained peptide evidence for 26,463 rat liver proteins. We validated 1,195 gene predictions, 83 splice events, 126 proteins with nonsynonymous variants, and 20 isoforms with nonsynonymous RNA editing. Quantitative RNA sequencing and proteomics data correlate highly between strains but poorly among each other, indicating extensive nongenetic regulation. Our multilevel analysis identified a genomic variant in the promoter of the most differentially expressed gene Cyp17a1, a previously reported top hit in genome-wide association studies for human hypertension, as a potential contributor to the hypertension phenotype in SHR rats. These results demonstrate the power of and need for integrative analysis for understanding genetic control of molecular dynamics and phenotypic diversity in a system-wide manner.
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Affiliation(s)
- Teck Yew Low
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Sebastiaan van Heesch
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Henk van den Toorn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Piero Giansanti
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Alba Cristobal
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Pim Toonen
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Sebastian Schafer
- Max-Delbruck-Center for Molecular Medicine (MDC), Robert-Rossle-Strasse 10, 13125 Berlin, Germany
| | - Norbert Hübner
- Max-Delbruck-Center for Molecular Medicine (MDC), Robert-Rossle-Strasse 10, 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Bas van Breukelen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Edwin Cuppen
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, the Netherlands.
| | - Victor Guryev
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
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184
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Kozak BU, van Rossum HM, Benjamin KR, Wu L, Daran JMG, Pronk JT, van Maris AJA. Replacement of the Saccharomyces cerevisiae acetyl-CoA synthetases by alternative pathways for cytosolic acetyl-CoA synthesis. Metab Eng 2013; 21:46-59. [PMID: 24269999 DOI: 10.1016/j.ymben.2013.11.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 10/03/2013] [Accepted: 11/11/2013] [Indexed: 10/26/2022]
Abstract
Cytosolic acetyl-coenzyme A is a precursor for many biotechnologically relevant compounds produced by Saccharomyces cerevisiae. In this yeast, cytosolic acetyl-CoA synthesis and growth strictly depend on expression of either the Acs1 or Acs2 isoenzyme of acetyl-CoA synthetase (ACS). Since hydrolysis of ATP to AMP and pyrophosphate in the ACS reaction constrains maximum yields of acetyl-CoA-derived products, this study explores replacement of ACS by two ATP-independent pathways for acetyl-CoA synthesis. After evaluating expression of different bacterial genes encoding acetylating acetaldehyde dehydrogenase (A-ALD) and pyruvate-formate lyase (PFL), acs1Δ acs2Δ S. cerevisiae strains were constructed in which A-ALD or PFL successfully replaced ACS. In A-ALD-dependent strains, aerobic growth rates of up to 0.27 h(-1) were observed, while anaerobic growth rates of PFL-dependent S. cerevisiae (0.20 h(-1)) were stoichiometrically coupled to formate production. In glucose-limited chemostat cultures, intracellular metabolite analysis did not reveal major differences between A-ALD-dependent and reference strains. However, biomass yields on glucose of A-ALD- and PFL-dependent strains were lower than those of the reference strain. Transcriptome analysis suggested that reduced biomass yields were caused by acetaldehyde and formate in A-ALD- and PFL-dependent strains, respectively. Transcript profiles also indicated that a previously proposed role of Acs2 in histone acetylation is probably linked to cytosolic acetyl-CoA levels rather than to direct involvement of Acs2 in histone acetylation. While demonstrating that yeast ACS can be fully replaced, this study demonstrates that further modifications are needed to achieve optimal in vivo performance of the alternative reactions for supply of cytosolic acetyl-CoA as a product precursor.
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Affiliation(s)
- Barbara U Kozak
- Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Harmen M van Rossum
- Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
| | | | - Liang Wu
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands.
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185
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Ferrández-Ayela A, Micol-Ponce R, Sánchez-García AB, Alonso-Peral MM, Micol JL, Ponce MR. Mutation of an Arabidopsis NatB N-alpha-terminal acetylation complex component causes pleiotropic developmental defects. PLoS One 2013; 8:e80697. [PMID: 24244708 PMCID: PMC3828409 DOI: 10.1371/journal.pone.0080697] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 10/14/2013] [Indexed: 12/22/2022] Open
Abstract
N-α-terminal acetylation is one of the most common, but least understood modifications of eukaryotic proteins. Although a high degree of conservation exists between the N-α-terminal acetylomes of plants and animals, very little information is available on this modification in plants. In yeast and humans, N-α-acetyltransferase complexes include a single catalytic subunit and one or two auxiliary subunits. Here, we report the positional cloning of TRANSCURVATA2 (TCU2), which encodes the auxiliary subunit of the NatB N-α-acetyltransferase complex in Arabidopsis. The phenotypes of loss-of-function tcu2 alleles indicate that NatB complex activity is required for flowering time regulation and for leaf, inflorescence, flower, fruit and embryonic development. In double mutants, tcu2 alleles synergistically interact with alleles of ARGONAUTE10, which encodes a component of the microRNA machinery. In summary, NatB-mediated N-α-terminal acetylation of proteins is pleiotropically required for Arabidopsis development and seems to be functionally related to the microRNA pathway.
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Affiliation(s)
| | - Rosa Micol-Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, Spain
| | | | | | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, Spain
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186
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Becker AH, Oh E, Weissman JS, Kramer G, Bukau B. Selective ribosome profiling as a tool for studying the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes. Nat Protoc 2013; 8:2212-39. [PMID: 24136347 DOI: 10.1038/nprot.2013.133] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A plethora of factors is involved in the maturation of newly synthesized proteins, including chaperones, membrane targeting factors and enzymes. Many factors act co-translationally through association with ribosome-nascent chain complexes (RNCs), but their target specificities and modes of action remain poorly understood. We developed selective ribosome profiling (SeRP) to identify substrate pools and points of RNC engagement of these factors. SeRP is based on sequencing mRNA fragments covered by translating ribosomes (general ribosome profiling (RP)), combined with a procedure to selectively isolate RNCs whose nascent polypeptides are associated with the factor of interest. Factor-RNC interactions are stabilized by cross-linking; the resulting factor-RNC adducts are nuclease-treated to generate monosomes, and then they are affinity purified. The ribosome-extracted mRNA footprints are converted to DNA libraries for deep sequencing. The protocol is specified for general RP and SeRP in bacteria. It was first applied to the chaperone trigger factor (TF) and is readily adaptable to other co-translationally acting factors, including eukaryotic factors. Factor-RNC purification and sequencing library preparation takes 7-8 d, and sequencing and data analysis can be completed in 5-6 d.
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Affiliation(s)
- Annemarie H Becker
- Center for Molecular Biology of the University of Heidelberg, German Cancer Research Center, DKFZ-ZMBH Alliance, Heidelberg, Germany
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187
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Katrukha IA, Gusev NB. Enigmas of cardiac troponin T phosphorylation. J Mol Cell Cardiol 2013; 65:156-8. [PMID: 24120912 DOI: 10.1016/j.yjmcc.2013.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 09/27/2013] [Accepted: 09/30/2013] [Indexed: 10/26/2022]
Affiliation(s)
- Ivan A Katrukha
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119991 Russian Federation
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188
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Schiza V, Molina-Serrano D, Kyriakou D, Hadjiantoniou A, Kirmizis A. N-alpha-terminal acetylation of histone H4 regulates arginine methylation and ribosomal DNA silencing. PLoS Genet 2013; 9:e1003805. [PMID: 24068969 PMCID: PMC3778019 DOI: 10.1371/journal.pgen.1003805] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 08/03/2013] [Indexed: 11/24/2022] Open
Abstract
Post-translational modifications of histones play a key role in DNA-based processes, like transcription, by modulating chromatin structure. N-terminal acetylation is unique among the numerous histone modifications because it is deposited on the N-alpha amino group of the first residue instead of the side-chain of amino acids. The function of this modification and its interplay with other internal histone marks has not been previously addressed. Here, we identified N-terminal acetylation of H4 (N-acH4) as a novel regulator of arginine methylation and chromatin silencing in Saccharomyces cerevisiae. Lack of the H4 N-alpha acetyltransferase (Nat4) activity results specifically in increased deposition of asymmetric dimethylation of histone H4 arginine 3 (H4R3me2a) and in enhanced ribosomal-DNA silencing. Consistent with this, H4 N-terminal acetylation impairs the activity of the Hmt1 methyltransferase towards H4R3 in vitro. Furthermore, combinatorial loss of N-acH4 with internal histone acetylation at lysines 5, 8 and 12 has a synergistic induction of H4R3me2a deposition and rDNA silencing that leads to a severe growth defect. This defect is completely rescued by mutating arginine 3 to lysine (H4R3K), suggesting that abnormal deposition of a single histone modification, H4R3me2a, can impact on cell growth. Notably, the cross-talk between N-acH4 and H4R3me2a, which regulates rDNA silencing, is induced under calorie restriction conditions. Collectively, these findings unveil a molecular and biological function for H4 N-terminal acetylation, identify its interplay with internal histone modifications, and provide general mechanistic implications for N-alpha-terminal acetylation, one of the most common protein modifications in eukaryotes. The genome of eukaryotic cells is packaged into nucleosomes consisting of an octamer of histone proteins that is wrapped around by DNA. Histone proteins are often modified with chemical groups that can influence the arrangement of nucleosomes and thereby affect DNA-based processes like transcription. Histone N-terminal acetylation, which comprises the addition of a chemical group at the tip of the histone tail, is an abundant modification whose function is unknown. In this work, we show that N-terminal acetylation of histone H4 can strongly inhibit the occurrence of a neighboring modification, namely dimethylation at the third arginine. To do this, N-terminal acetylation cooperates with other internal lysine acetylation marks. We find that the communication amongst these histone modifications is necessary for controlling the expression of ribosomal RNA genes that are required for protein synthesis and cell growth. Our experiments show that in the absence of both N-terminal acetylation and lysine acetylation there is a strong increase in H4 arginine 3 dimethylation levels leading to cell lethality. This growth defect can be rescued by a point mutation on H4 that blocks methylation at position 3. Together, our results unveil a molecular and biological function for the previously uncharacterized N-terminal acetylation of histones.
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Affiliation(s)
- Vassia Schiza
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Dimitris Kyriakou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
- * E-mail:
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189
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Wang D, Fang C, Zong NC, Liem DA, Cadeiras M, Scruggs SB, Yu H, Kim AK, Yang P, Deng M, Lu H, Ping P. Regulation of acetylation restores proteolytic function of diseased myocardium in mouse and human. Mol Cell Proteomics 2013; 12:3793-802. [PMID: 24037710 DOI: 10.1074/mcp.m113.028332] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteasome complexes play essential roles in maintaining cellular protein homeostasis and serve fundamental roles in cardiac function under normal and pathological conditions. A functional detriment in proteasomal activities has been recognized as a major contributor to the progression of cardiovascular diseases. Therefore, approaches to restore proteolytic function within the setting of the diseased myocardium would be of great clinical significance. In this study, we discovered that the cardiac proteasomal activity could be regulated by acetylation. Histone deacetylase (HDAC) inhibitors (suberoylanilide hydroxamic acid and sodium valproate) enhanced the acetylation of 20S proteasome subunits in the myocardium and led to an elevation of proteolytic capacity. This regulatory paradigm was present in both healthy and acutely ischemia/reperfusion (I/R) injured murine hearts, and HDAC inhibition in vitro restored proteolytic capacities to baseline sham levels in injured hearts. This mechanism of regulation was also viable in failing human myocardium. With 20S proteasomal complexes purified from murine myocardium treated with HDAC inhibitors in vivo, we confirmed that acetylation of 20S subunits directly, at least in part, presents a molecular explanation for the improvement in function. Furthermore, using high-resolution LC-MS/MS, we unraveled the first cardiac 20S acetylome, which identified the acetylation of nine N-termini and seven internal lysine residues. Acetylation on four lysine residues and four N-termini on cardiac proteasomes were novel discoveries of this study. In addition, the acetylation of five lysine residues was inducible via HDAC inhibition, which correlated with the enhancement of 20S proteasomal activity. Taken as a whole, our investigation unveiled a novel mechanism of proteasomal function regulation in vivo and established a new strategy for the potential rescue of compromised proteolytic function in the failing heart using HDAC inhibitors.
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Affiliation(s)
- Ding Wang
- Department of Physiology, UCLA School of Medicine, Los Angeles, California 90095
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190
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Cain JA, Solis N, Cordwell SJ. Beyond gene expression: the impact of protein post-translational modifications in bacteria. J Proteomics 2013; 97:265-86. [PMID: 23994099 DOI: 10.1016/j.jprot.2013.08.012] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 07/08/2013] [Accepted: 08/10/2013] [Indexed: 12/12/2022]
Abstract
The post-translational modification (PTM) of proteins plays a critical role in the regulation of a broad range of cellular processes in eukaryotes. Yet their role in governing similar systems in the conventionally presumed 'simpler' forms of life has been largely neglected and, until recently, was thought to occur only rarely, with some modifications assumed to be limited to higher organisms alone. Recent developments in mass spectrometry-based proteomics have provided an unparalleled power to enrich, identify and quantify peptides with PTMs. Additional modifications to biological molecules such as lipids and carbohydrates that are essential for bacterial pathophysiology have only recently been detected on proteins. Here we review bacterial protein PTMs, focusing on phosphorylation, acetylation, proteolytic degradation, methylation and lipidation and the roles they play in bacterial adaptation - thus highlighting the importance of proteomic techniques in a field that is only just in its infancy. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Joel A Cain
- School of Molecular Bioscience, School of Medical Sciences, The University of Sydney, 2006, Australia
| | - Nestor Solis
- School of Molecular Bioscience, School of Medical Sciences, The University of Sydney, 2006, Australia
| | - Stuart J Cordwell
- School of Molecular Bioscience, School of Medical Sciences, The University of Sydney, 2006, Australia; Discipline of Pathology, School of Medical Sciences, The University of Sydney, 2006, Australia.
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191
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Liszczak G, Goldberg JM, Foyn H, Petersson EJ, Arnesen T, Marmorstein R. Molecular basis for N-terminal acetylation by the heterodimeric NatA complex. Nat Struct Mol Biol 2013; 20:1098-105. [PMID: 23912279 PMCID: PMC3766382 DOI: 10.1038/nsmb.2636] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 06/19/2013] [Indexed: 12/23/2022]
Abstract
Amino-terminal acetylation is ubiquitous among eukaryotic proteins and controls a myriad of biological processes. Of the N-terminal acetyltransferases (NATs) that facilitate this co-translational modification, the heterodimeric NatA complex harbors the most diversity for substrate selection and modifies the majority of all amino-terminally acetylated proteins. Here, we report the X-ray crystal structure of the 100 kDa holo-NatA complex from Schizosaccharomyces pombe in the absence and presence of a bisubstrate peptide-CoA conjugate inhibitor, as well as the structure of the uncomplexed Naa10p catalytic subunit. The NatA-Naa15p auxiliary subunit contains 13 TPR motifs and adopts a ring-like topology that wraps around the NatA-Naa10p subunit, an interaction that alters the Naa10p active site for substrate-specific acetylation. These studies have implications for understanding the mechanistic details of other NAT complexes and how regulatory subunits modulate the activity of the broader family of protein acetyltransferases.
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Affiliation(s)
- Glen Liszczak
- 1] Program in Gene Expression and Regulation, Wistar Institute, Philadelphia, Pennsylvania, USA. [2] Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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192
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Kim I, Miller CR, Young DL, Fields S. High-throughput analysis of in vivo protein stability. Mol Cell Proteomics 2013; 12:3370-8. [PMID: 23897579 DOI: 10.1074/mcp.o113.031708] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Determining the half-life of proteins is critical for an understanding of virtually all cellular processes. Current methods for measuring in vivo protein stability, including large-scale approaches, are limited in their throughput or in their ability to discriminate among small differences in stability. We developed a new method, Stable-seq, which uses a simple genetic selection combined with high-throughput DNA sequencing to assess the in vivo stability of a large number of variants of a protein. The variants are fused to a metabolic enzyme, which here is the yeast Leu2 protein. Plasmids encoding these Leu2 fusion proteins are transformed into yeast, with the resultant fusion proteins accumulating to different levels based on their stability and leading to different doubling times when the yeast are grown in the absence of leucine. Sequencing of an input population of variants of a protein and the population of variants after leucine selection allows the stability of tens of thousands of variants to be scored in parallel. By applying the Stable-seq method to variants of the protein degradation signal Deg1 from the yeast Matα2 protein, we generated a high-resolution map that reveals the effect of ∼30,000 mutations on protein stability. We identified mutations that likely affect stability by changing the activity of the degron, by leading to translation from new start codons, or by affecting N-terminal processing. Stable-seq should be applicable to other organisms via the use of suitable reporter proteins, as well as to the analysis of complex mixtures of fusion proteins.
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Affiliation(s)
- Ikjin Kim
- Department of Genome Sciences, University of Washington, Box 355065, Seattle, Washington 98195
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193
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Friedmann DR, Marmorstein R. Structure and mechanism of non-histone protein acetyltransferase enzymes. FEBS J 2013; 280:5570-81. [PMID: 23742047 DOI: 10.1111/febs.12373] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 05/29/2013] [Accepted: 06/03/2013] [Indexed: 12/21/2022]
Abstract
Post-translational modification of proteins is ubiquitous and mediates many cellular processes, including intracellular localization, protein-protein interactions, enzyme activity, transcriptional regulation and protein stability. While the role of phosphorylation as a key post-translational modification has been well studied, the more evolutionarily conserved post-translational modification acetylation has only recently attracted attention as a key regulator of cellular events. Protein acetylation has been largely studied in the context of its role in histone modification and gene regulation, where histones are modified by histone acetyltransferases to promote transcription. However, more recent acetylomic and biochemical studies have revealed that acetylation is mediated by a broader family of protein acetyltransferases. The recent structure determination of several protein acetyltransferases has provided a wealth of molecular information regarding structural features of protein acetyltransferases, their enzymatic mechanisms, their mode of substrate-specific recognition and their regulatory elements. In this review, we briefly describe what is known about non-histone protein substrates, but mainly focus on a few recent structures of protein acetyltransferases to compare and contrast them with histone acetyltransferases to better understand the molecular basis for protein recognition and modification by this family of protein modification enzymes.
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Affiliation(s)
- David R Friedmann
- Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA, 19104, USA
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194
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Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding. Nat Struct Mol Biol 2013; 20:843-50. [DOI: 10.1038/nsmb.2615] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 05/15/2013] [Indexed: 12/23/2022]
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195
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N-α-acetyltransferase 10 protein is a negative regulator of 28S proteasome through interaction with PA28β. FEBS Lett 2013; 587:1630-7. [PMID: 23624078 DOI: 10.1016/j.febslet.2013.04.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/10/2013] [Accepted: 04/02/2013] [Indexed: 01/10/2023]
Abstract
N-α-acetyltransferase 10 protein (Naa10p) regulates various pathways associated with cancer cell proliferation, metastasis, apoptosis and autophagy. However, its role in protein quality control is unknown. Here, we report that Naa10p is physically associated with proteasome activator 28β (PA28β). Naa10p also interacts with PA28α in a PA28β-dependent manner. Naa10p negatively regulates PA28-dependent chymotrypsin-like proteasome activity in cancer cells and in a cell-free system reconstituted with purified proteins, which is not related to 26S proteasome. Acetyltransferase activity of Naa10p is not required for its effect on chymotrypsin-like proteasome activity. Therefore, our data reveal that Naa10p suppresses 28S proteasome activity through interaction with PA28β.
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196
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Shemorry A, Hwang CS, Varshavsky A. Control of protein quality and stoichiometries by N-terminal acetylation and the N-end rule pathway. Mol Cell 2013; 50:540-51. [PMID: 23603116 DOI: 10.1016/j.molcel.2013.03.018] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/04/2013] [Accepted: 03/12/2013] [Indexed: 11/19/2022]
Abstract
N(α)-terminal acetylation of cellular proteins was recently discovered to create specific degradation signals termed Ac/N-degrons and targeted by the Ac/N-end rule pathway. We show that Hcn1, a subunit of the APC/C ubiquitin ligase, contains an Ac/N-degron that is repressed by Cut9, another APC/C subunit and the ligand of Hcn1. Cog1, a subunit of the Golgi-associated COG complex, is also shown to contain an Ac/N-degron. Cog2 and Cog3, direct ligands of Cog1, can repress this degron. The subunit decoy technique was used to show that the long-lived endogenous Cog1 is destabilized and destroyed via its activated (unshielded) Ac/N-degron if the total level of Cog1 increased in a cell. Hcn1 and Cog1 are the first examples of protein regulation through the physiologically relevant transitions that shield and unshield natural Ac/N-degrons. This mechanistically straightforward circuit can employ the demonstrated conditionality of Ac/N-degrons to regulate subunit stoichiometries and other aspects of protein quality control.
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Affiliation(s)
- Anna Shemorry
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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197
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Aksnes H, Osberg C, Arnesen T. N-terminal acetylation by NatC is not a general determinant for substrate subcellular localization in Saccharomyces cerevisiae. PLoS One 2013; 8:e61012. [PMID: 23613772 PMCID: PMC3626706 DOI: 10.1371/journal.pone.0061012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 03/05/2013] [Indexed: 01/27/2023] Open
Abstract
N-terminal acetylation has been suggested to play a role in the subcellular targeting of proteins, in particular those acetylated by the N-terminal acetyltransferase complex NatC. Based on previous positional proteomics data revealing N-terminal acetylation status and the predicted NAT substrate classes, we selected 13 suitable NatC substrates for subcellular localization studies in Saccharomyces cerevisiae. Fluorescence microscopy analysis of GFP-tagged candidates in the presence or absence of the NatC catalytic subunit Naa30 (Mak3) revealed unaltered localization patterns for all 13 candidates, thus arguing against a general role for the N-terminal acetyl group as a localization determinant. Furthermore, all organelle-localized substrates indicated undisrupted structures, thus suggesting that absence of NatC acetylation does not have a vast effect on organelle morphology in yeast.
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Affiliation(s)
- Henriette Aksnes
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - Camilla Osberg
- 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
- * E-mail:
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198
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Foyn H, Jones JE, Lewallen D, Narawane R, Varhaug JE, Thompson PR, Arnesen T. Design, synthesis, and kinetic characterization of protein N-terminal acetyltransferase inhibitors. ACS Chem Biol 2013; 8:1121-7. [PMID: 23557624 DOI: 10.1021/cb400136s] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The N-termini of 80-90% of human proteins are acetylated by the N-terminal acetyltransferases (NATs), NatA-NatF. The major NAT complex, NatA, and particularly the catalytic subunit hNaa10 (ARD1) has been implicated in cancer development. For example, knockdown of hNaa10 results in cancer cell death and the arrest of cell proliferation. It also sensitized cancer cells to drug-induced cytotoxicity. Human NatE has a distinct substrate specificity and is essential for normal chromosome segregation. Thus, NAT inhibitors may potentially be valuable anticancer therapeutics, either directly or as adjuvants. Herein, we report the design and synthesis of the first inhibitors targeting these enzymes. Using the substrate specificity of the enzymes as a guide, we synthesized three bisubstrate analogues that potently and selectively inhibit the NatA complex (CoA-Ac-SES4; IC50 = 15.1 μM), hNaa10, the catalytic subunit of NatA (CoA-Ac-EEE4; Ki = 1.6 μM), and NatE/hNaa50 (CoA-Ac-MLG7; Ki* = 8 nM); CoA-Ac-EEE4 is a reversible competitive inhibitor of hNaa10, and CoA-Ac-MLG7 is a slow tight binding inhibitor of hNaa50. Our demonstration that it is possible to develop NAT selective inhibitors should assist future efforts to develop NAT inhibitors with more drug-like properties that can be used to chemically interrogate in vivo NAT function.
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Affiliation(s)
- Håvard Foyn
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
- Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
- Department of Chemistry, The Scripps Research Institute, 120 Scripps Way, Jupiter,
Florida 33458, United States
| | - Justin E. Jones
- Department of Chemistry, The Scripps Research Institute, 120 Scripps Way, Jupiter,
Florida 33458, United States
| | - Dan Lewallen
- Department of Chemistry, The Scripps Research Institute, 120 Scripps Way, Jupiter,
Florida 33458, United States
| | - Rashmi Narawane
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Jan Erik Varhaug
- Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
- Department of Surgical Sciences, University of Bergen, N-5020 Bergen, Norway
| | - Paul R. Thompson
- Department of Chemistry, The Scripps Research Institute, 120 Scripps Way, Jupiter,
Florida 33458, United States
| | - 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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199
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Alderson TR, Markley JL. Biophysical characterization of α-synuclein and its controversial structure. INTRINSICALLY DISORDERED PROTEINS 2013; 1:18-39. [PMID: 24634806 PMCID: PMC3908606 DOI: 10.4161/idp.26255] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 08/23/2013] [Indexed: 12/16/2022]
Abstract
α-synuclein, a presynaptic protein of poorly defined function, constitutes the main component of Parkinson disease-associated Lewy bodies. Extensive biophysical investigations have provided evidence that isolated α-synuclein is an intrinsically disordered protein (IDP) in vitro. Subsequently serving as a model IDP in numerous studies, α-synuclein has aided in the development of many technologies used to characterize IDPs and arguably represents the most thoroughly analyzed IDP to date. Recent reports, however, have challenged the disordered nature of α-synuclein inside cells and have instead proposed a physiologically relevant helical tetramer. Despite α-synuclein's rich biophysical history, a single coherent picture has not yet emerged concerning its in vivo structure, dynamics, and physiological role(s). We present herein a review of the biophysical discoveries, developments, and models pertinent to the characterization of α-synuclein's structure and analysis of the native tetramer controversy.
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Affiliation(s)
- T Reid Alderson
- Biochemistry Department; University of Wisconsin-Madison; Madison, WI USA
| | - John L Markley
- Biochemistry Department; University of Wisconsin-Madison; Madison, WI USA ; National Magnetic Resonance Facility at Madison; University of Wisconsin-Madison; Madison, WI USA
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200
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Zattas D, Adle DJ, Rubenstein EM, Hochstrasser M. N-terminal acetylation of the yeast Derlin Der1 is essential for Hrd1 ubiquitin-ligase activity toward luminal ER substrates. Mol Biol Cell 2013; 24:890-900. [PMID: 23363603 PMCID: PMC3608499 DOI: 10.1091/mbc.e12-11-0838] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Up to 70% of yeast proteins are N-terminally acetylated, but in few cases is the function known. The NatB Nα-acetyltransferase is essential for ER-associated degradation of luminal proteins (ERAD-L). Der1, an ERAD-L cofactor of the Hrd1 ubiquitin ligase, is acetylated by NatB and is the only N-acetylation substrate crucial to ERAD-L. Two conserved ubiquitin ligases, Hrd1 and Doa10, mediate most endoplasmic reticulum–associated protein degradation (ERAD) in yeast. Degradation signals (degrons) recognized by these ubiquitin ligases remain poorly characterized. Doa10 recognizes the Deg1 degron from the MATα2 transcription factor. We previously found that deletion of the gene (NAT3) encoding the catalytic subunit of the NatB N-terminal acetyltransferase weakly stabilized a Deg1-fusion protein. By contrast, a recent analysis of several MATα2 derivatives suggested that N-terminal acetylation of these proteins by NatB was crucial for recognition by Doa10. We now analyze endogenous MATα2 degradation in cells lacking NatB and observe minimal perturbation relative to wild-type cells. However, NatB mutation strongly impairs degradation of ER-luminal Hrd1 substrates. This unexpected defect derives from a failure of Der1, a Hrd1 complex subunit, to be N-terminally acetylated in NatB mutant yeast. We retargeted Der1 to another acetyltransferase to show that it is the only ERAD factor requiring N-terminal acetylation. Preventing Der1 acetylation stimulates its proteolysis via the Hrd1 pathway, at least partially accounting for the ERAD defect observed in the absence of NatB. These results reveal an important role for N-terminal acetylation in controlling Hrd1 ligase activity toward a specific class of ERAD substrates.
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Affiliation(s)
- Dimitrios Zattas
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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