N‐terminal modifications of cellular proteins: The enzymes involved, their substrate specificities and biological effects

Abstract

The vast majority of eukaryotic proteins are N‐terminally modified by one or more processing enzymes. Enzymes acting on the very first amino acid of a polypeptide include different peptidases, transferases, and ligases. Methionine aminopeptidases excise the initiator methionine leaving the nascent polypeptide with a newly exposed amino acid that may be further modified. N‐terminal acetyl‐, methyl‐, myristoyl‐, and palmitoyltransferases may attach an acetyl, methyl, myristoyl, or palmitoyl group, respectively, to the α‐amino group of the target protein N‐terminus. With the action of ubiquitin ligases, one or several ubiquitin molecules are transferred, and hence, constitute the N‐terminal modification. Modifications at protein N‐termini represent an important contribution to proteomic diversity and complexity, and are essential for protein regulation and cellular signaling. Consequently, dysregulation of the N‐terminal modifying enzymes is implicated in human diseases. We here review the different protein N‐terminal modifications occurring co‐ or post‐translationally with emphasis on the responsible enzymes and their substrate specificities.

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97. 97.

    Boisson B, Giglione C, Meinnel T. Unexpected protein families including cell defense components feature in the N-myristoylome of a higher eukaryote. J. Biol. Chem. 2003;278:43418-43429.

    Not in our library10.1074/jbc.m307321200

98. 98.

    Maurer-Stroh S, Eisenhaber B, Eisenhaber F. N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence. J. Mol. Biol. 2002;317:541-557.

    Not in our library10.1006/jmbi.2002.5426

99. 99.

    Maurer-Stroh S, Eisenhaber B, Eisenhaber F. N-terminal N-myristoylation of proteins: refinement of the sequence motif and its taxon-specific differences. J. Mol. Biol. 2002;317:523-540.

    Not in our library10.1006/jmbi.2002.5425

100. 100.
     Predicting N-terminal myristoylation sites in plant proteins · 2004

     Not checked
101. 101.

     Sugii M, Okada R, Matsuno H, Miyano S. Performance improvement in protein N-myristoyl classification by BONSAI with insignificant indexing symbol. Genome Inform. Int. Conf. Genome Inform. 2007;18:277-286.

     Not in our library

102. 102.

     Eisenhaber F, Eisenhaber B, Kubina W, Maurer-Stroh S, et al. Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1. Nucleic Acids Res. 2003;31:3631-3634.

     Not in our library10.1093/nar/gkg537

103. 103.

     Bologna G, Yvon C, Duvaud S, Veuthey AL. N-Terminal myristoylation predictions by ensembles of neural networks. Proteomics. 2004;4:1626-1632.

     Not in our library10.1002/pmic.200300783

104. 104.

     Suzuki T, Moriya K, Nagatoshi K, Ota Y, et al. Strategy for comprehensive identification of human N-myristoylated proteins using an insect cell-free protein synthesis system. Proteomics. 2010;10:1780-1793.

     Not in our library10.1002/pmic.200900783

105. 105.
     Global profiling of co- and post-translationally N-myristoylated proteomes in human cells · 2014

     No notice
106. 106.

     Linder ME, Middleton P, Hepler JR, Taussig R, et al. Lipid modifications of G proteins: alpha subunits are palmitoylated. Proc. Natl. Acad. Sci. USA. 1993;90:3675-3679.

     Not in our library10.1073/pnas.90.8.3675

107. 107.

     Kleuss C, Krause E. Galpha(s) is palmitoylated at the N-terminal glycine. EMBO J. 2003;22:826-832.

     Not in our library10.1093/emboj/cdg095

108. 108.

     Resh MD. Palmitoylation of ligands, receptors, and intracellular signaling molecules. Sci. STKE. 2006;2006:re14.

     Not in our library10.1126/stke.3592006re14

109. 109.

     Pepinsky RB, Zeng C, Wen D, Rayhorn P, et al. Identification of a palmitic acid-modified form of human Sonic hedgehog. J. Biol. Chem. 1998;273:14037-14045.

     Not in our library10.1074/jbc.273.22.14037

110. 110.

     Buglino JA, Resh MD. Hhat is a palmitoylacyltransferase with specificity for N-palmitoylation of Sonic Hedgehog. J. Biol. Chem. 2008;283:22076-22088.

     Not in our library10.1074/jbc.m803901200

111. 111.

     Chamoun Z, Mann RK, Nellen D, von Kessler DP, et al. Skinny hedgehog, an acyltransferase required for palmitoylation and activity of the hedgehog signal. Science. 2001;293:2080-2084.

     Not in our library10.1126/science.1064437

112. 112.

     Lee JD, Treisman JE. Sightless has homology to transmembrane acyltransferases and is required to generate active Hedgehog protein. Curr. Biol. 2001;11:1147-1152.

     Not in our library10.1016/s0960-9822(01)00323-2

113. 113.

     Micchelli CA, The, Selva I, Mogila E, Perrimon V, Rasp N. a putative transmembrane acyltransferase, is required for Hedgehog signaling. Development. 2002;129:843-851.

     Not in our library10.1242/dev.129.4.843

114. 114.

     Taylor FR, Wen D, Garber EA, Carmillo AN, et al. Enhanced potency of human Sonic hedgehog by hydrophobic modification. Biochemistry. 2001;40:4359-4371.

     Not in our library10.1021/bi002487u

115. 115.

     Hofmann K. A superfamily of membrane-bound O-acyltransferases with implications for wnt signaling. Trends Biochem. Sci. 2000;25:111-112.

     Not in our library10.1016/s0968-0004(99)01539-x

116. 116.

     Miura GI, Buglino J, Alvarado D, Lemmon MA, et al. Palmitoylation of the EGFR ligand Spitz by Rasp increases Spitz activity by restricting its diffusion. Dev. Cell. 2006;10:167-176.

     Not in our library10.1016/j.devcel.2005.11.017

117. 117.

     Miura GI, Treisman JE. Lipid modification of secreted signaling proteins. Cell Cycle. 2006;5:1184-1188.

     Not in our library10.4161/cc.5.11.2804

118. 118.

     Brosius J, Chen R. The primary structure of protein L16 located at the peptidyltransferase center of Escherichia coli ribosomes. FEBS Lett. 1976;68:105-109.

     Not in our library10.1016/0014-5793(76)80415-2

119. 119.

     Chang CN, Schwartz M, Chang FN. Identification and characterization of a new methylated amino acid in ribosomal protein L33 of Escherichia coli. Biochem. Biophys. Res. Commun. 1976;73:233-239.

     Not in our library10.1016/0006-291x(76)90698-7

120. 120.

     Wittmann-Liebold B, Pannenbecker R. Primary structure of protein L33 from the large subunit of the Escherichia coli ribosome. FEBS Lett. 1976;68:115-118.

     Not in our library10.1016/0014-5793(76)80417-6

121. 121.

     Chen T, Muratore TL, Schaner-Tooley CE, Shabanowitz J, et al. N-terminal alpha-methylation of RCC1 is necessary for stable chromatin association and normal mitosis. Nat. Cell Biol. 2007;9:596-U203.

     Not in our library10.1038/ncb1572

122. 122.

     Cai Q, Fu L, Wang Z, Gan N, et al. alpha-N-methylation of damaged DNA-binding protein 2 (DDB2) and its function in nucleotide excision repair. J. Biol. Chem. 2014;289:16046-16056.

     Not in our library10.1074/jbc.m114.558510

123. 123.

     Dai X, Otake K, You C, Cai Q, et al. Identification of novel alpha-n-methylation of CENP-B that regulates its binding to the centromeric DNA. J. Proteome Res. 2013;12:4167-4175.

     Not in our library10.1021/pr400498y

124. 124.

     Kimura Y, Kurata Y, Ishikawa A, Okayama A, et al. N-Terminal methylation of proteasome subunit Rpt1 in yeast. Proteomics. 2013;13:3167-3174.

     Not in our library10.1002/pmic.201300207

125. 125.

     Bailey AO, Panchenko T, Sathyan KM, Petkowski JJ, et al. Posttranslational modification of CENP-A influences the conformation of centromeric chromatin. Proc. Natl. Acad. Sci. USA. 2013;110:11827-11832.

     Not in our library10.1073/pnas.1300325110

126. 126.

     Hao Y, Macara IG. Regulation of chromatin binding by a conformational switch in the tail of the Ran exchange factor RCC1. J. Cell Biol. 2008;182:827-836.

     Not in our library10.1083/jcb.200803110

127. 127.

     Webb KJ, Lipson RS, Al-Hadid Q, Whitelegge JP, Clarke SG. Identification of Protein N-Terminal Methyltransferases in Yeast and Humans. Biochemistry. 2010;49:5225-5235.

     Not in our library10.1021/bi100428x

128. 128.

     Tooley CE, Petkowski JJ, Muratore-Schroeder TL, Balsbaugh JL, et al. NRMT is an alpha-N-methyltransferase that methylates RCC1 and retinoblastoma protein. Nature. 2010;466:1125-1128.

     Not in our library10.1038/nature09343

129. 129.

     Petkowski JJ, Bonsignore LA, Tooley JG, Wilkey DW, et al. NRMT2 is an N-terminal monomethylase that primes for its homologue NRMT1. Biochem. J. 2013;456:453-462.

     Not in our library10.1042/bj20131163

130. 130.

     Petkowski JJ, Schaner Tooley CE, Anderson LC, Shumilin IA, et al. Substrate specificity of mammalian N-terminal alpha-amino methyltransferase NRMT. Biochemistry. 2012;51:5942-5950.

     Not in our library10.1021/bi300278f

131. 131.

     Ciechanover A, Stanhill A. The complexity of recognition of ubiquitinated substrates by the 26S proteasome. Biochim. Biophys. Acta. 2014;1843:86-96.

     Not in our library10.1016/j.bbamcr.2013.07.007

132. 132.

     Varshavsky A. The ubiquitin system, an immense realm. Annu. Rev. Biochem. 2012;81:167-176.

     Not in our library10.1146/annurev-biochem-051910-094049

133. 133.

     Breitschopf K, Bengal E, Ziv T, Admon A, Ciechanover A. A novel site for ubiquitination: the N-terminal residue, and not internal lysines of MyoD, is essential for conjugation and degradation of the protein. EMBO J. 1998;17:5964-5973.

     Not in our library10.1093/emboj/17.20.5964

134. 134.

     Ben-Saadon R, Fajerman I, Ziv T, Hellman U, et al. The tumor suppressor protein p16(INK4a) and the human papillomavirus oncoprotein-58 E7 are naturally occurring lysine-less proteins that are degraded by the ubiquitin system. Direct evidence for ubiquitination at the N-terminal residue. J. Biol. Chem. 2004;279:41414-41421.

     Not in our library10.1074/jbc.m407201200

135. 135.

     Reinstein E, Scheffner M, Oren M, Ciechanover A, Schwartz A. Degradation of the E7 human papillomavirus oncoprotein by the ubiquitin-proteasome system: targeting via ubiquitination of the N-terminal residue. Oncogene. 2000;19:5944-5950.

     Not in our library10.1038/sj.onc.1203989

136. 136.

     Aviel S, Winberg G, Massucci M, Ciechanover A. Degradation of the epstein-barr virus latent membrane protein 1 (LMP1) by the ubiquitin-proteasome pathway. Targeting via ubiquitination of the N-terminal residue. J. Biol. Chem. 2000;275:23491-23499.

     Not in our library10.1074/jbc.m002052200

137. 137.

     Ikeda M, Ikeda A, Longnecker R. Lysine-independent ubiquitination of Epstein-Barr virus LMP2A. Virology. 2002;300:153-159.

     Not in our library10.1006/viro.2002.1562

138. 138.

     Coulombe P, Rodier G, Bonneil E, Thibault P, Meloche S. N-Terminal ubiquitination of extracellular signal-regulated kinase 3 and p21 directs their degradation by the proteasome. Mol, Cell. Biol. 2004;24:6140-6150.

     Not in our library10.1128/mcb.24.14.6140-6150.2004

139. 139.

     Bloom J, Amador V, Bartolini F, DeMartino G, Pagano M. Proteasome-mediated degradation of p21 via N-terminal ubiquitinylation. Cell. 2003;115:71-82.

     Not in our library10.1016/s0092-8674(03)00755-4

140. 140.

     Fajerman I, Schwartz AL, Ciechanover A. Degradation of the Id2 developmental regulator: targeting via N-terminal ubiquitination. Biochem. Biophys. Res. Commun. 2004;314:505-512.

     Not in our library10.1016/j.bbrc.2003.12.116

141. 141.

     Trausch-Azar JS, Lingbeck J, Ciechanover A, Schwartz AL. Ubiquitin-Proteasome-mediated degradation of Id1 is modulated by MyoD. J. Biol. Chem. 2004;279:32614-32619.

     Not in our library10.1074/jbc.m403794200

142. 142.

     Scaglione KM, Basrur V, Ashraf NS, Konen JR, et al. The ubiquitin-conjugating enzyme (E2) Ube2w ubiquitinates the N terminus of substrates. J. Biol. Chem. 2013;288:18784-18788.

     Not in our library10.1074/jbc.c113.477596

143. 143.

     Tatham MH, Plechanovova A, Jaffray EG, Salmen H, Hay RT. Ube2W conjugates ubiquitin to alpha-amino groups of protein N-termini. Biochem. J. 2013;453:137-145.

     Not in our library10.1042/bj20130244

144. 144.

     Noy T, Suad O, Taglicht D, Ciechanover A. HUWE1 ubiquitinates MyoD and targets it for proteasomal degradation. Biochem. Biophys. Res. Commun. 2012;418:408-413.

     Not in our library10.1016/j.bbrc.2012.01.045

145. 145.

     Vittal V, Shi L, Wenzel DM, Scaglione KM, et al. Intrinsic disorder drives N-terminal ubiquitination by Ube2w. Nat. Chem. Biol. 2015;11:83-89.

     Not in our library10.1038/nchembio.1700

146. 146.

     Bachmair A, Finley D, Varshavsky A. In vivo half-life of a protein is a function of its amino-terminal residue. Science. 1986;234:179-186.

     Not in our library10.1126/science.3018930

147. 147.

     Varshavsky A. The N-end rule: functions, mysteries, uses. Proc. Natl. Acad. Sci. USA. 1996;93:12142-12149.

     Not in our library10.1073/pnas.93.22.12142

148. 148.

     Bachmair A, Varshavsky A. The degradation signal in a short-lived protein. Cell. 1989;56:1019-1032.

     Not in our library10.1016/0092-8674(89)90635-1

149. 149.

     Gibbs DJ, Bacardit J, Bachmair A, Holdsworth MJ. The eukaryotic N-end rule pathway: conserved mechanisms and diverse functions. Trends Cell Biol. 2014;24:603-611.

     Not in our library10.1016/j.tcb.2014.05.001

150. 150.

     Varshavsky A. The N-end rule pathway and regulation by proteolysis. Protein Sci. 2011;20:1298-1345.

     Not in our library10.1002/pro.666

151. 151.

     Kim HK, Kim RR, Oh JH, Cho H, et al. The N-terminal methionine of cellular proteins as a degradation signal. Cell. 2014;156:158-169.

     Not in our library10.1016/j.cell.2013.11.031

152. 152.

     Hwang CS, Shemorry A, Varshavsky A. N-terminal acetylation of cellular proteins creates specific degradation signals. Science. 2010;327:973-977.

     Not in our library10.1126/science.1183147

153. 153.

     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;50:540-551.

     Not in our library10.1016/j.molcel.2013.03.018

154. 154.

     Tasaki T, Sriram SM, Park KS, Kwon YT. The N-end rule pathway. Annu. Rev. Biochem. 2012;81:261-289.

     Not in our library10.1146/annurev-biochem-051710-093308

155. 155.

     Giglione C, Vallon O, Meinnel T. Control of protein life-span by N-terminal methionine excision. EMBO J. 2003;22:13-23.

     Not in our library10.1093/emboj/cdg007

156. 156.

     Behnia R, Panic B, Whyte JR, Munro S. Targeting of the Arf-like GTPase Arl3p to the Golgi requires N-terminal acetylation and the membrane protein Sys1p. Nat. Cell Biol. 2004;6:405-413.

     Not in our library10.1038/ncb1120

157. 157.

     Murthi A, Hopper AK. Genome-wide screen for inner nuclear membrane protein targeting in Saccharomyces cerevisiae: roles for N-acetylation and an integral membrane protein. Genetics. 2005;170:1553-1560.

     Not in our library10.1534/genetics.105.043620

158. 158.

     Setty SR, Strochlic TI, Tong AH, Boone C, Burd CG. Golgi targeting of ARF-like GTPase Arl3p requires its Nalpha-acetylation and the integral membrane protein Sys1p. Nat. Cell Biol. 2004;6:414-419.

     Not in our library10.1038/ncb1121

159. 159.
     N-Terminal Acetylation Inhibits Protein Targeting to the Endoplasmic Reticulum · 2011

     No notice
160. 160.

     Scott DC, Monda JK, Bennett EJ, Harper JW, Schulman BA. N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex. Science. 2011;334:674-678.

     Not in our library10.1126/science.1209307

161. 161.

     Urbancikova M, Hitchcock-DeGregori SE. Requirement of amino-terminal modification for striated muscle alpha-tropomyosin function. J. Biol. Chem. 1994;269:24310-24315.

     Not in our library

162. 162.

     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.

     Not in our library10.1038/ncomms5383

163. 163.

     Arnesen T, Starheim KK, Van Damme P, Evjenth R, et al. The chaperone-like protein HYPK acts together with NatA in cotranslational N-terminal acetylation and prevention of Huntingtin aggregation. Mol, Cell. Biol. 2010;30:1898-1909.

     Not in our library10.1128/mcb.01199-09

164. 164.

     Dikiy I, Eliezer D. N-terminal acetylation stabilizes N-terminal helicity in lipid- and micelle-bound alpha-synuclein and increases its affinity for physiological membranes. J. Biol. Chem. 2014;289:3652-3665.

     Not in our library10.1074/jbc.m113.512459

165. 165.

     Myklebust LM, Van Damme P, Stove SI, Dorfel MJ, et al. Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects. Human Mol. Genet. 2015;24:1956-1976.

     Not in our library10.1093/hmg/ddu611

166. 166.

     Rope AF, Wang K, Evjenth R, Xing J, et al. Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am. J. Human Genet. 2011;89:28-43.

     Not in our library10.1016/j.ajhg.2011.05.017

167. 167.

     Popp B, Stove SI, Endele S, Myklebust LM, et al. De novo missense mutations in the NAA10 gene cause severe non-syndromic developmental delay in males and females. Eur. J. Human Genet. 2015;23:602-609.

     Not in our library10.1038/ejhg.2014.150

168. 168.

     Esmailpour T, Riazifar H, Liu L, Donkervoort S, et al. A splice donor mutation in NAA10 results in the dysregulation of the retinoic acid signalling pathway and causes Lenz microphthalmia syndrome. J. Med. Genet. 2014;51:185-196.

     Not in our library10.1136/jmedgenet-2013-101660

169. 169.

     Kalvik TV, Arnesen T. Protein N-terminal acetyltransferases in cancer. Oncogene. 2013;32:269-276.

     Not in our library10.1038/onc.2012.82

170. 170.

     Foyn H, Jones JE, Lewallen D, Narawane R, et al. Design, synthesis, and kinetic characterization of protein N-terminal acetyltransferase inhibitors. ACS Chem. Biol. 2013;8:1121-1127.

     Not in our library10.1021/cb400136s

171. 171.

     Silva DR, Martinho RG. Developmental roles of Protein N-terminal acetylation. Proteomics. 2015;15:2402-2409.

     Not in our library10.1002/pmic.201400631

172. 172.

     Dawber RJ, Hebbes S, Herpers B, Docquier F, van den Heuvel M. Differential range and activity of various forms of the Hedgehog protein. BMC Dev. Biol. 2005;5:21.

     Not in our library10.1186/1471-213x-5-21

173. 173.

     Lee JD, Kraus P, Gaiano N, Nery S, et al. An acylatable residue of Hedgehog is differentially required in Drosophila and mouse limb development. Dev. Biol. 2001;233:122-136.

     Not in our library10.1006/dbio.2001.0218

174. 174.

     Pasca di Magliano M, Hebrok M. Hedgehog signalling in cancer formation and maintenance. Nat. Rev. Cancer. 2003;3:903-911.

     Not in our library10.1038/nrc1229

175. 175.

     Hayashi N, Titani K. N-myristoylated proteins, key components in intracellular signal transduction systems enabling rapid and flexible cell responses. Proc. Jpn. Acad. Ser. B Phys. Biol. Sci. 2010;86:494-508.

     Not in our library10.2183/pjab.86.494

176. 176.

     Resh MD. Fatty acylation of proteins: new insights into membrane targeting of myristoylated and palmitoylated proteins. Biochim. Biophys. Acta. 1999;1451:1-16.

     Not in our library10.1016/s0167-4889(99)00075-0

177. 177.

     Yin G, Ji C, Wu T, Shen Z, et al. Cloning, characterization and subcellular localization of a gene encoding a human Ubiquitin-conjugating enzyme (E2) homologous to the Arabidopsis thaliana UBC-16 gene product. Front. Biosci. 2006;11:1500-1507.

     Not in our library10.2741/1899

178. 178.

     Gao J, Aksoy BA, Dogrusoz U, Dresdner G, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci. Signal. 2013;6:p11.

     Not in our library10.1126/scisignal.2004088

179. 179.

     Mittag T, Marzahn MR. Protein disorder: wagging a tail at ubiquitin. Nat. Chem. Biol. 2015;11:7-8.

     Not in our library10.1038/nchembio.1716

180. 180.

     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.

     Not in our library10.1371/journal.pgen.1003805

181. 181.

     Utsumi T, Sato M, Nakano K, Takemura D, et al. Amino acid residue penultimate to the amino-terminal gly residue strongly affects two cotranslational protein modifications, N-myristoylation and N-acetylation. J. Biol. Chem. 2001;276:10505-10513.

     Not in our library10.1074/jbc.m006134200

182. 182.

     Van Damme P, Hole K, Gevaert K, Arnesen T. N-terminal acetylome analysis reveals the specificity of Naa50 (Nat5) and suggests a kinetic competition between N-terminal acetyltransferases and methionine aminopeptidases. Proteomics. 2015;15:2436-2446.

     Not in our library10.1002/pmic.201400575

Cited by papers we hold 2

• Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications · 2023
  No notice
• Spotlight on protein N-terminal acetylation · 2018
  No notice

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