1
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Gaddelapati SC, George S, Moola A, Sengodan K, Palli SR. N(alpha)-acetyltransferase 40-mediated histone acetylation plays an important role in ecdysone regulation of metamorphosis in the red flour beetle, Tribolium castaneum. Commun Biol 2024; 7:521. [PMID: 38702540 PMCID: PMC11068786 DOI: 10.1038/s42003-024-06212-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 04/18/2024] [Indexed: 05/06/2024] Open
Abstract
Histone acetylation, a crucial epigenetic modification, is governed by histone acetyltransferases (HATs), that regulate many biological processes. Functions of HATs in insects are not well understood. We identified 27 HATs and determined their functions using RNA interference (RNAi) in the model insect, Tribolium castaneum. Among HATs studied, N-alpha-acetyltransferase 40 (NAA40) knockdown caused a severe phenotype of arrested larval development. The steroid hormone, ecdysone induced NAA40 expression through its receptor, EcR (ecdysone receptor). Interestingly, ecdysone-induced NAA40 regulates EcR expression. NAA40 acetylates histone H4 protein, associated with the promoters of ecdysone response genes: EcR, E74, E75, and HR3, and causes an increase in their expression. In the absence of ecdysone and NAA40, histone H4 methylation by arginine methyltransferase 1 (ART1) suppressed the above genes. However, elevated ecdysone levels at the end of the larval period induced NAA40, promoting histone H4 acetylation and increasing the expression of ecdysone response genes. NAA40 is also required for EcR, and steroid-receptor co-activator (SRC) mediated induction of E74, E75, and HR3. These findings highlight the key role of ecdysone-induced NAA40-mediated histone acetylation in the regulation of metamorphosis.
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Affiliation(s)
- Sharath Chandra Gaddelapati
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Smitha George
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Anilkumar Moola
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Karthi Sengodan
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Subba Reddy Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA.
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2
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Fernández E, Bogaert A, Timmerman E, Staes A, Impens F, Gevaert K. A Strong Cation Exchange Chromatography Protocol for Examining N-Terminal Proteoforms. Methods Mol Biol 2022; 2477:293-309. [PMID: 35524124 DOI: 10.1007/978-1-0716-2257-5_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Especially in eukaryotes, the N-terminal acetylation status of a protein reveals translation initiation sites and substrate specificities and activities of N-terminal acetyltransferases (NATs). Here, we discuss a bottom-up proteomics protocol for the enrichment of N-terminal peptides via strong cation exchange chromatography. This protocol is based on depleting internal tryptic peptides from proteome digests through their retention on strong cation exchangers, leaving N-terminally acetylated/blocked peptides enriched among the nonretained peptides. As such, one can identify novel N-terminal proteoforms and quantify the degree of N-terminal protein acetylation.
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Affiliation(s)
- Esperanza Fernández
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Annelies Bogaert
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Evy Timmerman
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - An Staes
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Francis Impens
- VIB Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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3
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Van Damme P. Charting the N-Terminal Acetylome: A Comprehensive Map of Human NatA Substrates. Int J Mol Sci 2021; 22:ijms221910692. [PMID: 34639033 PMCID: PMC8509067 DOI: 10.3390/ijms221910692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/10/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
N-terminal acetylation (Nt-acetylation) catalyzed by conserved N-terminal acetyltransferases or NATs embodies a modification with one of the highest stoichiometries reported for eukaryotic protein modifications to date. Comprising the catalytic N-alpha acetyltransferase (NAA) subunit NAA10 plus the ribosome anchoring regulatory subunit NAA15, NatA represents the major acetyltransferase complex with up to 50% of all mammalian proteins representing potential substrates. Largely in consequence of the essential nature of NatA and its high enzymatic activity, its experimentally confirmed mammalian substrate repertoire remained poorly charted. In this study, human NatA knockdown conditions achieving near complete depletion of NAA10 and NAA15 expression resulted in lowered Nt-acetylation of over 25% out of all putative NatA targets identified, representing an up to 10-fold increase in the reported number of substrate N-termini affected upon human NatA perturbation. Besides pointing to less efficient NatA substrates being prime targets, several putative NatE substrates were shown to be affected upon human NatA knockdown. Intriguingly, next to a lowered expression of ribosomal proteins and proteins constituting the eukaryotic 48S preinitiation complex, steady-state levels of protein N-termini additionally point to NatA Nt-acetylation deficiency directly impacting protein stability of knockdown affected targets.
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Affiliation(s)
- Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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4
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Jonckheere V, Van Damme P. N-Terminal Acetyltransferase Naa40p Whereabouts Put into N-Terminal Proteoform Perspective. Int J Mol Sci 2021; 22:ijms22073690. [PMID: 33916271 PMCID: PMC8037211 DOI: 10.3390/ijms22073690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/28/2021] [Accepted: 03/28/2021] [Indexed: 11/21/2022] Open
Abstract
The evolutionary conserved N-alpha acetyltransferase Naa40p is among the most selective N-terminal acetyltransferases (NATs) identified to date. Here we identified a conserved N-terminally truncated Naa40p proteoform named Naa40p25 or short Naa40p (Naa40S). Intriguingly, although upon ectopic expression in yeast, both Naa40p proteoforms were capable of restoring N-terminal acetylation of the characterized yeast histone H2A Naa40p substrate, the Naa40p histone H4 substrate remained N-terminally free in human haploid cells specifically deleted for canonical Naa40p27 or 237 amino acid long Naa40p (Naa40L), but expressing Naa40S. Interestingly, human Naa40L and Naa40S displayed differential expression and subcellular localization patterns by exhibiting a principal nuclear and cytoplasmic localization, respectively. Furthermore, Naa40L was shown to be N-terminally myristoylated and to interact with N-myristoyltransferase 1 (NMT1), implicating NMT1 in steering Naa40L nuclear import. Differential interactomics data obtained by biotin-dependent proximity labeling (BioID) further hints to context-dependent roles of Naa40p proteoforms. More specifically, with Naa40S representing the main co-translationally acting actor, the interactome of Naa40L was enriched for nucleolar proteins implicated in ribosome biogenesis and the assembly of ribonucleoprotein particles, overall indicating a proteoform-specific segregation of previously reported Naa40p activities. Finally, the yeast histone variant H2A.Z and the transcriptionally regulatory protein Lge1 were identified as novel Naa40p substrates, expanding the restricted substrate repertoire of Naa40p with two additional members and further confirming Lge1 as being the first redundant yNatA and yNatD substrate identified to date.
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5
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N α-terminal acetylation of proteins by NatA and NatB serves distinct physiological roles in Saccharomyces cerevisiae. Cell Rep 2021; 34:108711. [PMID: 33535049 DOI: 10.1016/j.celrep.2021.108711] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 10/10/2020] [Accepted: 01/09/2021] [Indexed: 11/22/2022] Open
Abstract
N-terminal (Nt) acetylation is a highly prevalent co-translational protein modification in eukaryotes, catalyzed by at least five Nt acetyltransferases (Nats) with differing specificities. Nt acetylation has been implicated in protein quality control, but its broad biological significance remains elusive. We investigate the roles of the two major Nats of S. cerevisiae, NatA and NatB, by performing transcriptome, translatome, and proteome profiling of natAΔ and natBΔ mutants. Our results reveal a range of NatA- and NatB-specific phenotypes. NatA is implicated in systemic adaptation control, because natAΔ mutants display altered expression of transposons, sub-telomeric genes, pheromone response genes, and nuclear genes encoding mitochondrial ribosomal proteins. NatB predominantly affects protein folding, because natBΔ mutants, to a greater extent than natA mutants, accumulate protein aggregates, induce stress responses, and display reduced fitness in the absence of the ribosome-associated chaperone Ssb. These phenotypic differences indicate that controlling Nat activities may serve to elicit distinct cellular responses.
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6
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Weidenhausen J, Kopp J, Armbruster L, Wirtz M, Lapouge K, Sinning I. Structural and functional characterization of the N-terminal acetyltransferase Naa50. Structure 2021; 29:413-425.e5. [PMID: 33400917 DOI: 10.1016/j.str.2020.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/28/2020] [Accepted: 12/08/2020] [Indexed: 10/22/2022]
Abstract
The majority of eukaryotic proteins is modified by N-terminal acetylation, which plays a fundamental role in protein homeostasis, localization, and complex formation. N-terminal acetyltransferases (NATs) mainly act co-translationally on newly synthesized proteins at the ribosomal tunnel exit. NatA is the major NAT consisting of Naa10 catalytic and Naa15 auxiliary subunits, and with Naa50 forms the NatE complex. Naa50 has recently been identified in Arabidopsis thaliana and is important for plant development and stress response regulation. Here, we determined high-resolution X-ray crystal structures of AtNaa50 in complex with AcCoA and a bisubstrate analog. We characterized its substrate specificity, determined its enzymatic parameters, and identified functionally important residues. Even though Naa50 is conserved among species, we highlight differences between Arabidopsis and yeast, where Naa50 is catalytically inactive but binds CoA conjugates. Our study provides insights into Naa50 conservation, species-specific adaptations, and serves as a basis for further studies of NATs in plants.
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Affiliation(s)
| | - Jürgen Kopp
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Laura Armbruster
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany.
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7
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Mueller F, Friese A, Pathe C, da Silva RC, Rodriguez KB, Musacchio A, Bange T. Overlap of NatA and IAP substrates implicates N-terminal acetylation in protein stabilization. SCIENCE ADVANCES 2021; 7:7/3/eabc8590. [PMID: 33523899 PMCID: PMC7810383 DOI: 10.1126/sciadv.abc8590] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/24/2020] [Indexed: 05/15/2023]
Abstract
SMAC/DIABLO and HTRA2 are mitochondrial proteins whose amino-terminal sequences, known as inhibitor of apoptosis binding motifs (IBMs), bind and activate ubiquitin ligases known as inhibitor of apoptosis proteins (IAPs), unleashing a cell's apoptotic potential. IBMs comprise a four-residue, loose consensus sequence, and binding to IAPs requires an unmodified amino terminus. Closely related, IBM-like N termini are present in approximately 5% of human proteins. We show that suppression of the N-alpha-acetyltransferase NatA turns these cryptic IBM-like sequences into very efficient IAP binders in cell lysates and in vitro and ultimately triggers cellular apoptosis. Thus, amino-terminal acetylation of IBM-like motifs in NatA substrates shields them from IAPs. This previously unrecognized relationship suggests that amino-terminal acetylation is generally protective against protein degradation in human cells. It also identifies IAPs as agents of a general quality control mechanism targeting unacetylated rogues in metazoans.
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Affiliation(s)
- Franziska Mueller
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Alexandra Friese
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Claudio Pathe
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Richard Cardoso da Silva
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Kenny Bravo Rodriguez
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany.
- Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
| | - Tanja Bange
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany.
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich
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8
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Jazurek-Ciesiolka M, Ciesiolka A, Komur AA, Urbanek-Trzeciak MO, Krzyzosiak WJ, Fiszer A. RAN Translation of the Expanded CAG Repeats in the SCA3 Disease Context. J Mol Biol 2020; 432:166699. [PMID: 33157084 DOI: 10.1016/j.jmb.2020.10.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 01/08/2023]
Abstract
Spinocerebellar ataxia type 3 (SCA3) is a progressive neurodegenerative disorder caused by a CAG repeat expansion in the ATXN3 gene encoding the ataxin-3 protein. Despite extensive research the exact pathogenic mechanisms of SCA3 are still not understood in depth. In the present study, to gain insight into the toxicity induced by the expanded CAG repeats in SCA3, we comprehensively investigated repeat-associated non-ATG (RAN) translation in various cellular models expressing translated or non-canonically translated ATXN3 sequences with an increasing number of CAG repeats. We demonstrate that two SCA3 RAN proteins, polyglutamine (polyQ) and polyalanine (polyA), are found only in the case of CAG repeats of pathogenic length. Despite having distinct cellular localization, RAN polyQ and RAN polyA proteins are very often coexpressed in the same cell, impairing nuclear integrity and inducing apoptosis. We provide for the first time mechanistic insights into SCA3 RAN translation indicating that ATXN3 sequences surrounding the repeat region have an impact on SCA3 RAN translation initiation and efficiency. We revealed that RAN translation of polyQ proteins starts at non-cognate codons upstream of the CAG repeats, whereas RAN polyA proteins are likely translated within repeats. Furthermore, integrated stress response activation enhances SCA3 RAN translation. Our findings suggest that the ATXN3 sequence context plays an important role in triggering SCA3 RAN translation and that SCA3 RAN proteins may cause cellular toxicity.
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Affiliation(s)
- Magdalena Jazurek-Ciesiolka
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Adam Ciesiolka
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Alicja A Komur
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Martyna O Urbanek-Trzeciak
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Agnieszka Fiszer
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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9
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Kemp PR, Paul R, Hinken AC, Neil D, Russell A, Griffiths MJ. Metabolic profiling shows pre-existing mitochondrial dysfunction contributes to muscle loss in a model of ICU-acquired weakness. J Cachexia Sarcopenia Muscle 2020; 11:1321-1335. [PMID: 32677363 PMCID: PMC7567140 DOI: 10.1002/jcsm.12597] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 05/01/2020] [Accepted: 05/27/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Surgery can lead to significant muscle loss, which increases recovery time and associates with increased mortality. Muscle loss is not uniform, with some patients losing significant muscle mass and others losing relatively little, and is likely to be accompanied by marked changes in circulating metabolites and proteins. Determining these changes may help understand the variability and identify novel therapeutic approaches or markers of muscle wasting. METHODS To determine the association between muscle loss and circulating metabolites, we studied 20 male patients (median age, 70.5, interquartile range, 62.5-75) undergoing aortic surgery. Muscle mass was determined before and 7 days after surgery and blood samples were taken before surgery, and 1, 3, and 7 days after surgery. The circulating metabolome and proteome were determined using commercial services (Metabolon and SomaLogic). RESULTS Ten patients lost more than 10% of the cross-sectional area of the rectus femoris (RFCSA ) and were defined as wasting. Metabolomic analysis showed that 557 circulating metabolites were altered following surgery (q < 0.05) in the whole cohort and 104 differed between wasting and non-wasting patients (q < 0.05). Weighted genome co-expression network analysis, identified clusters of metabolites, both before and after surgery, that associated with muscle mass and function (r = -0.72, p = 6 × 10-4 with RFCSA on Day 0, P = 3 × 10-4 with RFCSA on Day 7 and r = -0.73, P = 5 × 10-4 with hand-grip strength on Day 7). These clusters were mainly composed of acyl carnitines and dicarboxylates indicating that pre-existing mitochondrial dysfunction contributes to muscle loss following surgery. Surgery elevated cortisol to the same extent in wasting and non-wasting patients, but the cortisol:cortisone ratio was higher in the wasting patients (Day 3 P = 0.043 and Day 7 P = 0.016). Wasting patients also showed a greater increase in circulating nucleotides 3 days after surgery. Comparison of the metabolome with inflammatory markers identified by SOMAscan® showed that pre-surgical mitochondrial dysfunction was associated with growth differentiation factor 15 (GDF-15) (r = 0.79, P = 2 × 10-4 ) and that GDF-15, interleukin (IL)-8), C-C motif chemokine 23 (CCL-23), and IL-15 receptor subunit alpha (IL-15RA) contributed to metabolic changes in response to surgery. CONCLUSIONS We show that pre-existing mitochondrial dysfunction and reduced cortisol inactivation contribute to muscle loss following surgery. The data also implicate GDF-15 and IL-15RA in mitochondrial dysfunction.
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Affiliation(s)
- Paul R Kemp
- Cardiovascular and Respiratory Interface Section, National Heart and Lung Institute, Imperial College London, South Kensington Campus, London, UK
| | - Richard Paul
- Cardiovascular and Respiratory Interface Section, National Heart and Lung Institute, Imperial College London, South Kensington Campus, London, UK.,Department of Intensive Care, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Aaron C Hinken
- Muscle Metabolism Discovery Performance Unit, GlaxoSmithKline, Inc, Collegeville, PA, USA
| | - David Neil
- Muscle Metabolism Discovery Performance Unit, GlaxoSmithKline, Inc, Collegeville, PA, USA
| | - Alan Russell
- Muscle Metabolism Discovery Performance Unit, GlaxoSmithKline, Inc, Collegeville, PA, USA.,Edgewise Therapeutics, Boulder, CO, USA
| | - Mark J Griffiths
- Cardiovascular and Respiratory Interface Section, National Heart and Lung Institute, Imperial College London, South Kensington Campus, London, UK
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10
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Du X, Lu J, Yang L, Bao H, Zhang L, Yan G, Fang C, Lu H. Rapid and Easy Enrichment Strategy for Naturally Acetylated N Termini Based on LysN Digestion and Amine-Reactive Resin Capture. Anal Chem 2020; 92:8315-8322. [PMID: 32433867 DOI: 10.1021/acs.analchem.0c00695] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein N-terminal acetylation (Nα-acetylation) is one of the most common modifications in both eukaryotes and prokaryotes. Although studies have shown that Nα-acetylation plays important roles in protein assembly, stability, and location, the physiological role has not been fully elucidated. Therefore, a robust and large-scale analytical method is important for a better understanding of Nα-acetylation. Here, an enrichment strategy was presented based on LysN digestion and amine-reactive resin capture to study naturally acetylated protein N termini. Since LysN protease cleaves at the amino-terminus of the lysine residue, all resulting peptides except naturally acetylated N-terminal peptides contain free amino groups and can be removed by coupling with AminoLink Resin. Therefore, the naturally acetylated N-terminal peptides were left in solution and enriched for further liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. The method was very simple and fast, which contained no additional chemical derivatization except protein reduction and alkylation necessarily needed in bottom-up proteomics. It could be used to study acetylated N termini from complex biological samples without bias toward different peptides with various physicochemical properties. The enrichment specificity was above 99% when it was applied in HeLa cell lysates. Neo-N termini generated by endogenous degradation could be directly distinguished without the use of stable-isotope labeling because no chemical derivatization was introduced in this method. Furthermore, this method was highly complementary to the traditional analytical methods for protein N termini based on trypsin only with ArgC-like activity. Therefore, the described method was beneficial to naturally acetylated protein N termini profiling.
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Affiliation(s)
- Xiaoxian Du
- Fudan University Shanghai Cancer Center and Department of Chemistry, Fudan University, Shanghai 200032, P.R. China.,Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Jingtian Lu
- Fudan University Shanghai Cancer Center and Department of Chemistry, Fudan University, Shanghai 200032, P.R. China.,Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Lijun Yang
- Fudan University Shanghai Cancer Center and Department of Chemistry, Fudan University, Shanghai 200032, P.R. China.,Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Huimin Bao
- Fudan University Shanghai Cancer Center and Department of Chemistry, Fudan University, Shanghai 200032, P.R. China
| | - Lei Zhang
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Guoquan Yan
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Caiyun Fang
- Fudan University Shanghai Cancer Center and Department of Chemistry, Fudan University, Shanghai 200032, P.R. China
| | - Haojie Lu
- Fudan University Shanghai Cancer Center and Department of Chemistry, Fudan University, Shanghai 200032, P.R. China.,Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China.,NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P.R. China
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11
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Lapteva YS, Vologzhannikova AA, Sokolov AS, Ismailov RG, Uversky VN, Permyakov SE. In Vitro N-Terminal Acetylation of Bacterially Expressed Parvalbumins by N-Terminal Acetyltransferases from Escherichia coli. Appl Biochem Biotechnol 2020; 193:1365-1378. [PMID: 32394317 DOI: 10.1007/s12010-020-03324-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/23/2020] [Indexed: 11/28/2022]
Abstract
Most eukaryotic proteins are N-terminally acetylated (Nt-acetylated) by specific N-terminal acetyltransferases (NATs). Although this co-/post-translational protein modification may affect different aspects of protein functioning, it is typically neglected in studies of bacterially expressed eukaryotic proteins, lacking this modification. To overcome this limitation of bacterial expression, we have probed the efficiency of recombinant Escherichia coli NATs (RimI, RimJ, and RimL) with regard to in vitro Nt-acetylation of several parvalbumins (PAs) expressed in E. coli. PA is a calcium-binding protein of vertebrates, which is sensitive to Nt-acetylation. Our analyses revealed that only metal-free PAs were prone to Nt-acetylation (up to 100%), whereas Ca2+ binding abolished this modification, thereby indicating that Ca2+-induced structural stabilization of PAs impedes their Nt-acetylation. RimJ and RimL were active towards all PAs with N-terminal serine. Their activity towards PAs beginning with alanine was PA-specific, suggesting the importance of the subsequent residues. RimI showed the least activity regardless of the PA studied. Overall, NATs from E. coli are suited for post-translational Nt-acetylation of bacterially expressed eukaryotic proteins with decreased structural stability.
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Affiliation(s)
- Yulia S Lapteva
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russia.
| | - Alisa A Vologzhannikova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russia
| | - Andrey S Sokolov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russia
| | - Ramis G Ismailov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russia
| | - Vladimir N Uversky
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russia. .,Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| | - Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russia
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12
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Li L, Yan G, Zhang X. A rapid and efficient method for N-termini analysis in short-lived proteins. Talanta 2019; 204:367-371. [DOI: 10.1016/j.talanta.2019.06.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 06/02/2019] [Accepted: 06/08/2019] [Indexed: 02/05/2023]
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13
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Abstract
Protein α‐N‐terminal methylation is catalyzed by protein N‐terminal methyltransferases. The prevalent occurrence of this methylation in ribosomes, myosin, and histones implies its function in protein–protein interactions. Although its full spectrum of function has not yet been outlined, recent discoveries have revealed the emerging roles of α‐N‐terminal methylation in protein–chromatin interactions, DNA damage repair, and chromosome segregation. Herein, an overview of the discovery of protein N‐terminal methyltransferases and functions of α‐N‐terminal methylation is presented. In addition, substrate recognition, mechanisms, and inhibition of N‐terminal methyltransferases are reviewed. Opportunities and gaps in protein α‐N‐terminal methylation are also discussed.
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Affiliation(s)
- Rong Huang
- Department of Medicinal Chemistry and Molecular PharmacologyCenter for Cancer Research, Institute for Drug DiscoveryPurdue University West Lafayette IN 47907 USA
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14
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Kaushal P, Kwon Y, Ju S, Lee C. An SDS-PAGE based proteomic approach for N-terminome profiling. Analyst 2019; 144:7001-7009. [DOI: 10.1039/c9an01616c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Schematic diagram of the SDS-PAGE based N-termini enrichment (GelNrich) workflow.
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Affiliation(s)
- Prashant Kaushal
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Division of Bio-Medical Science & Technology
| | - Yumi Kwon
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Department of Life Science and Research Institute for Natural Sciences
| | - Shinyeong Ju
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Department of Life Science and Research Institute for Natural Sciences
| | - Cheolju Lee
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Division of Bio-Medical Science & Technology
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15
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Abstract
Fatty acid amides represent a diverse and underappreciated family of lipids found in vertebrates and invertebrates. The most recognized, most studied, and best understood members of the fatty acid amide family are N-arachidonoylethanolamine (anandamide) and oleamide. Over 70 other fatty acid amides have been identified from biological systems and these non-anandamide and non-oleamide fatty acid amides are not well understood: their cellular functions, transport, biosynthesis, and degradation are, at best, partially elucidated. Most of the fatty acid amides are “orphan” ligands for “orphan” or unknown receptors. Interest in the fatty acid amides will wane without a more complete understanding of their function in vivo and most of these lipids will be mentioned in a few sentences in reviews on ananamide and/or olemide. In this commentary, we suggest that one strategy to dramatically increase our understanding of any member of the fatty acid amide family is the design, synthesis, and proper use of binding-based profiling probes (BBPPs) based on the structure of a specific fatty acid amide. A BBPP is an analog of a fatty acid amide that enables the controlled covalent attachment of the probe to a fatty acid amide-binding protein and, also, possesses a chemical moiety that will allow the purification and/or detection of the BBPP-labeled proteins. The identification of the proteins that specifically bind a fatty acid amide will foster a better understanding of the function, transport, and metabolism of a fatty acid amide.
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Affiliation(s)
- David J Merkler
- Department of Chemistry, University of South Florida, Tampa, FL, USA
| | - James W Leahy
- Department of Chemistry, University of South Florida, Tampa, FL, USA.,Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL USA.,Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL USA
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16
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Thompson CR, Champion MM, Champion PA. Quantitative N-Terminal Footprinting of Pathogenic Mycobacteria Reveals Differential Protein Acetylation. J Proteome Res 2018; 17:3246-3258. [PMID: 30080413 DOI: 10.1021/acs.jproteome.8b00373] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
N-terminal acetylation (NTA) is a post-transcriptional modification of proteins that is conserved from bacteria to humans. In bacteria, the enzymes that mediate protein NTA also promote antimicrobial resistance. In pathogenic mycobacteria, which cause human tuberculosis and other chronic infections, NTA has been linked to pathogenesis and stress response, yet the fundamental biology underlying NTA of mycobacterial proteins remains unclear. We enriched, defined, and quantified the NT-acetylated populations of both cell-associated and secreted proteins from both the human pathogen, Mycobacterium tuberculosis, and the nontuberculous opportunistic pathogen, Mycobacterium marinum. We used a parallel N-terminal enrichment strategy from proteolytic digests coupled to charge-based selection and stable isotope ratio mass spectrometry. We show that NTA of the mycobacterial proteome is abundant, diverse, and primarily on Thr residues, which is unique compared with other bacteria. We isolated both the acetylated and unacetylated forms of 256 proteins, indicating that NTA of mycobacterial proteins is homeostatic. We identified 16 mycobacterial proteins with differential levels of NTA on the cytoplasmic and secreted forms, linking protein modification and localization. Our findings reveal novel biology underlying the NTA of mycobacterial proteins, which may provide a basis to understand NTA in mycobacterial physiology, pathogenesis, and antimicrobial resistance.
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17
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Ahmed MS, Shahjaman M, Kabir E, Kamruzzaman M. Prediction of Protein Acetylation Sites using Kernel Naive Bayes Classifier Based on Protein Sequences Profiling. Bioinformation 2018; 14:213-218. [PMID: 30108418 PMCID: PMC6077816 DOI: 10.6026/97320630014213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 04/29/2018] [Accepted: 04/29/2018] [Indexed: 12/11/2022] Open
Abstract
Lysine acetylation is one of the decisive categories of protein post-translational modification (PTM), it is convoluted in many significant cellular developments and severe diseases in the biological system. The experimental identification of protein-acetylated sites is painstaking, time-consuming and expensive. Hence, there is significant interest in the development of computational approaches for consistent prediction of acetylation sites using protein sequences. Features selection from protein sequences plays a significant role for acetylation sites prediction. We describe an improved feature selection approach for acetylation sites prediction based on kernel naive Bayes classifier (KNBC). We have shown that KNBC generated from selected features by a new feature selection method outperforms than the existing methods for identification of acetylation sites. The sensitivity, specificity, ACC (Accuracy), MCC (Matthews Correlation Coefficient) and AUC (Area under Curve of ROC) in our proposed method are as follows 80.71%, 93.39%, 76.73%, 41.37% and 83.0% with the optimum window size is 47. Thus the kernel naive Bayes classifier finds application in acetylation site prediction.
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Affiliation(s)
- Md. Shakil Ahmed
- Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh
| | - Md. Shahjaman
- Department of Statistics, Begum Rokeya University, Rangpur-5400, Bangladesh
| | - Enamul Kabir
- School of Agricultural, Computational and Environmental Sciences, University of Southern Queensland, Australia
| | - Md. Kamruzzaman
- Data Science for Knowledge Creation Research Center, Seoul National University, Korea
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18
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Huang J, Wang J, Li Q, Zhang Y, Zhang X. Enzyme and Chemical Assisted N-Terminal Blocked Peptides Analysis, ENCHANT, as a Selective Proteomics Approach Complementary to Conventional Shotgun Approach. J Proteome Res 2017; 17:212-221. [DOI: 10.1021/acs.jproteome.7b00521] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jingnan Huang
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jie Wang
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qingqing Li
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yang Zhang
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xumin Zhang
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
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19
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Feng Z, Wang H, Chen X, Xu B. Self-Assembling Ability Determines the Activity of Enzyme-Instructed Self-Assembly for Inhibiting Cancer Cells. J Am Chem Soc 2017; 139:15377-15384. [PMID: 28990765 PMCID: PMC5669277 DOI: 10.1021/jacs.7b07147] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Enzyme-instructed
self-assembly (EISA) represents a dynamic continuum
of supramolecular nanostructures that selectively inhibits cancer
cells via simultaneously targeting multiple hallmark capabilities
of cancer, but how to design the small molecules for EISA from the
vast molecular space remains an unanswered question. Here we show
that the self-assembling ability of small molecules controls the anticancer
activity of EISA. Examining the EISA precursor analogues consisting
of an N-capped d-tetrapeptide, a phosphotyrosine residue,
and a diester or a diamide group, we find that, regardless of the
stereochemistry and the regiochemistry of their tetrapeptidic backbones,
the anticancer activities of these precursors largely match their
self-assembling abilities. Additional mechanistic studies confirm
that the assemblies of the small peptide derivatives result in cell
death, accompanying significant rearrangement of cytoskeletal proteins
and plasma membranes. These results imply that the diester or diamide
derivatives of the d-tetrapeptides self-assemble pericellularly,
as well as intracellularly, to result in cell death. As the first
case to correlate thermodynamic properties (e.g., self-assembling
ability) of small molecules with the efficacy of a molecule process
against cancer cells, this work provides an important insight for
developing a molecular dynamic continuum for potential cancer therapy,
as well as understanding the cytotoxicity of pathogenic assemblies.
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Affiliation(s)
- Zhaoqianqi Feng
- Department of Chemistry, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
| | - Huaimin Wang
- Department of Chemistry, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
| | - Xiaoyi Chen
- Department of Chemistry, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
| | - Bing Xu
- Department of Chemistry, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
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20
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DeFilippis AP, Trainor PJ, Hill BG, Amraotkar AR, Rai SN, Hirsch GA, Rouchka EC, Bhatnagar A. Identification of a plasma metabolomic signature of thrombotic myocardial infarction that is distinct from non-thrombotic myocardial infarction and stable coronary artery disease. PLoS One 2017; 12:e0175591. [PMID: 28414761 PMCID: PMC5393610 DOI: 10.1371/journal.pone.0175591] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 03/28/2017] [Indexed: 12/13/2022] Open
Abstract
Aims Current non-invasive diagnostics for acute myocardial infarction (MI) identify myocardial necrosis rather than the primary cause and therapeutic target—plaque disruption and resultant thrombosis. The aim of this study was to identify changes specific to plaque disruption and pathological thrombosis that are distinct from acute myocardial necrosis. Methods and results We quantified 1,032 plasma metabolites by mass spectrometry in 11 thrombotic MI, 12 non-thrombotic MI, and 15 stable coronary artery disease (CAD) subjects at two acute phase (time of catheterization [T0], six hours [T6]) and one quiescent (>3 months follow-up) time points. A statistical classifier was constructed utilizing baseline (T0) abundances of a parsimonious set of 17 qualifying metabolites. Qualifying metabolites were those that demonstrated a significant change between the quiescent phase and the acute phase and that were distinct from any change seen in non-thrombotic MI or stable CAD subjects. Classifier performance as estimated by 10-fold cross-validation was suggestive of high sensitivity and specificity for differentiating thrombotic from non-thrombotic MI and stable CAD subjects at presentation. Nineteen metabolites demonstrated an intra-subject change from time of acute thrombotic MI presentation to the quiescent state that was distinct from any change measured in both the non-thrombotic MI and stable CAD subjects undergoing cardiac catheterization over the same time course (false discovery rate <5%). Conclusions We have identified a candidate metabolic signature that differentiates acute thrombotic MI from quiescent state after MI, from acute non-thrombotic MI, and from stable CAD. Further validation of these metabolites is warranted given their potential as diagnostic biomarkers and novel therapeutic targets for the prevention or treatment of acute MI.
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Affiliation(s)
- Andrew P. DeFilippis
- Department of Medicine, Division of Cardiovascular Medicine, Diabetes and Obesity Center, University of Louisville, Louisville, Kentucky, United States of America
- Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
| | - Patrick J. Trainor
- Department of Medicine, Division of Bioinformatics, University of Louisville, Louisville, Kentucky, United States of America
| | - Bradford G. Hill
- Department of Medicine, Division of Cardiovascular Medicine, Diabetes and Obesity Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Alok R. Amraotkar
- Department of Medicine, Division of Cardiovascular Medicine, Diabetes and Obesity Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Shesh N. Rai
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, Kentucky, United States of America
| | - Glenn A. Hirsch
- Department of Medicine, Division of Cardiovascular Medicine, Diabetes and Obesity Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Eric C. Rouchka
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, Kentucky, United States of America
| | - Aruni Bhatnagar
- Department of Medicine, Division of Cardiovascular Medicine, Diabetes and Obesity Center, University of Louisville, Louisville, Kentucky, United States of America
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21
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Reddi R, Saddanapu V, Chinthapalli DK, Sankoju P, Sripadi P, Addlagatta A. Human Naa50 Protein Displays Broad Substrate Specificity for Amino-terminal Acetylation: DETAILED STRUCTURAL AND BIOCHEMICAL ANALYSIS USING TETRAPEPTIDE LIBRARY. J Biol Chem 2016; 291:20530-8. [PMID: 27484799 DOI: 10.1074/jbc.m116.730432] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Indexed: 11/06/2022] Open
Abstract
Amino-terminal acetylation is a critical co-translational modification of the newly synthesized proteins in a eukaryotic cell carried out by six amino-terminal acetyltransferases (NATs). All NATs contain at least one catalytic subunit, and some contain one or two additional auxiliary subunits. For example, NatE is a complex of Naa10, Naa50, and Naa15 (auxiliary). In the present study, the crystal structure of human Naa50 suggested the presence of CoA and acetylated tetrapeptide (AcMMXX) that have co-purified with the protein. Biochemical and thermal stability studies on the tetrapeptide library with variations in the first and second positions confirm our results from the crystal structure that a peptide with Met-Met in the first two positions is the best substrate for this enzyme. In addition, Naa50 acetylated all MXAA peptides except for MPAA. Transcriptome analysis of 10 genes that make up six NATs in humans from eight different cell lines suggests that components of NatE are transcribed in all cell lines, whereas others are variable. Because Naa10 is reported to acetylate all amino termini that are devoid of methionine and Naa50 acetylates all other peptides that are followed by methionine, we believe that NatE complex can be a major contributor for amino-terminal acetylation at the ribosome exit tunnel.
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Affiliation(s)
| | | | - Dinesh Kumar Chinthapalli
- National Centre for Mass Spectrometry, Council of Scientific and Industrial Research-Indian Institute of Chemical Technology, Hyderabad, Telangana 500 607, India
| | | | - Prabhakar Sripadi
- National Centre for Mass Spectrometry, Council of Scientific and Industrial Research-Indian Institute of Chemical Technology, Hyderabad, Telangana 500 607, India
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22
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Lai ZW, Weisser J, Nilse L, Costa F, Keller E, Tholen M, Kizhakkedathu JN, Biniossek M, Bronsert P, Schilling O. Formalin-Fixed, Paraffin-Embedded Tissues (FFPE) as a Robust Source for the Profiling of Native and Protease-Generated Protein Amino Termini. Mol Cell Proteomics 2016; 15:2203-13. [PMID: 27087653 PMCID: PMC5083106 DOI: 10.1074/mcp.o115.056515] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 04/12/2016] [Indexed: 11/06/2022] Open
Abstract
Dysregulated proteolysis represents a hallmark of numerous diseases. In recent years, increasing number of studies has begun looking at the protein termini in hope to unveil the physiological and pathological functions of proteases in clinical research. However, the availability of cryopreserved tissue specimens is often limited. Alternatively, formalin-fixed, paraffin-embedded (FFPE) tissues offer an invaluable resource for clinical research. Pathologically relevant tissues are often stored as FFPE, which represent the most abundant resource of archived human specimens. In this study, we established a robust workflow to investigate native and protease-generated protein N termini from FFPE specimens. We demonstrate comparable N-terminomes of cryopreserved and formalin-fixed tissue, thereby showing that formalin fixation/paraffin embedment does not proteolytically damage proteins. Accordingly, FFPE specimens are fully amenable to N-terminal analysis. Moreover, we demonstrate feasibility of FFPE-degradomics in a quantitative N-terminomic study of FFPE liver specimens from cathepsin L deficient or wild-type mice. Using a machine learning approach in combination with the previously determined cathepsin L specificity, we successfully identify a number of potential cathepsin L cleavage sites. Our study establishes FFPE specimens as a valuable alternative to cryopreserved tissues for degradomic studies.
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Affiliation(s)
- Zon Weng Lai
- From the ‡Institute of Molecular Medicine and Cell Research
| | | | - Lars Nilse
- From the ‡Institute of Molecular Medicine and Cell Research
| | | | - Eva Keller
- From the ‡Institute of Molecular Medicine and Cell Research
| | - Martina Tholen
- From the ‡Institute of Molecular Medicine and Cell Research
| | - Jayachandran N Kizhakkedathu
- ¶Department of Pathology and Laboratory Medicine and Department of Chemistry, Centre of Chemistry, University of British Columbia, Vancouver, Canada
| | | | - Peter Bronsert
- ‖Department of Pathology, **German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Schilling
- From the ‡Institute of Molecular Medicine and Cell Research, **German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany ‡‡BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany;
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23
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Tholen S, Wolf C, Mayer B, Knopf JD, Löffek S, Qian Y, Kizhakkedathu JN, Biniossek ML, Franzke CW, Schilling O. Skin Barrier Defects Caused by Keratinocyte-Specific Deletion of ADAM17 or EGFR Are Based on Highly Similar Proteome and Degradome Alterations. J Proteome Res 2016; 15:1402-17. [PMID: 27089454 DOI: 10.1021/acs.jproteome.5b00691] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Keratinocyte-specific deletion of ADAM17 in mice impairs terminal differentiation of keratinocytes leading to severe epidermal barrier defects. Mice deficient for ADAM17 in keratinocytes phenocopy mice with a keratinocyte-specific deletion of epidermal growth factor receptor (EGFR), which highlights the role of ADAM17 as a "ligand sheddase" of EGFR ligands. In this study, we aim for the first proteomic/degradomic approach to characterize the disruption of the ADAM17-EGFR signaling axis and its consequences for epidermal barrier formation. Proteomic profiling of the epidermal proteome of mice deficient for either ADAM17 or EGFR in keratinocytes at postnatal days 3 and 10 revealed highly similar protein alterations for ADAM17 and EGFR deficiency. These include massive proteome alterations of structural and regulatory components important for barrier formation such as transglutaminases, involucrin, filaggrin, and filaggrin-2. Cleavage site analysis using terminal amine isotopic labeling of substrates revealed increased proteolytic processing of S100 fused-type proteins including filaggrin-2. Alterations in proteolytic processing are supported by altered abundance of numerous proteases upon keratinocyte-specific Adam17 or Egfr deletion, among them kallikreins, cathepsins, and their inhibitors. This study highlights the essential role of proteolytic processing for maintenance of a functional epidermal barrier. Furthermore, it suggests that most defects in formation of the postnatal epidermal barrier upon keratinocyte-specific ADAM17 deletion are mediated via EGFR.
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Affiliation(s)
- Stefan Tholen
- Institute of Molecular Medicine and Cell Research, University of Freiburg , 79104 Freiburg, Germany
| | - Cristina Wolf
- Department of Dermatology, University Medical Center Freiburg , 79104 Freiburg, Germany
| | - Bettina Mayer
- Institute of Molecular Medicine and Cell Research, University of Freiburg , 79104 Freiburg, Germany
| | - Julia D Knopf
- Institute of Molecular Medicine and Cell Research, University of Freiburg , 79104 Freiburg, Germany
| | - Stefanie Löffek
- Department of Dermatology, University Medical Center Freiburg , 79104 Freiburg, Germany
| | - Yawen Qian
- Department of Dermatology, University Medical Center Freiburg , 79104 Freiburg, Germany
| | - Jayachandran N Kizhakkedathu
- Department of Pathology and Laboratory Medicine and Department of Chemistry, Centre for Blood Research, University of British Columbia , Vancouver, British Columbia V6T 1Z3, Canada
| | - Martin L Biniossek
- Institute of Molecular Medicine and Cell Research, University of Freiburg , 79104 Freiburg, Germany
| | - Claus-Werner Franzke
- Department of Dermatology, University Medical Center Freiburg , 79104 Freiburg, Germany
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research, University of Freiburg , 79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg , D-79104 Freiburg, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
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24
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Chang YY, Hsu CH. Multiple Conformations of the Loop Region Confers Heat-Resistance on SsArd1, a Thermophilic NatA. Chembiochem 2015; 17:214-7. [PMID: 26593285 DOI: 10.1002/cbic.201500568] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Indexed: 11/10/2022]
Abstract
Structural comparison indicates that the loop region between β3 and β4 of SsArd1 is extended relative to the corresponding region in mesophilic Nats, and forms a plastic hydrogen-bond network mainly at two serine residues. Strikingly, two single-point mutants showed ∼3 °C decrease in melting temperature, and two other variants showed ∼7 °C decrease; this correlated with significantly reduced enzymatic activity. To our knowledge, this is the first discovery of a loop region capable of remarkably improving protein thermostability. This provides a novel route to engineer heat-resistant proteins.
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Affiliation(s)
- Yu-Yung Chang
- Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Chun-Hua Hsu
- Department of Agricultural Chemistry, Center for Systems Biology, Genome and Systems Biology Degree Program, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
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25
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Hirano H, Kimura Y, Kimura A. Biological significance of co- and post-translational modifications of the yeast 26S proteasome. J Proteomics 2015; 134:37-46. [PMID: 26642761 DOI: 10.1016/j.jprot.2015.11.016] [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] [Received: 07/09/2015] [Revised: 11/04/2015] [Accepted: 11/16/2015] [Indexed: 02/05/2023]
Abstract
UNLABELLED In yeast (Saccharomyces cerevisiae), co- and post-translational modifications of the 26S proteasome, a large protein complex, were comprehensively detected by proteomic techniques, and their functions were investigated. The presence, number, site, and state of co- and post-translational modifications of the 26S proteasome differ considerably among yeast, human, and mouse. The roles of phosphorylation, N(α)-acetylation, N(α)-myristoylation, N(α)-methylation, and N-terminal truncation in the yeast 26S proteasome were investigated. Although there is only one modification site for either N(α)-acetylation, N(α)-myristoylation, or N(α)-methylation, these modifications play an important role in the functions of the yeast proteasome. In contrast, there are many phosphorylation sites in the yeast 26S proteasome. However, the phosphorylation patterns might be a few, suggesting that tiny modifications exert considerable effects on the function of the proteasome. BIOLOGICAL SIGNIFICANCE Protein co- and post-translational modifications produce different protein species which often have different functions. The yeast 26S proteasome, a large protein complex, consisting of many subunits has a number of co- and post-translational modification sites. This review describes the effects of the modifications on the function of the protein complex. This article is part of a Special Issue entitled: Protein species. Guest Editors: Peter Jungblut, Hartmut Schlüter and Bernd Thiede.
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Affiliation(s)
- Hisashi Hirano
- Yokohama City University, Advanced Medical Research Center, Japan.
| | - Yayoi Kimura
- Yokohama City University, Advanced Medical Research Center, Japan
| | - Ayuko Kimura
- Yokohama City University, Advanced Medical Research Center, Japan
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26
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Berry IJ, Steele JR, Padula MP, Djordjevic SP. The application of terminomics for the identification of protein start sites and proteoforms in bacteria. Proteomics 2015; 16:257-72. [DOI: 10.1002/pmic.201500319] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/21/2015] [Accepted: 09/30/2015] [Indexed: 01/11/2023]
Affiliation(s)
- Iain J. Berry
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Joel R. Steele
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Matthew P. Padula
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Steven P. Djordjevic
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
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27
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Marino G, Eckhard U, Overall CM. Protein Termini and Their Modifications Revealed by Positional Proteomics. ACS Chem Biol 2015; 10:1754-64. [PMID: 26042555 DOI: 10.1021/acschembio.5b00189] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A myriad of co- and post-translational modifications occur at protein N- and C-termini, resulting in an extra layer of proteome complexity and an additional source of protein regulation. Here, we review N- and C-terminal modifications and the contemporary positional proteomics techniques used to isolate protein terminal peptides from complex protein mixtures and characterize their diversity and occurrence in biological systems. Furthermore, these degradomics strategies--often referred to as N- and C-terminomics--represent dedicated high-throughput techniques to study proteolysis in dynamic living systems. Over the past decade, terminomics studies have provided indispensable information on the functional states of individual proteins, cell types, tissues, and biological processes and delivered fundamental new data for the Human Proteome Project, including high confidence identifications of many so-called "missing proteins", which had not been identified by traditional proteomics analyses.
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Affiliation(s)
- Giada Marino
- Centre
for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ulrich Eckhard
- Centre
for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher M. Overall
- Centre
for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department
of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
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Eckhard U, Marino G, Abbey SR, Tharmarajah G, Matthew I, Overall CM. The Human Dental Pulp Proteome and N-Terminome: Levering the Unexplored Potential of Semitryptic Peptides Enriched by TAILS to Identify Missing Proteins in the Human Proteome Project in Underexplored Tissues. J Proteome Res 2015; 14:3568-82. [DOI: 10.1021/acs.jproteome.5b00579] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ulrich Eckhard
- Centre
for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Giada Marino
- Centre
for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Simon R. Abbey
- Centre
for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Grace Tharmarajah
- Department
of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Ian Matthew
- Department
of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Christopher M. Overall
- Centre
for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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Fletcher AJ, Christensen DE, Nelson C, Tan CP, Schaller T, Lehner PJ, Sundquist WI, Towers GJ. TRIM5α requires Ube2W to anchor Lys63-linked ubiquitin chains and restrict reverse transcription. EMBO J 2015; 34:2078-95. [PMID: 26101372 PMCID: PMC4551353 DOI: 10.15252/embj.201490361] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 05/18/2015] [Accepted: 05/20/2015] [Indexed: 11/26/2022] Open
Abstract
TRIM5α is an antiviral, cytoplasmic, E3 ubiquitin (Ub) ligase that assembles on incoming retroviral capsids and induces their premature dissociation. It inhibits reverse transcription of the viral genome and can also synthesize unanchored polyubiquitin (polyUb) chains to stimulate innate immune responses. Here, we show that TRIM5α employs the E2 Ub-conjugating enzyme Ube2W to anchor the Lys63-linked polyUb chains in a process of TRIM5α auto-ubiquitination. Chain anchoring is initiated, in cells and in vitro, through Ube2W-catalyzed monoubiquitination of TRIM5α. This modification serves as a substrate for the elongation of anchored Lys63-linked polyUb chains, catalyzed by the heterodimeric E2 enzyme Ube2N/Ube2V2. Ube2W targets multiple TRIM5α internal lysines with Ub especially lysines 45 and 50, rather than modifying the N-terminal amino group, which is instead αN-acetylated in cells. E2 depletion or Ub mutation inhibits TRIM5α ubiquitination in cells and restores restricted viral reverse transcription, but not infection. Our data indicate that the stepwise formation of anchored Lys63-linked polyUb is a critical early step in the TRIM5α restriction mechanism and identify the E2 Ub-conjugating cofactors involved.
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Affiliation(s)
- Adam J Fletcher
- MRC Centre of Medical Molecular Virology, Division of Infection and Immunity, University College London, London, UK
| | - Devin E Christensen
- Department of Biochemistry and HSC Core Facilities, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Chad Nelson
- Department of Biochemistry and HSC Core Facilities, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Choon Ping Tan
- MRC Centre of Medical Molecular Virology, Division of Infection and Immunity, University College London, London, UK
| | - Torsten Schaller
- MRC Centre of Medical Molecular Virology, Division of Infection and Immunity, University College London, London, UK
| | - Paul J Lehner
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Wesley I Sundquist
- Department of Biochemistry and HSC Core Facilities, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Greg J Towers
- MRC Centre of Medical Molecular Virology, Division of Infection and Immunity, University College London, London, UK
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Giglione C, Fieulaine S, Meinnel T. N-terminal protein modifications: Bringing back into play the ribosome. Biochimie 2015; 114:134-46. [PMID: 25450248 DOI: 10.1016/j.biochi.2014.11.008] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022]
Abstract
N-terminal protein modifications correspond to the first modifications which in principle any protein may undergo, before translation is completed by the ribosome. This class of essential modifications can have different nature or function and be catalyzed by a variety of dedicated enzymes. Here, we review the current state of the major N-terminal co-translational modifications, with a particular emphasis to their catalysts, which belong to metalloprotease and acyltransferase clans. The earliest of these modifications corresponds to the N-terminal methionine excision, an ubiquitous and essential process leading to the removal of the first methionine. N-alpha acetylation occurs also in all Kingdoms although its extent appears to be significantly increased in higher eukaryotes. Finally, N-myristoylation is a crucial pathway existing only in eukaryotes. Recent studies dealing on how some of these co-translational modifiers might work in close vicinity of the ribosome is starting to provide new information on when these modifications exactly take place on the elongating nascent chain and the interplay with other ribosome biogenesis factors taking in charge the nascent chains. Here a comprehensive overview of the recent advances in the field of N-terminal protein modifications is given.
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Affiliation(s)
- Carmela Giglione
- CNRS, Institut des Sciences du Végétal, 1 Avenue de la Terrasse, Bât 23A, F-91198 Gif sur Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France.
| | - Sonia Fieulaine
- CNRS, Institut des Sciences du Végétal, 1 Avenue de la Terrasse, Bât 23A, F-91198 Gif sur Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
| | - Thierry Meinnel
- CNRS, Institut des Sciences du Végétal, 1 Avenue de la Terrasse, Bât 23A, F-91198 Gif sur Yvette, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France.
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31
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The biological functions of Naa10 - From amino-terminal acetylation to human disease. Gene 2015; 567:103-31. [PMID: 25987439 DOI: 10.1016/j.gene.2015.04.085] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/20/2015] [Accepted: 04/27/2015] [Indexed: 01/07/2023]
Abstract
N-terminal acetylation (NTA) is one of the most abundant protein modifications known, and the N-terminal acetyltransferase (NAT) machinery is conserved throughout all Eukarya. Over the past 50 years, the function of NTA has begun to be slowly elucidated, and this includes the modulation of protein-protein interaction, protein-stability, protein function, and protein targeting to specific cellular compartments. Many of these functions have been studied in the context of Naa10/NatA; however, we are only starting to really understand the full complexity of this picture. Roughly, about 40% of all human proteins are substrates of Naa10 and the impact of this modification has only been studied for a few of them. Besides acting as a NAT in the NatA complex, recently other functions have been linked to Naa10, including post-translational NTA, lysine acetylation, and NAT/KAT-independent functions. Also, recent publications have linked mutations in Naa10 to various diseases, emphasizing the importance of Naa10 research in humans. The recent design and synthesis of the first bisubstrate inhibitors that potently and selectively inhibit the NatA/Naa10 complex, monomeric Naa10, and hNaa50 further increases the toolset to analyze Naa10 function.
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Zhou Y, Zhang N, Li BQ, Huang T, Cai YD, Kong XY. A method to distinguish between lysine acetylation and lysine ubiquitination with feature selection and analysis. J Biomol Struct Dyn 2015; 33:2479-90. [PMID: 25616595 DOI: 10.1080/07391102.2014.1001793] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lysine acetylation and ubiquitination are two primary post-translational modifications (PTMs) in most eukaryotic proteins. Lysine residues are targets for both types of PTMs, resulting in different cellular roles. With the increasing availability of protein sequences and PTM data, it is challenging to distinguish the two types of PTMs on lysine residues. Experimental approaches are often laborious and time consuming. There is an urgent need for computational tools to distinguish between lysine acetylation and ubiquitination. In this study, we developed a novel method, called DAUFSA (distinguish between lysine acetylation and lysine ubiquitination with feature selection and analysis), to discriminate ubiquitinated and acetylated lysine residues. The method incorporated several types of features: PSSM (position-specific scoring matrix) conservation scores, amino acid factors, secondary structures, solvent accessibilities, and disorder scores. By using the mRMR (maximum relevance minimum redundancy) method and the IFS (incremental feature selection) method, an optimal feature set containing 290 features was selected from all incorporated features. A dagging-based classifier constructed by the optimal features achieved a classification accuracy of 69.53%, with an MCC of .3853. An optimal feature set analysis showed that the PSSM conservation score features and the amino acid factor features were the most important attributes, suggesting differences between acetylation and ubiquitination. Our study results also supported previous findings that different motifs were employed by acetylation and ubiquitination. The feature differences between the two modifications revealed in this study are worthy of experimental validation and further investigation.
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Affiliation(s)
- You Zhou
- a The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine , Shanghai 200031 , P.R. China
| | - Ning Zhang
- b Department of Biomedical Engineering, Tianjin Key Lab of BME Measurement , Tianjin University , Tianjin 300072 , P.R. China
| | - Bi-Qing Li
- c Key Laboratory of Systems Biology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200031 , P.R. China
| | - Tao Huang
- a The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine , Shanghai 200031 , P.R. China.,d Department of Genetics and Genomic Sciences , Icahn School of Medicine at Mount Sinai , New York , NY 10029 , USA
| | - Yu-Dong Cai
- e Institute of Systems Biology , Shanghai University , Shanghai 200444 , P.R. China
| | - Xiang-Yin Kong
- a The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine , Shanghai 200031 , P.R. China
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33
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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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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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Ouidir T, Jarnier F, Cosette P, Jouenne T, Hardouin J. Characterization of N-terminal protein modifications in Pseudomonas aeruginosa PA14. J Proteomics 2014; 114:214-25. [PMID: 25464366 DOI: 10.1016/j.jprot.2014.11.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/10/2014] [Accepted: 11/01/2014] [Indexed: 01/26/2023]
Abstract
UNLABELLED Even though protein initiator methionine excision (NME) and N-terminal acetylation (NTA) have been relatively well investigated in eukaryotic proteomes, few studies were dedicated to these modifications in bacteria up to now. In this work, we investigated, for the first time, the N-terminal proteome of the bacterium Pseudomonas aeruginosa PA14 by studying the NME and NTA processes using proteomic approaches. For NME, most of proteins had their initiator Met cleaved (63%) and the nature of the penultimate residue seems to be essential for this cleavage. Concerning NTA, two methods were applied (protein fractionation and peptide enrichment). This allowed us to identify 117 Nα-acetylated proteins, among them 113 have not yet been described as modified in bacteria. Most often, the non-acetylated form was over-represented compared to the acetylated form, arguing that this latter was a minor part of the total abundance of a given protein. Furthermore, some proteins with acetylated initiator methionine were observed. The present work significantly enlarges the number of N-terminally modified proteins in bacteria and confirms that these modifications are a general and fundamental process, not only restricted to eukaryotes. BIOLOGICAL SIGNIFICANCE Protein modifications in prokaryotes have been detected more recently than in eukaryotes. Methionine cleavage and N-terminal acetylation are two common protein N-terminal modifications. Despite their importance in bacterial processes, they are less investigated. The characterization of N-terminal acetylation in bacteria is a challenge because no antibody exists and it is a less frequent modification than in eukaryotes. We used proteomic approaches (enrichment, fractionation, nanoLC-MS/MS, and bioinformatic analyses) to investigate the N-terminal methionine excision and to profile the N-terminal acetylome of P. aeruginosa strain PA14. From our results, around 60% of the proteins had their iMet cleaved. In total, 117 proteins were identified constituting the largest dataset in prokaryotes. Among them, proteins kept their initiator methionine and were acetylated. These results may facilitate the design of experiments to better understand the role of acetylation at the protein N-terminus of P. aeruginosa PA14.
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Affiliation(s)
- Tassadit Ouidir
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76820 Mont-Saint-Aignan, France; Normandy Univ, UR, France; PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France
| | - Frédérique Jarnier
- Normandy Univ, UR, France; PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France
| | - Pascal Cosette
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76820 Mont-Saint-Aignan, France; Normandy Univ, UR, France; PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France
| | - Thierry Jouenne
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76820 Mont-Saint-Aignan, France; Normandy Univ, UR, France; PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France
| | - Julie Hardouin
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76820 Mont-Saint-Aignan, France; Normandy Univ, UR, France; PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France.
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Kucharova V, Wiker HG. Proteogenomics in microbiology: taking the right turn at the junction of genomics and proteomics. Proteomics 2014; 14:2360-675. [PMID: 25263021 DOI: 10.1002/pmic.201400168] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 08/18/2014] [Accepted: 09/23/2014] [Indexed: 12/14/2022]
Abstract
High-accuracy and high-throughput proteomic methods have completely changed the way we can identify and characterize proteins. MS-based proteomics can now provide a unique supplement to genomic data and add a new level of information to the interpretation of genomic sequences. Proteomics-driven genome annotation has become especially relevant in microbiology where genomes are sequenced on a daily basis and limitations of an in silico driven annotation process are well recognized. In this review paper, we outline different strategies on how one can design a proteogenomic experiment, for example on genome-sequenced (synonymous proteogenomics) versus unsequenced organisms (ortho-proteogenomics) or with the aid of other "omic" data such as RNA-seq. We touch upon many challenges that are encountered during a typical proteogenomic study, mostly concerning bioinformatics methods and downstream data analysis, but also related to creation and use of sequence databases. A large list of proteogenomic case studies of different microorganisms is provided to illustrate the mapping of MS/MS-derived peptide spectra to genomic DNA sequences. These investigations have led to accurate determination of translational initiation sites, pointed out eventual read-throughs or programmed frameshifts, detected signal peptide processing or other protein maturation events, removed questionable annotation assignments, and provided evidence for predicted hypothetical proteins.
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Affiliation(s)
- Veronika Kucharova
- Department of Clinical Science, The Gade Research Group for Infection and Immunity, University of Bergen, Norway
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37
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Identification of phosphatidylcholine transfer protein-like in the parasite Entamoeba histolytica. Biochimie 2014; 107 Pt B:223-34. [PMID: 25223890 DOI: 10.1016/j.biochi.2014.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 09/04/2014] [Indexed: 11/22/2022]
Abstract
Caveolin is the protein marker of caveola-mediated endocytosis. Previously, we demonstrated by immunoblotting and immunofluorescence that an anti-chick embryo caveolin-1 monoclonal antibody (mAb) recognizes a protein in amoeba extracts. Nevertheless, the caveolin-1 gene is absent in the Entamoeba histolytica genome database. In this work, the goal was to isolate, identify and characterize the protein that cross-reacts with chick embryo caveolin-1. We identified the protein using a proteomic approach, and the complete gene was cloned and sequenced. The identified protein, E. histolytica phosphatidylcholine transfer protein-like (EhPCTP-L), is a member of the StAR-related lipid transfer (START) protein superfamily. The human homolog binds and transfers phosphatidylcholine (PC) and phosphatidylethanolamine (PE) between model membranes in vitro; however, the physiological role of PCTP-L remains elusive. Studies in silico showed that EhPCTP-L has a central START domain and also contains a C-terminal intrinsically disordered region. The anti-rEhPCTP-L antibody demonstrated that EhPCTP-L is found in the plasma membrane and cytosol, which is in agreement with previous reports on the human counterpart. This result points to the plasma membrane as one possible target membrane for EhPCTP-L. Furthermore, assays using filipin and nystatin showed down regulation of EhPCTP-L, in an apparently cholesterol-independent way. Interestingly, EhPCTP-L binds primarily to anionic phospholipids phosphatidylserine (PS) and phosphatidic acid (PA), while its mammalian counterpart HsPCTP-L binds neutral phospholipids PC and PE. The present study provides information that helps reveal the possible function and regulation of PCTP-L expression in the primitive eukaryotic parasite E. histolytica.
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38
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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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39
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Hou T, Zheng G, Zhang P, Jia J, Li J, Xie L, Wei C, Li Y. LAceP: lysine acetylation site prediction using logistic regression classifiers. PLoS One 2014; 9:e89575. [PMID: 24586884 PMCID: PMC3930742 DOI: 10.1371/journal.pone.0089575] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 01/22/2014] [Indexed: 11/19/2022] Open
Abstract
Background Lysine acetylation is a crucial type of protein post-translational modification, which is involved in many important cellular processes and serious diseases. However, identification of protein acetylated sites through traditional experiment methods is time-consuming and laborious. Those methods are not suitable to identify a large number of acetylated sites quickly. Therefore, computational methods are still very valuable to accelerate lysine acetylated site finding. Result In this study, many biological characteristics of acetylated sites have been investigated, such as the amino acid sequence around the acetylated sites, the physicochemical property of the amino acids and the transition probability of adjacent amino acids. A logistic regression method was then utilized to integrate these information for generating a novel lysine acetylation prediction system named LAceP. When compared with existing methods, LAceP overwhelms most of state-of-the-art methods. Especially, LAceP has a more balanced prediction capability for positive and negative datasets. Conclusion LAceP can integrate different biological features to predict lysine acetylation with high accuracy. An online web server is freely available at http://www.scbit.org/iPTM/.
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Affiliation(s)
- Ting Hou
- School of Biological Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Center for Bioinformation Technology, Shanghai, China
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guangyong Zheng
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (GZ); (CCW); (YXL)
| | - Pingyu Zhang
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jia Jia
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Jing Li
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Chaochun Wei
- Shanghai Center for Bioinformation Technology, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (GZ); (CCW); (YXL)
| | - Yixue Li
- School of Biological Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Center for Bioinformation Technology, Shanghai, China
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (GZ); (CCW); (YXL)
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40
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Bland C, Hartmann EM, Christie-Oleza JA, Fernandez B, Armengaud J. N-Terminal-oriented proteogenomics of the marine bacterium roseobacter denitrificans Och114 using N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) labeling and diagonal chromatography. Mol Cell Proteomics 2014; 13:1369-81. [PMID: 24536027 DOI: 10.1074/mcp.o113.032854] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Given the ease of whole genome sequencing with next-generation sequencers, structural and functional gene annotation is now purely based on automated prediction. However, errors in gene structure are frequent, the correct determination of start codons being one of the main concerns. Here, we combine protein N termini derivatization using (N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP Ac-OSu) as a labeling reagent with the COmbined FRActional DIagonal Chromatography (COFRADIC) sorting method to enrich labeled N-terminal peptides for mass spectrometry detection. Protein digestion was performed in parallel with three proteases to obtain a reliable automatic validation of protein N termini. The analysis of these N-terminal enriched fractions by high-resolution tandem mass spectrometry allowed the annotation refinement of 534 proteins of the model marine bacterium Roseobacter denitrificans OCh114. This study is especially efficient regarding mass spectrometry analytical time. From the 534 validated N termini, 480 confirmed existing gene annotations, 41 highlighted erroneous start codon annotations, five revealed totally new mis-annotated genes; the mass spectrometry data also suggested the existence of multiple start sites for eight different genes, a result that challenges the current view of protein translation initiation. Finally, we identified several proteins for which classical genome homology-driven annotation was inconsistent, questioning the validity of automatic annotation pipelines and emphasizing the need for complementary proteomic data. All data have been deposited to the ProteomeXchange with identifier PXD000337.
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Affiliation(s)
- Céline Bland
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
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41
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Lichti CF, Wildburger NC, Emmett MR, Mostovenko E, Shavkunov AS, Strain SK, Nilsson CL. Post-translational Modifications in the Human Proteome. TRANSLATIONAL BIOINFORMATICS 2014. [DOI: 10.1007/978-94-017-9202-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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42
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Huesgen PF, Alami M, Lange PF, Foster LJ, Schröder WP, Overall CM, Green BR. Proteomic amino-termini profiling reveals targeting information for protein import into complex plastids. PLoS One 2013; 8:e74483. [PMID: 24066144 PMCID: PMC3774753 DOI: 10.1371/journal.pone.0074483] [Citation(s) in RCA: 34] [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: 06/03/2013] [Accepted: 08/01/2013] [Indexed: 01/14/2023] Open
Abstract
In organisms with complex plastids acquired by secondary endosymbiosis from a photosynthetic eukaryote, the majority of plastid proteins are nuclear-encoded, translated on cytoplasmic ribosomes, and guided across four membranes by a bipartite targeting sequence. In-depth understanding of this vital import process has been impeded by a lack of information about the transit peptide part of this sequence, which mediates transport across the inner three membranes. We determined the mature N-termini of hundreds of proteins from the model diatom Thalassiosira pseudonana, revealing extensive N-terminal modification by acetylation and proteolytic processing in both cytosol and plastid. We identified 63 mature N-termini of nucleus-encoded plastid proteins, deduced their complete transit peptide sequences, determined a consensus motif for their cleavage by the stromal processing peptidase, and found evidence for subsequent processing by a plastid methionine aminopeptidase. The cleavage motif differs from that of higher plants, but is shared with other eukaryotes with complex plastids.
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Affiliation(s)
- Pitter F. Huesgen
- Centre for Blood Research and Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Meriem Alami
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Philipp F. Lange
- Centre for Blood Research and Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Leonard J. Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wolfgang P. Schröder
- Centre for Blood Research and Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry and Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Christopher M. Overall
- Centre for Blood Research and Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Beverley R. Green
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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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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Vanderperre B, Lucier JF, Bissonnette C, Motard J, Tremblay G, Vanderperre S, Wisztorski M, Salzet M, Boisvert FM, Roucou X. Direct detection of alternative open reading frames translation products in human significantly expands the proteome. PLoS One 2013; 8:e70698. [PMID: 23950983 PMCID: PMC3741303 DOI: 10.1371/journal.pone.0070698] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 06/20/2013] [Indexed: 01/04/2023] Open
Abstract
A fully mature mRNA is usually associated to a reference open reading frame encoding a single protein. Yet, mature mRNAs contain unconventional alternative open reading frames (AltORFs) located in untranslated regions (UTRs) or overlapping the reference ORFs (RefORFs) in non-canonical +2 and +3 reading frames. Although recent ribosome profiling and footprinting approaches have suggested the significant use of unconventional translation initiation sites in mammals, direct evidence of large-scale alternative protein expression at the proteome level is still lacking. To determine the contribution of alternative proteins to the human proteome, we generated a database of predicted human AltORFs revealing a new proteome mainly composed of small proteins with a median length of 57 amino acids, compared to 344 amino acids for the reference proteome. We experimentally detected a total of 1,259 alternative proteins by mass spectrometry analyses of human cell lines, tissues and fluids. In plasma and serum, alternative proteins represent up to 55% of the proteome and may be a potential unsuspected new source for biomarkers. We observed constitutive co-expression of RefORFs and AltORFs from endogenous genes and from transfected cDNAs, including tumor suppressor p53, and provide evidence that out-of-frame clones representing AltORFs are mistakenly rejected as false positive in cDNAs screening assays. Functional importance of alternative proteins is strongly supported by significant evolutionary conservation in vertebrates, invertebrates, and yeast. Our results imply that coding of multiple proteins in a single gene by the use of AltORFs may be a common feature in eukaryotes, and confirm that translation of unconventional ORFs generates an as yet unexplored proteome.
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Affiliation(s)
- Benoît Vanderperre
- Département de biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec, Canada
| | - Jean-François Lucier
- Département de microbiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec, Canada
| | - Cyntia Bissonnette
- Département de biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec, Canada
| | - Julie Motard
- Département de biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec, Canada
| | - Guillaume Tremblay
- Département de biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec, Canada
| | - Solène Vanderperre
- Département de biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec, Canada
| | - Maxence Wisztorski
- PRISM, Laboratoire de Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, EA 4550, SN3, Université Lille 1, Villeneuve d'Ascq, France
| | - Michel Salzet
- PRISM, Laboratoire de Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, EA 4550, SN3, Université Lille 1, Villeneuve d'Ascq, France
| | - François-Michel Boisvert
- Département d'anatomie et de biologie cellulaire, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec, Canada
| | - Xavier Roucou
- Département de biochimie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Québec, Canada
- * E-mail:
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Differential isotope dansylation labeling combined with liquid chromatography mass spectrometry for quantification of intact and N-terminal truncated proteins. Anal Chim Acta 2013; 792:79-85. [DOI: 10.1016/j.aca.2013.05.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 05/14/2013] [Accepted: 05/22/2013] [Indexed: 11/19/2022]
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46
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Chen SH, Chen CR, Chen SH, Li DT, Hsu JL. Improved N(α)-acetylated peptide enrichment following dimethyl labeling and SCX. J Proteome Res 2013; 12:3277-87. [PMID: 23745983 DOI: 10.1021/pr400127j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Protein N-terminal acetylation is one of the most common modifications occurring co- and post-translationally on either eukaryote or prokaryote proteins. However, compared to other protein modifications, the physiological role of protein N-terminal acetylation is relatively unclear. To explore the biological functions of protein N-terminal acetylation, a robust and large-scale method for qualitative and quantitative analysis of this modification is required. Enrichment of N(α)-acetylated peptides or depletion of the free N-terminal and internal tryptic peptides prior to analysis by mass spectrometry are necessary based on current technologies. This study demonstrated a simple strong cation exchange (SCX) fractionation method to selectively enrich N(α)-acetylated tryptic peptides via dimethyl labeling without the need for tedious protective labeling and depleting procedures. This method was introduced for the comprehensive analysis of N-terminal acetylated proteins from HepG2 cells. Several hundred N-terminal acetylation sites were readily identified in a single SCX flow-through fraction. Moreover, the N(α)-acetylated peptides of some protein isoforms were simultaneously observed in the SCX flow-through fraction, which indicated that this approach can be utilized to discriminate protein isoforms with very similar full sequences but different N-terminal sequences, such as β-actin/γ-actin, ERK1/ERK2, α-centractin/β-centractin, and ADP/ATP translocase 2 and 3. Compared to other methods, this method is relatively simple and can be directly implemented in a two-dimensional separation (SCX-RP)-mass spectrometry scheme for quantitative N-terminal proteomics using stable-isotope dimethyl labeling.
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Affiliation(s)
- Sin-Hong Chen
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan
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47
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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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48
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Exploring the accessible conformations of N-terminal acetylated α-synuclein. FEBS Lett 2013; 587:1128-38. [PMID: 23499431 DOI: 10.1016/j.febslet.2013.02.049] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 02/28/2013] [Accepted: 02/28/2013] [Indexed: 11/21/2022]
Abstract
Alpha synuclein (αsyn) fibrils are found in the Lewy Bodies of patients with Parkinson's disease (PD). The aggregation of the αsyn monomer to soluble oligomers and insoluble fibril aggregates is believed to be one of the causes of PD. Recently, the view of the native state of αsyn as a monomeric ensemble was challenged by a report suggesting that αsyn exists in its native state as a helical tetramer. This review reports on our current understanding of αsyn within the context of these recent developments and describes the work performed by a number of groups to address the monomer/tetramer debate. A number of in depth studies have subsequently shown that both non-acetylated and acetylated αsyn purified under mild conditions are primarily monomer. A description of the accessible states of acetylated αsyn monomer and the ability of αsyn to self-associate is explored.
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49
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Liu CC, Zhu HY, Dong XM, Ning DL, Wang HX, Li WH, Yang CP, Wang BC. Identification and analysis of the acetylated status of poplar proteins reveals analogous N-terminal protein processing mechanisms with other eukaryotes. PLoS One 2013; 8:e58681. [PMID: 23536812 PMCID: PMC3594182 DOI: 10.1371/journal.pone.0058681] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 02/05/2013] [Indexed: 11/22/2022] Open
Abstract
Background The N-terminal protein processing mechanism (NPM) including N-terminal Met excision (NME) and N-terminal acetylation (Nα-acetylation) represents a common protein co-translational process of some eukaryotes. However, this NPM occurred in woody plants yet remains unknown. Methodology/Principal Findings To reveal the NPM in poplar, we investigated the Nα-acetylation status of poplar proteins during dormancy by combining tandem mass spectrometry with TiO2 enrichment of acetylated peptides. We identified 58 N-terminally acetylated (Nα-acetylated) proteins. Most proteins (47, >81%) are subjected to Nα-acetylation following the N-terminal removal of Met, indicating that Nα-acetylation and NME represent a common NPM of poplar proteins. Furthermore, we confirm that poplar shares the analogous NME and Nα-acetylation (NPM) to other eukaryotes according to analysis of N-terminal features of these acetylated proteins combined with genome-wide identification of the involving methionine aminopeptidases (MAPs) and N-terminal acetyltransferase (Nat) enzymes in poplar. The Nα-acetylated reactions and the involving enzymes of these poplar proteins are also identified based on those of yeast and human, as well as the subcellular location information of these poplar proteins. Conclusions/Significance This study represents the first extensive investigation of Nα-acetylation events in woody plants, the results of which will provide useful resources for future unraveling the regulatory mechanisms of Nα-acetylation of proteins in poplar.
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Affiliation(s)
- Chang-Cai Liu
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, Heilongjiang, China
- Laboratory for Chemical Defense and Microscale Analysis, Hubei Nanxing General Chemical Factory, Zhijiang, Hubei, China
| | - Hang-Yong Zhu
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, Heilongjiang, China
- Bureau of Garden and Park, Qitaihe, Heilongjiang, China
| | - Xiu-Mei Dong
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, Heilongjiang, China
| | - De-Li Ning
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, Heilongjiang, China
| | - Hong-Xia Wang
- Institute of Basic Medical Sciences, National Center for Biomedical Analysis, Beijing, China
| | - Wei-Hua Li
- Institute of Basic Medical Sciences, National Center for Biomedical Analysis, Beijing, China
| | - Chuan-Ping Yang
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, Heilongjiang, China
- * E-mail: (C-PY); (B-CW)
| | - Bai-Chen Wang
- State Key Laboratory of Forest Genetics and Tree Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, Heilongjiang, China
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- * E-mail: (C-PY); (B-CW)
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50
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RegulatING chromatin regulators: post-translational modification of the ING family of epigenetic regulators. Biochem J 2013; 450:433-42. [DOI: 10.1042/bj20121632] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The five human ING genes encode at least 15 splicing isoforms, most of which affect cell growth, differentiation and apoptosis through their ability to alter gene expression by epigenetic mechanisms. Since their discovery in 1996, ING proteins have been classified as type II tumour suppressors on the basis of reports describing their down-regulation and mislocalization in a variety of cancer types. In addition to their regulation by transcriptional mechanisms, understanding the range of PTMs (post-translational modifications) of INGs is important in understanding how ING functions are fine-tuned in the physiological setting and how they add to the repertoire of activities affected by the INGs. In the present paper we review the different PTMs that have been reported to occur on INGs. We discuss the PTMs that modulate ING function under normal conditions and in response to a variety of stresses. We also describe the ING PTMs that have been identified by several unbiased MS-based PTM enrichment techniques and subsequent proteomic analysis. Among the ING PTMs identified to date, a subset has been characterized for their biological significance and have been shown to affect processes including subcellular localization, interaction with enzymatic complexes and ING protein half-life. The present review aims to highlight the emerging role of PTMs in regulating ING function and to suggest additional pathways and functions where PTMs may effect ING function.
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