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Van V, Smith AT. ATE1-Mediated Post-Translational Arginylation Is an Essential Regulator of Eukaryotic Cellular Homeostasis. ACS Chem Biol 2020; 15:3073-3085. [PMID: 33228359 DOI: 10.1021/acschembio.0c00677] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Arginylation is a protein post-translational modification catalyzed by arginyl-tRNA transferases (ATE1s), which are critical enzymes conserved across all eukaryotes. Arginylation is a key step in the Arg N-degron pathway, a hierarchical cellular signaling pathway that links the ubiquitin-dependent degradation of a protein to the identity of its N-terminal amino acid side chain. The fidelity of ATE1-catalyzed arginylation is imperative, as this post-translational modification regulates several essential biological processes such as cardiovascular maturation, chromosomal segregation, and even the stress response. While the process of ATE1-catalyzed arginylation has been studied in detail at the cellular level, much remains unknown about the structure of this important enzyme, its mechanism of action, and its regulation. In this work, we detail the current state of knowledge on ATE1-catalyzed arginylation, and we discuss both ongoing and future directions that will reveal the structural and mechanistic details of this essential eukaryotic cellular regulator.
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Affiliation(s)
- Verna Van
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Aaron T. Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
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Moutiez M, Belin P, Gondry M. Aminoacyl-tRNA-Utilizing Enzymes in Natural Product Biosynthesis. Chem Rev 2017; 117:5578-5618. [DOI: 10.1021/acs.chemrev.6b00523] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Mireille Moutiez
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Pascal Belin
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Muriel Gondry
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
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Fung AWS, Payoe R, Fahlman RP. Perspectives and Insights into the Competition for Aminoacyl-tRNAs between the Translational Machinery and for tRNA Dependent Non-Ribosomal Peptide Bond Formation. Life (Basel) 2015; 6:life6010002. [PMID: 26729173 PMCID: PMC4810233 DOI: 10.3390/life6010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 12/23/2015] [Accepted: 12/25/2015] [Indexed: 12/19/2022] Open
Abstract
Aminoacyl-tRNA protein transferases catalyze the transfer of amino acids from aminoacyl-tRNAs to polypeptide substrates. Different forms of these enzymes are found in the different kingdoms of life and have been identified to be central to a wide variety of cellular processes. L/F-transferase is the sole member of this class of enzyme found in Escherichia coli and catalyzes the transfer of leucine to the N-termini of proteins which result in the targeted degradation of the modified protein. Recent investigations on the tRNA specificity of L/F-transferase have revealed the unique recognition nucleotides for a preferred Leu-tRNALeu isoacceptor substrate. In addition to discussing this tRNA selectivity by L/F-transferase, we present and discuss a hypothesis and its implications regarding the apparent competition for this aminoacyl-tRNA between L/F-transferase and the translational machinery. Our discussion reveals a hypothetical involvement of the bacterial stringent response that occurs upon amino acid limitation as a potential cellular event that may reduce this competition and provide the opportunity for L/F-transferase to readily increase its access to the pool of aminoacylated tRNA substrates.
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Affiliation(s)
- Angela W S Fung
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, 474-MSB Edmonton, AB T6G 2H7, Canada.
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada.
| | - Roshani Payoe
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, 474-MSB Edmonton, AB T6G 2H7, Canada.
- Institute of Technology, Faculty of Science and Technology, University of Tartu, Noorse St 1, Tartu 50411, Estonia.
| | - Richard P Fahlman
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, 474-MSB Edmonton, AB T6G 2H7, Canada.
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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Abstract
Arginylation is an enzymatic reaction in which arginyl-tRNA protein transferase 1 (ATE1, EC 2.3.2.8) conjugates a single arginyl moiety from aminoacylated tRNA(Arg) onto a target polypeptide. We established arginylation for in vitro labeling of peptides with N-terminal acidic amino acids. Consistent with prior knowledge, arginylated peptides flanked by basic amino acids result in rich redundant MS/MS fragment spectra using various precursor fragmentation modes. Arginylation carried out by ATE1 is a fast method for labeling peptides. Sequence-specific proteolytic digest of proteins is best carried out using a double digest of proteins by Lys-C and Asp-N to generate peptides with a basic amino acid on the C-terminus and an acidic amino acid on the N-terminus. Under these conditions, arginylation is specific for N-terminal acidic amino acids and results in a near 2× sequence coverage in the MS/MS spectrum are achieved.
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Affiliation(s)
- H Alexander Ebhardt
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, HPT E 61, Auguste-Piccard-Hof 1, 8093, Zürich, Switzerland,
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Ebhardt HA, Nan J, Chaulk SG, Fahlman RP, Aebersold R. Enzymatic generation of peptides flanked by basic amino acids to obtain MS/MS spectra with 2× sequence coverage. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:2735-2743. [PMID: 25380496 PMCID: PMC4241039 DOI: 10.1002/rcm.7069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 10/01/2014] [Accepted: 10/02/2014] [Indexed: 06/04/2023]
Abstract
RATIONALE Tandem mass (MS/MS) spectra generated by collision-induced dissociation (CID) typically lack redundant peptide sequence information in the form of e.g. b- and y-ion series due to frequent use of sequence-specific endopeptidases cleaving C- or N-terminal to Arg or Lys residues. METHODS Here we introduce arginyl-tRNA protein transferase (ATE, EC 2.3.2.8) for proteomics. ATE recognizes acidic amino acids or oxidized Cys at the N-terminus of a substrate peptide and conjugates an arginine from an aminoacylated tRNA(Arg) onto the N-terminus of the substrate peptide. This enzymatic reaction is carried out under physiological conditions and, in combination with Lys-C/Asp-N double digest, results in arginylated peptides with basic amino acids on both termini. RESULTS We demonstrate that in vitro arginylation of peptides using yeast arginyl tRNA protein transferase 1 (yATE1) is a robust enzymatic reaction, specific to only modifying N-terminal acidic amino acids. Precursors originating from arginylated peptides generally have an increased protonation state compared with their non-arginylated forms. Furthermore, the product ion spectra of arginylated peptides show near complete 2× fragment ladders within the same MS/MS spectrum using commonly available electrospray ionization peptide fragmentation modes. Unexpectedly, arginylated peptides generate complete y- and c-ion series using electron transfer dissociation (ETD) despite having an internal proline residue. CONCLUSIONS We introduce a rapid enzymatic method to generate peptides flanked on either terminus by basic amino acids, resulting in a rich, redundant MS/MS fragment pattern.
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Affiliation(s)
- H Alexander Ebhardt
- Department of Biology, Institute of Molecular Systems Biology, ETH ZürichAuguste-Piccard-Hof 1, 8093, Zürich, Switzerland
| | - Jie Nan
- Department of Biology, Institute of Molecular Systems Biology, ETH ZürichAuguste-Piccard-Hof 1, 8093, Zürich, Switzerland
| | - Steven G Chaulk
- Department of Biochemistry, University of AlbertaEdmonton, Alberta, Canada
| | - Richard P Fahlman
- Department of Biochemistry, University of AlbertaEdmonton, Alberta, Canada
- Department of Oncology, University of AlbertaEdmonton, Alberta, Canada
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH ZürichAuguste-Piccard-Hof 1, 8093, Zürich, Switzerland
- Competence Center for Systems Physiology and Metabolic DiseasesZürich, Switzerland
- Faculty of Science, University of ZürichZürich, Switzerland
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Fung AWS, Leung CCY, Fahlman RP. The determination of tRNALeu recognition nucleotides for Escherichia coli L/F transferase. RNA (NEW YORK, N.Y.) 2014; 20:1210-1222. [PMID: 24935875 PMCID: PMC4105747 DOI: 10.1261/rna.044529.114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/28/2014] [Indexed: 06/03/2023]
Abstract
Escherichia coli leucyl/phenylalanyl-tRNA protein transferase catalyzes the tRNA-dependent post-translational addition of amino acids onto the N-terminus of a protein polypeptide substrate. Based on biochemical and structural studies, the current tRNA recognition model by L/F transferase involves the identity of the 3' aminoacyl adenosine and the sequence-independent docking of the D-stem of an aminoacyl-tRNA to the positively charged cluster on L/F transferase. However, this model does not explain the isoacceptor preference observed 40 yr ago. Using in vitro-transcribed tRNA and quantitative MALDI-ToF MS enzyme activity assays, we have confirmed that, indeed, there is a strong preference for the most abundant leucyl-tRNA, tRNA(Leu) (anticodon 5'-CAG-3') isoacceptor for L/F transferase activity. We further investigate the molecular mechanism for this preference using hybrid tRNA constructs. We identified two independent sequence elements in the acceptor stem of tRNA(Leu) (CAG)-a G₃:C₇₀ base pair and a set of 4 nt (C₇₂, A₄:U₆₉, C₆₈)-that are important for the optimal binding and catalysis by L/F transferase. This maps a more specific, sequence-dependent tRNA recognition model of L/F transferase than previously proposed.
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Affiliation(s)
- Angela Wai Shan Fung
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | | | - Richard Peter Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7 Department of Oncology, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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Cruz-Morales P, Vijgenboom E, Iruegas-Bocardo F, Girard G, Yáñez-Guerra LA, Ramos-Aboites HE, Pernodet JL, Anné J, van Wezel GP, Barona-Gómez F. The genome sequence of Streptomyces lividans 66 reveals a novel tRNA-dependent peptide biosynthetic system within a metal-related genomic island. Genome Biol Evol 2013; 5:1165-75. [PMID: 23709624 PMCID: PMC3698927 DOI: 10.1093/gbe/evt082] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The complete genome sequence of the original isolate of the model actinomycete Streptomyces lividans 66, also referred to as 1326, was deciphered after a combination of next-generation sequencing platforms and a hybrid assembly pipeline. Comparative analysis of the genomes of S. lividans 66 and closely related strains, including S. coelicolor M145 and S. lividans TK24, was used to identify strain-specific genes. The genetic diversity identified included a large genomic island with a mosaic structure, present in S. lividans 66 but not in the strain TK24. Sequence analyses showed that this genomic island has an anomalous (G + C) content, suggesting recent acquisition and that it is rich in metal-related genes. Sequences previously linked to a mobile conjugative element, termed plasmid SLP3 and defined here as a 94 kb region, could also be identified within this locus. Transcriptional analysis of the response of S. lividans 66 to copper was used to corroborate a role of this large genomic island, including two SLP3-borne “cryptic” peptide biosynthetic gene clusters, in metal homeostasis. Notably, one of these predicted biosynthetic systems includes an unprecedented nonribosomal peptide synthetase—tRNA-dependent transferase biosynthetic hybrid organization. This observation implies the recruitment of members of the leucyl/phenylalanyl-tRNA-protein transferase family to catalyze peptide bond formation within the biosynthesis of natural products. Thus, the genome sequence of S. lividans 66 not only explains long-standing genetic and phenotypic differences but also opens the door for further in-depth comparative genomic analyses of model Streptomyces strains, as well as for the discovery of novel natural products following genome-mining approaches.
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Affiliation(s)
- Pablo Cruz-Morales
- Evolution of Metabolic Diversity Laboratory, Laboratorio Nacional de Genómica para la Biodiversidad, Langebio, Cinvestav-IPN, Irapuato, México
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Kawaguchi J, Maejima K, Kuroiwa H, Taki M. Kinetic analysis of the leucyl/phenylalanyl-tRNA-protein transferase with acceptor peptides possessing different N-terminal penultimate residues. FEBS Open Bio 2013; 3:252-5. [PMID: 23905007 PMCID: PMC3722611 DOI: 10.1016/j.fob.2013.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 06/05/2013] [Accepted: 06/06/2013] [Indexed: 11/20/2022] Open
Abstract
The introduction of non-natural amino acids at the N-terminus of peptides/proteins using leucyl/phenylalanyl-tRNA-protein transferase (L/F-transferase) is a useful technique for protein engineering. To accelerate the chemoenzymatic reaction, here we systematically optimized the N-terminal penultimate residue of the acceptor peptide. Positively charged, small, or hydrophilic amino acids at this position show positive effects for the reaction. Kinetic analysis of peptides possessing different penultimate residues suggests that the side chain of the residue affects peptide-binding affinity towards the L/F-transferase. These findings also provide biological insight into the effect of the penultimate amino acid on substrate specificity of natural proteins to be degraded via the N-end rule pathway. A systematic kinetic analysis of L/F-transferase with different acceptor peptides. L/F-transferase discriminates the N-terminal penultimate residue of substrate peptides. The side chain of this residue affects the peptide binding affinity for L/F-transferase. Ser or Arg is this position optimizes introduction of non-natural amino acids into peptides The N-terminal penultimate residue of a protein may affect its stability in vivo.
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Affiliation(s)
- Jun Kawaguchi
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering, The University of Electro-Communications (UEC), 7-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
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Xu Z, Payoe R, Fahlman RP. The C-terminal proteolytic fragment of the breast cancer susceptibility type 1 protein (BRCA1) is degraded by the N-end rule pathway. J Biol Chem 2012; 287:7495-502. [PMID: 22262859 PMCID: PMC3293596 DOI: 10.1074/jbc.m111.301002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 01/05/2012] [Indexed: 01/27/2023] Open
Abstract
The breast cancer susceptibility type 1 gene product (BRCA1) is cleaved by caspases upon the activation of apoptotic pathways. After proteolysis the C-terminal fragment has been reported to translocate to the cytoplasm and promote cell death. Here we report that the C-terminal fragment is unstable in cells as it is targeted for degradation by the N-end rule pathway. The data reveals that mutating the wild type N-terminal aspartate, of the C-terminal fragment, to valine stabilizes the fragment. If the N terminus is mutated to another N-terminal destabilizing residue, like arginine, the C-terminal fragment remains unstable in cells. Last, the C-terminal fragment of BRCA1 is stable in cells lacking ATE1, a component of the N-end rule pathway.
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Affiliation(s)
- Zhizhong Xu
- From the Departments of Biochemistry and
- Oncology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | | | - Richard P. Fahlman
- From the Departments of Biochemistry and
- Oncology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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