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Abstract
Ubiquitination involves the covalent attachment of the protein ubiquitin to substrates. It can be reversed by the action of deubiquitinating enzymes (DUBs), thereby providing an important layer of regulation. Originally believed to be restricted to lysine residues, it is emerging that additional amino acids, including serine, threonine and cysteine, are also modified. It remains unknown which DUBs might target these unusual sites for deubiquitination. Herein, we develop representative model substrates and screen 53 DUBs for non-lysine activity, thereby providing important insights into DUB function. Strikingly, we find that a poorly studied DUB class has potent and highly selective serine/threonine activity. These findings suggest that non-lysine ubiquitination rivals the regulatory sophistication of its conventional counterpart and might serve distinct cellular functions. The reversibility of ubiquitination by the action of deubiquitinating enzymes (DUBs) serves as an important regulatory layer within the ubiquitin system. Approximately 100 DUBs are encoded by the human genome, and many have been implicated with pathologies, including neurodegeneration and cancer. Non-lysine ubiquitination is chemically distinct, and its physiological importance is emerging. Here, we couple chemically and chemoenzymatically synthesized ubiquitinated lysine and threonine model substrates to a mass spectrometry-based DUB assay. Using this platform, we profile two-thirds of known catalytically active DUBs for threonine esterase and lysine isopeptidase activity and find that most DUBs demonstrate dual selectivity. However, with two anomalous exceptions, the ovarian tumor domain DUB class demonstrates specific (iso)peptidase activity. Strikingly, we find the Machado–Joseph disease (MJD) class to be unappreciated non-lysine DUBs with highly specific ubiquitin esterase activity rivaling the efficiency of the most active isopeptidases. Esterase activity is dependent on the canonical catalytic triad, but proximal hydrophobic residues appear to be general determinants of non-lysine activity. Our findings also suggest that ubiquitin esters have appreciable cellular stability and that non-lysine ubiquitination is an integral component of the ubiquitin system. Its regulatory sophistication is likely to rival that of canonical ubiquitination.
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Romestand B, Rolland JL, Commeyras A, Coussot G, Desvignes I, Pascal R, Vandenabeele-Trambouze O. Dendrigraft Poly-l-lysine: A Non-Immunogenic Synthetic Carrier for Antibody Production. Biomacromolecules 2010; 11:1169-73. [DOI: 10.1021/bm9012056] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Bernard Romestand
- IFREMER, Université Montpellier 2, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5119, Ecosystèmes Lagunaires, place E. Bataillon, CC80, 34095 Montpellier cedex 5, France, COLCOM, Cap-Alpha, Av. de l’Europe, Clapiers, 34940 Montpellier Cedex 9, and Institut des Biomolécules Max Mousseron, Centre National de la Recherche Scientifique, Université de Montpellier 1, Université de Montpellier 2, Unité Mixte de Recherche 5247, place E. Bataillon, CC17006, 34095 Montpellier cedex 5, France
| | - Jean-Luc Rolland
- IFREMER, Université Montpellier 2, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5119, Ecosystèmes Lagunaires, place E. Bataillon, CC80, 34095 Montpellier cedex 5, France, COLCOM, Cap-Alpha, Av. de l’Europe, Clapiers, 34940 Montpellier Cedex 9, and Institut des Biomolécules Max Mousseron, Centre National de la Recherche Scientifique, Université de Montpellier 1, Université de Montpellier 2, Unité Mixte de Recherche 5247, place E. Bataillon, CC17006, 34095 Montpellier cedex 5, France
| | - Auguste Commeyras
- IFREMER, Université Montpellier 2, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5119, Ecosystèmes Lagunaires, place E. Bataillon, CC80, 34095 Montpellier cedex 5, France, COLCOM, Cap-Alpha, Av. de l’Europe, Clapiers, 34940 Montpellier Cedex 9, and Institut des Biomolécules Max Mousseron, Centre National de la Recherche Scientifique, Université de Montpellier 1, Université de Montpellier 2, Unité Mixte de Recherche 5247, place E. Bataillon, CC17006, 34095 Montpellier cedex 5, France
| | - Gaëlle Coussot
- IFREMER, Université Montpellier 2, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5119, Ecosystèmes Lagunaires, place E. Bataillon, CC80, 34095 Montpellier cedex 5, France, COLCOM, Cap-Alpha, Av. de l’Europe, Clapiers, 34940 Montpellier Cedex 9, and Institut des Biomolécules Max Mousseron, Centre National de la Recherche Scientifique, Université de Montpellier 1, Université de Montpellier 2, Unité Mixte de Recherche 5247, place E. Bataillon, CC17006, 34095 Montpellier cedex 5, France
| | - Isabelle Desvignes
- IFREMER, Université Montpellier 2, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5119, Ecosystèmes Lagunaires, place E. Bataillon, CC80, 34095 Montpellier cedex 5, France, COLCOM, Cap-Alpha, Av. de l’Europe, Clapiers, 34940 Montpellier Cedex 9, and Institut des Biomolécules Max Mousseron, Centre National de la Recherche Scientifique, Université de Montpellier 1, Université de Montpellier 2, Unité Mixte de Recherche 5247, place E. Bataillon, CC17006, 34095 Montpellier cedex 5, France
| | - Robert Pascal
- IFREMER, Université Montpellier 2, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5119, Ecosystèmes Lagunaires, place E. Bataillon, CC80, 34095 Montpellier cedex 5, France, COLCOM, Cap-Alpha, Av. de l’Europe, Clapiers, 34940 Montpellier Cedex 9, and Institut des Biomolécules Max Mousseron, Centre National de la Recherche Scientifique, Université de Montpellier 1, Université de Montpellier 2, Unité Mixte de Recherche 5247, place E. Bataillon, CC17006, 34095 Montpellier cedex 5, France
| | - Odile Vandenabeele-Trambouze
- IFREMER, Université Montpellier 2, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5119, Ecosystèmes Lagunaires, place E. Bataillon, CC80, 34095 Montpellier cedex 5, France, COLCOM, Cap-Alpha, Av. de l’Europe, Clapiers, 34940 Montpellier Cedex 9, and Institut des Biomolécules Max Mousseron, Centre National de la Recherche Scientifique, Université de Montpellier 1, Université de Montpellier 2, Unité Mixte de Recherche 5247, place E. Bataillon, CC17006, 34095 Montpellier cedex 5, France
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Abstract
The introduction of noncanonical amino acids and biophysical probes into peptides and proteins, and total or segmental isotopic labelling has the potential to greatly aid the determination of protein structure, function and protein-protein interactions. To obtain a peptide as large as possible by solid-phase peptide synthesis, native chemical ligation was introduced to enable synthesis of proteins of up to 120 amino acids in length. After the discovery of inteins, with their self-splicing properties and their application in protein synthesis, the semisynthetic methodology, expressed protein ligation, was developed to circumvent size limitation problems. Today, diverse expression vectors are available that allow the production of N- and C-terminal fragments that are needed for ligation to produce large amounts and high purity protein(s) (protein alpha-thioesters and peptides or proteins with N-terminal Cys). Unfortunately, expressed protein ligation is still limited mainly by the requirement of a Cys residue. Of course, additional Cys residues can be introduced into the sequence by site directed mutagenesis or synthesis, however, those mutations may disturb protein structure and function. Recently, alternative ligation approaches have been developed that do not require Cys residues. Accordingly, it is theoretically possible to obtain each modified protein using ligation strategies.
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Affiliation(s)
- Ralf David
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Germany
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