2024
77-Coux O, Farràs R, Abbas M, Barrio R, Blattner C, Brix K, et al. ProteoCure: A European network to fine-tune the proteome. Biochimie 2024:S0300908424001408. https://doi.org/10.1016/j.biochi.2024.06.004.
76-Küry S, Stanton JE, Van Woerden G, Hsieh T-C, Rosenfelt C, Scott-Boyer MP, et al. Unveiling the crucial neuronal role of the proteasomal ATPase subunit gene PSMC5 in neurodevelopmental proteasomopathies 2024. https://doi.org/10.1101/2024.01.13.24301174.
75-Mascaro M, D’Ambrosio L, Lazzari E, Almoguera B, Swafiri ST, Zanchetta ME, et al. A unique missense mutation in the RING domain impairs MID1 E3 ubiquitin ligase activity and localisation and is associated with uncommon Opitz Syndrome-like signs. Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease 2024;1870:167126. https://doi.org/10.1016/j.bbadis.2024.167126.
74-Merino‐Cacho L, Barroso‐Gomila O, Hernández‐Sánchez S, Ramirez J, Mayor U, Sutherland JD, et al. Biotin‐Based Strategies to Explore the World of Ubiquitin and Ubiquitin‐Like Modifiers. ChemBioChem 2024;25:e202300746. https://doi.org/10.1002/cbic.202300746.
73-Bernardino R, Carvalho AS, Hall MJ, Alves L, Leão R, Sayyid R, et al. Profiling of urinary extracellular vesicle protein signatures from patients with cribriform and intraductal prostate carcinoma in a cross-sectional study. Sci Rep 2024;14:25065. https://doi.org/10.1038/s41598-024-75272-w.
72-Ketteler R, Kiso K, Von Chamier L, Agrotis A. ATG5 is dispensable for ATG8ylation of cellular proteins. Autophagy Reports 2024;3:2392450. https://doi.org/10.1080/27694127.2024.2392450.
71-Forbord KM, Lunde NN, Bosnjak-Olsen T, Johansen HT, Solberg R, Jafari A. Legumain is a paracrine regulator of osteoblast differentiation and mediates the inhibitory effect of TGF-β1 on osteoblast maturation. Front Endocrinol 2024;15:1445049. https://doi.org/10.3389/fendo.2024.1445049.
70-Bedja-Iacona L, Richard E, Marouillat S, Brulard C, Alouane T, Beltran S, et al. Post-Translational Variants of Major Proteins in Amyotrophic Lateral Sclerosis Provide New Insights into the Pathophysiology of the Disease. IJMS 2024;25:8664. https://doi.org/10.3390/ijms25168664.
69-Ayuso-García P, Sánchez-Rueda A, Velasco-Avilés S, Tamayo-Caro M, Ferrer-Pinós A, Huarte-Sebastian C, et al. Neddylation orchestrates the complex transcriptional and posttranscriptional program that drives Schwann cell myelination. Sci Adv 2024;10:eadm7600. https://doi.org/10.1126/sciadv.adm7600.
68-Zhou X, Mahdizadeh SJ, Le Gallo M, Eriksson LA, Chevet E, Lafont E. UFMylation: a ubiquitin-like modification. Trends in Biochemical Sciences 2024;49:52–67. https://doi.org/10.1016/j.tibs.2023.10.004.
67-Bernardino R, Carvalho AS, Hall MJ, Alves L, Leão R, Sayyid R, et al. Profiling of urinary extracellular vesicle protein signatures from patients with cribriform and intraductal prostate carcinoma in a cross-sectional study. Sci Rep 2024;14:25065. https://doi.org/10.1038/s41598-024-75272-w.
66-Sala-Gaston J, Pérez-Villegas EM, Armengol JA, Rawlins LE, Baple EL, Crosby AH, et al. Autophagy dysregulation via the USP20-ULK1 axis in the HERC2-related neurodevelopmental disorder. Cell Death Discov 2024;10:163. https://doi.org/10.1038/s41420-024-01931-6.
65-Zolg S, Donzelli L, Geiss-Friedlander R. N-terminal processing by dipeptidyl peptidase 9: Cut and Go! Biochimie 2024:S030090842400052X. https://doi.org/10.1016/j.biochi.2024.03.002.
64-Ebstein F, Latypova X, Sharon Hung KY, Prado MA, Lee B-H, Möller S, et al. Biallelic USP14 variants cause a syndromic neurodevelopmental disorder. Genetics in Medicine 2024;26:101120. https://doi.org/10.1016/j.gim.2024.101120.
63-Xu S, Gierisch ME, Barchi E, Poser I, Alberti S, Salomons FA, et al. Chemical inhibition of the integrated stress response impairs the ubiquitin-proteasome system. Commun Biol 2024;7:1282. https://doi.org/10.1038/s42003-024-06974-0.
62-Mahdizadeh SJ, Grandén J, Pelizzari-Raymundo D, Guillory X, Carlesso A, Chevet E, et al. Different binding modalities of quercetin to inositol-requiring enzyme 1 of S. cerevisiae and human lead to opposite regulation. Commun Chem 2024;7:6. https://doi.org/10.1038/s42004-023-01092-0.
61-Shahmoradi Ghahe S, Drabikowski K, Topf U. Identification of a non-canonical function of prefoldin subunit 5 in proteasome assembly 2024. https://doi.org/10.1101/2024.04.22.590501.
60-Deb W, Rosenfelt C, Vignard V, Papendorf JJ, Möller S, Wendlandt M, et al. PSMD11 loss-of-function variants correlate with a neurobehavioral phenotype, obesity, and increased interferon response. The American Journal of Human Genetics 2024;111:1352–69. https://doi.org/10.1016/j.ajhg.2024.05.016.
59-Srinivasan V, Soliymani R, Ivanova L, Eriksson O, Peitsaro N, Lalowski M, et al. USP14 regulates pS129 α-synuclein levels and oxidative stress in human SH-SY5Y dopaminergic cells 2024. https://doi.org/10.1101/2024.05.09.592905.
58-Martín-Villanueva S, Galmozzi CV, Ruger-Herreros C, Kressler D, De La Cruz J. The Beak of Eukaryotic Ribosomes: Life, Work and Miracles. Biomolecules 2024;14:882. https://doi.org/10.3390/biom14070882.
57-Oliveira BR, Nehlmeier I, Kempf AM, Venugopalan V, Rehders M, Ceniza MEP, et al. Cytoskeletal β-tubulin and cysteine cathepsin L deregulation by SARS-CoV-2 spike protein interaction with the neuronal model cell line SH-SY5Y. Biochimie 2024:S0300908424000440. https://doi.org/10.1016/j.biochi.2024.02.006.
56-Boumali R, Urli L, Naim M, Soualmia F, Kinugawa K, Petropoulos I, et al. Kallikrein-related peptidase’s significance in Alzheimer’s disease pathogenesis: A comprehensive survey. Biochimie 2024:S0300908424000762. https://doi.org/10.1016/j.biochi.2024.04.001.
55-Escalera-Balsera A, Robles-Bolivar P, Parra-Perez AM, Murillo-Cuesta S, Chua HC, Rodríguez-de La Rosa L, et al. A rare haplotype of the GJD3 gene segregating in familial Meniere Disease interferes with connexin assembly 2024. https://doi.org/10.1101/2024.01.16.24300842.
54-Eirich J, Boyer J-B, Armbruster L, Ivanauskaite A, De La Torre C, Meinnel T, et al. Light Changes Promote Distinct Responses of Plastid Protein Acetylation Marks. Molecular & Cellular Proteomics 2024;23:100845. https://doi.org/10.1016/j.mcpro.2024.100845.
53-Van Midden KP, Mantz M, Fonovič M, Gazvoda M, Svete J, Huesgen PF, et al. Mechanistic insights into CrCEP1: A dual-function cysteine protease with endo- and transpeptidase activity. International Journal of Biological Macromolecules 2024;271:132505. https://doi.org/10.1016/j.ijbiomac.2024.132505.
52-Buggiani J, Meinnel T, Giglione C, Frottin F. Advances in nuclear proteostasis of metazoans. Biochimie 2024:S0300908424000816. https://doi.org/10.1016/j.biochi.2024.04.006.
51-Bouvier C, Lawrence R, Cavallo F, Xolalpa W, Jordan A, Hjerpe R, et al. Breaking Bad Proteins—Discovery Approaches and the Road to Clinic for Degraders. Cells 2024;13:578. https://doi.org/10.3390/cells13070578.
50-Filippopoulou C, Thomé CC, Perdikari S, Ntini E, Simos G, Bohnsack KE, et al. Hypoxia-driven deSUMOylation of EXOSC10 promotes adaptive changes in the transcriptome profile. Cell Mol Life Sci 2024;81:58. https://doi.org/10.1007/s00018-023-05035-9.
49-Al Rawi S, Simpson L, Agnarsdóttir G, McDonald NQ, Chernuha V, Elpeleg O, et al. Study of an FBXO7patient mutation reveals Fbxo7 and PI 31 co‐regulate proteasomes and mitochondria. The FEBS Journal 2024;291:2565–89. https://doi.org/10.1111/febs.17114.
48-Desroys Du Roure P, Lajoie L, Mallavialle A, Alcaraz LB, Mansouri H, Fenou L, et al. A novel Fc-engineered cathepsin D-targeting antibody enhances ADCC, triggers tumor-infiltrating NK cell recruitment, and improves treatment with paclitaxel and enzalutamide in triple-negative breast cancer. J Immunother Cancer 2024;12:e007135. https://doi.org/10.1136/jitc-2023-007135.
47-Pineau R, Le Reste PJ, Avril T, Jarry U, Chevet E, Pelizzari-Raymundo D. Protocol to generate two distinct standard-of-care murine glioblastoma models for evaluating novel combination therapies. STAR Protocols 2024;5:103304. https://doi.org/10.1016/j.xpro.2024.103304.
46-Guedes JP, Boyer JB, Elurbide J, Carte B, Redeker V, Sago L, et al. NatB Protects Procaspase-8 from UBR4-Mediated Degradation and Is Required for Full Induction of the Extrinsic Apoptosis Pathway. Molecular and Cellular Biology 2024;44:358–71. https://doi.org/10.1080/10985549.2024.2382453.
45-Seoane R, Lama-Díaz T, Romero AM, El Motiam A, Martínez-Férriz A, Vidal S, et al. SUMOylation modulates eIF5A activities in both yeast and pancreatic ductal adenocarcinoma cells. Cell Mol Biol Lett 2024;29:15. https://doi.org/10.1186/s11658-024-00533-5.
2023
| 44-Taibi V, Polo S, Maspero E. Monitoring HECT Ubiquitination Activity In Vitro. Methods Mol Biol. 2023;2602: 81–92. doi:10.1007/978-1-0716-2859-1_6 |
| 43-Sengupta S, Pick E. The Ubiquitin-like Proteins of Saccharomyces cerevisiae. Biomolecules. 2023;13: 734. doi:10.3390/biom13050734 |
| 42-Samra N, Jansen NS, Morani I, Kakun RR, Zaid R, Paperna T, et al. Exome sequencing links the SUMO protease SENP7 with fatal arthrogryposis multiplex congenita, early respiratory failure and neutropenia. J Med Genet. 2023;60: 1133–1141. doi:10.1136/jmg-2023-109267 |
| 41-Sala-Gaston J, Costa-Sastre L, Pedrazza L, Martinez-Martinez A, Ventura F, Rosa JL. Regulation of MAPK Signaling Pathways by the Large HERC Ubiquitin Ligases. International Journal of Molecular Sciences. 2023;24: 4906. doi:10.3390/ijms24054906 |
| 40-Saad S, Berda E, Klein Y, Issa S, Pick E. Strategies for Monitoring “Ubiquitin C-Terminal Hydrolase 1” (Yuh1) Activity. In: Rodriguez MS, Barrio R, editors. The Ubiquitin Code. New York, NY: Springer US; 2023. pp. 107–122. doi:10.1007/978-1-0716-2859-1_8 |
| 30-Rosa JL. Regulation of Ubiquitin Family Signaling in Disease. International Journal of Molecular Sciences. 2023;24: 6735. doi:10.3390/ijms24076735 |
| 29-Rodriguez MS, Barrio R, editors. The Ubiquitin Code. New York, NY: Springer US; 2023. doi:10.1007/978-1-0716-2859-1 |
| 28-Quinet G, Génin P, Belgareh-Touzé N, Ozturk O, Weil R, Cohen MM, et al. Analysis of ATG8 Family Members Using LC3-Interacting Regions (LIR)-Based Molecular Traps. In: Rodriguez MS, Barrio R, editors. The Ubiquitin Code. New York, NY: Springer US; 2023. pp. 191–204. doi:10.1007/978-1-0716-2859-1_14 |
| 27-Pelizzari-Raymundo D, Doultsinos D, Pineau R, Sauzay C, Koutsandreas T, Langlais T, et al. A novel IRE1 kinase inhibitor for adjuvant glioblastoma treatment. iScience. 2023;26. doi:10.1016/j.isci.2023.106687 |
| 26-Pedrazza L, Martinez-Martinez A, Sánchez-de-Diego C, Valer JA, Pimenta-Lopes C, Sala-Gaston J, et al. HERC1 deficiency causes osteopenia through transcriptional program dysregulation during bone remodeling. Cell Death Dis. 2023;14: 1–11. doi:10.1038/s41419-023-05549-x |
| 25-Papendorf JJ, Ebstein F, Alehashemi S, Piotto DGP, Kozlova A, Terreri MT, et al. Identification of eight novel proteasome variants in five unrelated cases of proteasome-associated autoinflammatory syndromes (PRAAS). Frontiers in Immunology. 2023;14. Available: https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2023.1190104 |
| 24-Matthiesen R, Rodriguez MS, Carvalho AS. A Computational Tool for Analysis of Mass Spectrometry Data of Ubiquitin-Enriched Samples. In: Rodriguez MS, Barrio R, editors. The Ubiquitin Code. New York, NY: Springer US; 2023. pp. 205–214. doi:10.1007/978-1-0716-2859-1_15 |
| 23-Martínez-Férriz A, Gandía C, Pardo-Sánchez JM, Fathinajafabadi A, Ferrando A, Farràs R. Eukaryotic Initiation Factor 5A2 localizes to actively translating ribosomes to promote cancer cell protrusions and invasive capacity. Cell Commun Signal. 2023;21: 1–15. doi:10.1186/s12964-023-01076-6 |
| 22-Martínez-Alonso M, Gandioso A, Thibaudeau C, Qin X, Arnoux P, Demeubayeva N, et al. A Novel Near-IR Absorbing Ruthenium(II) Complex as Photosensitizer for Photodynamic Therapy and its Cetuximab Bioconjugates. ChemBioChem. 2023;24: e202300203. doi:10.1002/cbic.202300203 |
| 21-Ilter M, Schulze-Niemand E, Naumann M, Stein M. Structural Dynamics of Lys11-Selective Deubiquitinylase Cezanne-1 during the Catalytic Cycle. J Chem Inf Model. 2023;63: 2084–2094. doi:10.1021/acs.jcim.2c01281 |
| 20-Guedes JP, Boyer JB, Elurbide J, Carte B, Redeker V, Sago L, et al. NatB-dependent acetylation protects procaspase-8 from UBR4-mediated degradation and is required for full induction of the extrinsic apoptosis pathway. bioRxiv; 2023. p. 2023.09.25.559278. doi:10.1101/2023.09.25.559278 |
| 19-Gonzalez-Santamarta M, Ceccato L, Carvalho AS, Rain J-C, Matthiesen R, Rodriguez MS. Isolation and Mass Spectrometry Identification of K48 and K63 Ubiquitin Proteome Using Chain-Specific Nanobodies. In: Rodriguez MS, Barrio R, editors. The Ubiquitin Code. New York, NY: Springer US; 2023. pp. 125–136. doi:10.1007/978-1-0716-2859-1_9 |
| 18-Elabd S, Pauletto E, Solozobova V, Eickhoff N, Padrao N, Zwart W, et al. TRIM25 targets p300 for degradation. Life Sci Alliance. 2023;6: e202301980. doi:10.26508/lsa.202301980 |
| 17-Dubiel D, da Fonseca PCA, Valášek LS, Schulze-Niemand E, Naumann M. ZOMES: Cell physiology determined by PCI complexes and protein turnover. Biochimica et Biophysica Acta (BBA) – Molecular Cell Research. 2023;1870: 119402. doi:10.1016/j.bbamcr.2022.119402 |
| 16-David A, Chazeirat T, Saidi A, Lalmanach G, Lecaille F. The Interplay of Glycosaminoglycans and Cysteine Cathepsins in Mucopolysaccharidosis. Biomedicines. 2023;11: 810. doi:10.3390/biomedicines11030810 |
| 15-Creutznacher R, Schulze-Niemand E, König P, Stanojlovic V, Mallagaray A, Peters T, et al. Conformational Control of Fast Asparagine Deamidation in a Norovirus Capsid Protein. Biochemistry. 2023;62: 1032–1043. doi:10.1021/acs.biochem.2c00656 |
| 14-Barroso-Gomila O, Merino-Cacho L, Muratore V, Perez C, Taibi V, Maspero E, et al. BioE3 identifies specific substrates of ubiquitin E3 ligases. Nat Commun. 2023;14: 7656. doi:10.1038/s41467-023-43326-8 |
| 13-Barroso-Gomila O, Mayor U, Barrio R, Sutherland JD. SUMO-ID: A Strategy for the Identification of SUMO-Dependent Proximal Interactors. Methods Mol Biol. 2023;2602: 177–189. doi:10.1007/978-1-0716-2859-1_13 |
| 12-Arnesen T, Aksnes H, Giglione C. Protein Termini 2022: central roles of protein ends. Trends in Biochemical Sciences. 2023;48: 495–499. doi:10.1016/j.tibs.2023.02.008 |
2022
| 11-Schulze-Niemand E, Naumann M, Stein M. Substrate-assisted activation and selectivity of the bacterial RavD effector deubiquitinylase. Proteins: Structure, Function, and Bioinformatics. 2022;90: 947–958. doi:10.1002/prot.26286 |
| 10-Sala-Gaston J, Pedrazza L, Ramirez J, Martinez-Martinez A, Rawlins LE, Baple EL, et al. HERC2 deficiency activates C-RAF/MKK3/p38 signalling pathway altering the cellular response to oxidative stress. Cell Mol Life Sci. 2022;79: 548. doi:10.1007/s00018-022-04586-7 |
| 9-Rivière F, Dian C, Dutheil RF, Monassa P, Giglione C, Meinnel T. Structural and Large-scale Analysis Unveil the Intertwined Paths Promoting NMT-catalyzed Lysine and Glycine Myristoylation. Journal of Molecular Biology. 2022;434: 167843. doi:10.1016/j.jmb.2022.167843 |
| 8-Nagamalleswari E, Bakshi K, Breucker J, Gschweitl M, González-Prieto R, Eisenhardt N, et al. UBC9 and EME1 sumoylation foster ribosomal DNA damage repair in CPT response. bioRxiv; 2022. p. 2022.04.11.487628. doi:10.1101/2022.04.11.487628 |
| 7-Meinnel T, Giglione C. N-terminal modifications, the associated processing machinery, and their evolution in plastid-containing organisms. Journal of Experimental Botany. 2022;73: 6013–6033. doi:10.1093/jxb/erac290 |
| 6-Mann G, Sulkshane P, Sadhu P, Ziv T, Glickman MH, Brik A. Antibody for Serine 65 Phosphorylated Ubiquitin Identifies PLK1-Mediated Phosphorylation of Mitotic Proteins and APC1. Molecules. 2022;27: 4867. doi:10.3390/molecules27154867 |
| 5-Denamur S, Chazeirat T, Maszota-Zieleniak M, Vivès RR, Saidi A, Zhang F, et al. Binding of heparan sulfate to human cystatin C modulates inhibition of cathepsin L: Putative consequences in mucopolysaccharidosis. Carbohydrate Polymers. 2022;293: 119734. doi:10.1016/j.carbpol.2022.119734 |
| 4-De Azevedo J, Mourtada J, Bour C, Devignot V, Schultz P, Borel C, et al. The EXTREME Regimen Associating Cetuximab and Cisplatin Favors Head and Neck Cancer Cell Death and Immunogenicity with the Induction of an Anti-Cancer Immune Response. Cells. 2022;11: 2866. doi:10.3390/cells11182866 |
| 3-Bakshi K, Nagamalleswari E, Breucker J, Eisenhardt N, Tiwari R, González-Prieto R, et al. Multi-level monitoring of EME1-MUS81 in CPT induced nucleolar rDNA repair. bioRxiv; 2022. p. 2022.04.11.487769. doi:10.1101/2022.04.11.487769 |
| 2-Badie A, Gaiddon C, Mellitzer G. Histone Deacetylase Functions in Gastric Cancer: Therapeutic Target? Cancers. 2022;14: 5472. doi:10.3390/cancers14215472 |
| 1-Araújo SJ, Barrio R. Editorial: 17th Spanish Society for Developmental Biology Meeting: New Trends in Developmental Biology. Frontiers in Cell and Developmental Biology. 2022;10. Available: https://www.frontiersin.org/articles/10.3389/fcell.2022.897989 |