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Blanco-Touriñán N, Pérez-Alemany J, Bourbousse C, Latrasse D, Ait-Mohamed O, Benhamed M, Barneche F, Blázquez MA, Gallego-Bartolomé J, Alabadí D. The plant POLYMERASE-ASSOCIATED FACTOR1 complex links transcription and H2B monoubiquitination genome wide. Plant Physiol 2024; 195:640-651. [PMID: 38285074 PMCID: PMC11060679 DOI: 10.1093/plphys/kiae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/30/2024]
Abstract
The evolutionarily conserved POLYMERASE-ASSOCIATED FACTOR1 complex (Paf1C) participates in transcription, and research in animals and fungi suggests that it facilitates RNA POLYMERASE II (RNAPII) progression through chromatin. We examined the genomic distribution of the EARLY FLOWERING7 (ELF7) and VERNALIZATION INDEPENDENCE3 subunits of Paf1C in Arabidopsis (Arabidopsis thaliana). The occupancy of both subunits was confined to thousands of gene bodies and positively associated with RNAPII occupancy and the level of gene expression, supporting a role as a transcription elongation factor. We found that monoubiquitinated histone H2B, which marks most transcribed genes, was strongly reduced genome wide in elf7 seedlings. Genome-wide profiling of RNAPII revealed that in elf7 mutants, RNAPII occupancy was reduced throughout the gene body and at the transcription end site of Paf1C-targeted genes, suggesting a direct role for the complex in transcription elongation. Overall, our observations suggest a direct functional link between Paf1C activity, monoubiquitination of histone H2B, and the transition of RNAPII to productive elongation. However, for several genes, Paf1C may also act independently of H2Bub deposition or occupy these genes more stable than H2Bub marking, possibly reflecting the dynamic nature of Paf1C association and H2Bub turnover during transcription.
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Affiliation(s)
- Noel Blanco-Touriñán
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), 46022 Valencia, Spain
| | - Jaime Pérez-Alemany
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), 46022 Valencia, Spain
| | - Clara Bourbousse
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (CNRS), CNRS, INSERM, Université PSL, 75230 Paris, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (Université Paris-Saclay-CNRS), 91190 Gif-sur-Yvette, France
| | - Ouardia Ait-Mohamed
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (CNRS), CNRS, INSERM, Université PSL, 75230 Paris, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (Université Paris-Saclay-CNRS), 91190 Gif-sur-Yvette, France
| | - Fredy Barneche
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (CNRS), CNRS, INSERM, Université PSL, 75230 Paris, France
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), 46022 Valencia, Spain
| | | | - David Alabadí
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), 46022 Valencia, Spain
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Cavaco M, Valle J, Flores I, Andreu D, A. R. B. Castanho M. Estimating peptide half-life in serum from tunable, sequence-related physicochemical properties. Clin Transl Sci 2021; 14:1349-1358. [PMID: 33641212 PMCID: PMC8301568 DOI: 10.1111/cts.12985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/30/2020] [Accepted: 12/25/2020] [Indexed: 01/05/2023] Open
Abstract
Proteolytic instability is a critical limitation for peptide-based products. Although significant efforts are devoted to stabilize sequences against proteases/peptidases in plasma/serum, such approaches tend to be rather empirical, unspecific, time-consuming, and frequently not cost-effective. A more rational and potentially rewarding alternative is to identify the chemical grounds of susceptibility to enzymatic degradation of peptides so that proteolytic resistance can be tuned by manipulation of key chemical properties. In this regard, we conducted a meta-analysis of literature published over the last decade reporting experimental data on the lifetimes of peptides exposed to proteolytic conditions. Our initial database contained 579 entries and was curated with regard to amino acid sequence, chemical modification, terminal half-life (t1/2 ) or other stability readouts, type of stability assay, and biological application of the study. Although the majority of entries in the database corresponded to (slightly or substantially) modified peptides, we chose to focus on unmodified ones, as we aimed to decipher intrinsic characteristics of peptide proteolytic susceptibility. Specifically, we developed a multivariable regression model to unravel those peptide properties with most impact on proteolytic stability and thus potential t1/2 predicting ability. Model validation was done by two different approaches. First, a library of peptides spanning a large interval of properties that modulate stability was synthesized and their t1/2 in human serum were experimentally determined. Second, the t1/2 of 21 selected peptides approved for clinical use or in clinical trials were recorded and matched with the model-estimated values. With both approaches, good correlation between experimental and predicted t1/2 data was observed.
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Affiliation(s)
- Marco Cavaco
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaLisboaPortugal
- Proteomics and Protein Chemistry UnitDepartment of Experimental and Health SciencesPompeu Fabra UniversityBarcelonaSpain
| | - Javier Valle
- Proteomics and Protein Chemistry UnitDepartment of Experimental and Health SciencesPompeu Fabra UniversityBarcelonaSpain
| | - Isabel Flores
- Instituto das Políticas Públicas e Sociais do ISCTELisboaPortugal
| | - David Andreu
- Proteomics and Protein Chemistry UnitDepartment of Experimental and Health SciencesPompeu Fabra UniversityBarcelonaSpain
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Kober KI, Cano A, Géraud C, Sipilä K, Mobasseri SA, Philippeos C, Pisco AO, Stannard A, Martin A, Salvador F, Santos V, Boutros M, Rognoni E, Watt FM. Loxl2 is dispensable for dermal development, homeostasis and tumour stroma formation. PLoS One 2018; 13:e0199679. [PMID: 29953488 PMCID: PMC6023175 DOI: 10.1371/journal.pone.0199679] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/12/2018] [Indexed: 12/31/2022] Open
Abstract
Lysyl oxidase-like 2 (LOXL2) is a copper-dependent monoamine oxidase that contributes to the remodelling of the extracellular matrix (ECM) by cross linkage of collagen and elastin fibres and has emerged as a potential therapeutic target in cancer and fibrosis. In the skin, LOXL2 is essential for epidermal cell polarity and differentiation. However, its role in the dermis has not been evaluated. We found that Loxl2 is dispensable for mouse dermal development, maturation and homeostasis, yet affects dermal stiffness. Neither loss of Loxl2 nor increased Loxl2 expression affected dermal architecture following treatment with the phorbol ester TPA. Furthermore, Loxl2 expression did not alter the stroma of DMBA-TPA-induced tumours. We conclude that, although Loxl2 is expressed in both dermis and epidermis, its function appears largely confined to the epidermis.
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Affiliation(s)
- Katharina Isabelle Kober
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Amparo Cano
- Departamento de Bioquímica, UAM, Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Red, CIBERONC, Madrid, Spain
| | - Cyrill Géraud
- Section of Clinical and Molecular Dermatology, Department of Dermatology, Venereology and Allergology and European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kalle Sipilä
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy’s Hospital, London, United Kingdom
| | - Seyedeh Atefeh Mobasseri
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy’s Hospital, London, United Kingdom
| | - Christina Philippeos
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy’s Hospital, London, United Kingdom
| | - Angela Oliveira Pisco
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy’s Hospital, London, United Kingdom
| | - Andrew Stannard
- Department of Physics, King’s College London, Strand, London, United Kingdom
| | - Alberto Martin
- Departamento de Bioquímica, UAM, Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Red, CIBERONC, Madrid, Spain
| | - Fernando Salvador
- Departamento de Bioquímica, UAM, Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Red, CIBERONC, Madrid, Spain
| | - Vanesa Santos
- Departamento de Bioquímica, UAM, Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, IdiPAZ, Madrid, Spain
- Centro de Investigación Biomédica en Red, CIBERONC, Madrid, Spain
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Emanuel Rognoni
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy’s Hospital, London, United Kingdom
- * E-mail: (ER); (FMW)
| | - Fiona M. Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy’s Hospital, London, United Kingdom
- * E-mail: (ER); (FMW)
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