1
|
Rodríguez-López M, Bordin N, Lees J, Scholes H, Hassan S, Saintain Q, Kamrad S, Orengo C, Bähler J. Broad functional profiling of fission yeast proteins using phenomics and machine learning. eLife 2023; 12:RP88229. [PMID: 37787768 PMCID: PMC10547477 DOI: 10.7554/elife.88229] [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] [Indexed: 10/04/2023] Open
Abstract
Many proteins remain poorly characterized even in well-studied organisms, presenting a bottleneck for research. We applied phenomics and machine-learning approaches with Schizosaccharomyces pombe for broad cues on protein functions. We assayed colony-growth phenotypes to measure the fitness of deletion mutants for 3509 non-essential genes in 131 conditions with different nutrients, drugs, and stresses. These analyses exposed phenotypes for 3492 mutants, including 124 mutants of 'priority unstudied' proteins conserved in humans, providing varied functional clues. For example, over 900 proteins were newly implicated in the resistance to oxidative stress. Phenotype-correlation networks suggested roles for poorly characterized proteins through 'guilt by association' with known proteins. For complementary functional insights, we predicted Gene Ontology (GO) terms using machine learning methods exploiting protein-network and protein-homology data (NET-FF). We obtained 56,594 high-scoring GO predictions, of which 22,060 also featured high information content. Our phenotype-correlation data and NET-FF predictions showed a strong concordance with existing PomBase GO annotations and protein networks, with integrated analyses revealing 1675 novel GO predictions for 783 genes, including 47 predictions for 23 priority unstudied proteins. Experimental validation identified new proteins involved in cellular aging, showing that these predictions and phenomics data provide a rich resource to uncover new protein functions.
Collapse
Affiliation(s)
- María Rodríguez-López
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Nicola Bordin
- University College London, Institute of Structural and Molecular BiologyLondonUnited Kingdom
| | - Jon Lees
- University College London, Institute of Structural and Molecular BiologyLondonUnited Kingdom
- University of BristolBristolUnited Kingdom
| | - Harry Scholes
- University College London, Institute of Structural and Molecular BiologyLondonUnited Kingdom
| | - Shaimaa Hassan
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
- Helwan University, Faculty of PharmacyCairoEgypt
| | - Quentin Saintain
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Stephan Kamrad
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| | - Christine Orengo
- University College London, Institute of Structural and Molecular BiologyLondonUnited Kingdom
| | - Jürg Bähler
- University College London, Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentLondonUnited Kingdom
| |
Collapse
|
2
|
de Seny D, Baiwir D, Bianchi E, Cobraiville G, Deroyer C, Poulet C, Malaise O, Paulissen G, Kaiser MJ, Hauzeur JP, Mazzucchelli G, Delvenne P, Malaise M. New Proteins Contributing to Immune Cell Infiltration and Pannus Formation of Synovial Membrane from Arthritis Diseases. Int J Mol Sci 2021; 23:ijms23010434. [PMID: 35008858 PMCID: PMC8745719 DOI: 10.3390/ijms23010434] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 01/15/2023] Open
Abstract
An inflamed synovial membrane plays a major role in joint destruction and is characterized by immune cells infiltration and fibroblast proliferation. This proteomic study considers the inflammatory process at the molecular level by analyzing synovial biopsies presenting a histological inflammatory continuum throughout different arthritis joint diseases. Knee synovial biopsies were obtained from osteoarthritis (OA; n = 9), chronic pyrophosphate arthropathy (CPPA; n = 7) or rheumatoid arthritis (RA; n = 8) patients. The histological inflammatory score was determined using a semi-quantitative scale based on synovial hyperplasia, lymphocytes, plasmocytes, neutrophils and macrophages infiltration. Proteomic analysis was performed by liquid chromatography-mass spectrometry (LC-MS/MS). Differentially expressed proteins were confirmed by immunohistochemistry. Out of the 1871 proteins identified and quantified by LC-MS/MS, 10 proteins (LAP3, MANF, LCP1, CTSZ, PTPRC, DNAJB11, EML4, SCARA5, EIF3K, C1orf123) were differentially expressed in the synovial membrane of at least one of the three disease groups (RA, OA and CPPA). Significant increased expression of the seven first proteins was detected in RA and correlated to the histological inflammatory score. Proteomics is therefore a powerful tool that provides a molecular pattern to the classical histology usually applied for synovitis characterization. Except for LCP1, CTSZ and PTPRC, all proteins have never been described in human synovitis.
Collapse
Affiliation(s)
- Dominique de Seny
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
- Correspondence: ; Tel.: +32-366-24-74
| | - Dominique Baiwir
- GIGA Proteomics Facility, University of Liège, 4000 Liège, Belgium; (D.B.); (P.D.)
| | - Elettra Bianchi
- Department of Pathology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium;
| | - Gaël Cobraiville
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
| | - Céline Deroyer
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
| | - Christophe Poulet
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
| | - Olivier Malaise
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
| | - Geneviève Paulissen
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
| | - Marie-Joëlle Kaiser
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
| | - Jean-Philippe Hauzeur
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, 4000 Liège, Belgium;
| | - Philippe Delvenne
- GIGA Proteomics Facility, University of Liège, 4000 Liège, Belgium; (D.B.); (P.D.)
| | - Michel Malaise
- Laboratory and Service of Rheumatology, GIGA Research, Centre Hospitalier Universitaire de Liège, University of Liège, 4000 Liège, Belgium; (G.C.); (C.D.); (C.P.); (O.M.); (G.P.); (M.-J.K.); (J.-P.H.); (M.M.)
| |
Collapse
|
3
|
Jaswal S, Anand V, Ali SA, Jena MK, Kumar S, Kaushik JK, Mohanty AK. TMT based deep proteome analysis of buffalo mammary epithelial cells and identification of novel protein signatures during lactogenic differentiation. FASEB J 2021; 35:e21621. [PMID: 33977573 DOI: 10.1096/fj.202002476rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 01/04/2023]
Abstract
The lactating mammary gland harbours numerous matured alveoli with their lumen surrounded by differentiated mammary epithelial cells (MECs), which are exclusively involved in milk synthesis and secretion. Buffalo (Bubalus bubalis) is the second major milk-producing animal, and its physiology is different from cattle. The complete protein machinery involved in MECs differentiation is still not defined in ruminants, in particular, buffalo. Therefore, we have studied the differential expression of regulated proteins in the in vitro grown buffalo MECs (BuMECs) at different time points (on 3, 6, 12, and 15 days) of their differentiation in the presence of lactogenic hormones. TMT-based MS analysis identified 4,934 proteins; of them, 681 were differentially expressed proteins (DEPs). The principal component analysis suggested a highly heterogeneous expression of DEPs at the four-time points of hormone treatment, with most of them (307) attained the highest expression on 12 days. Bioinformatics analysis revealed the association of DEPs with 24 KEGG pathways. We observed few new proteins, namely ABCA13, IVL, VPS37, CZIB, RFX7, Rab5, TTLL12, SMEK1, GDI2, and TMEM131 in BuMECs. The function of one of the highly upregulated proteins, namely involucrin in the differentiation of BuMECs was confirmed based on biochemical inhibition assay. The results further conclude that the proteins with higher abundance can be considered as the potential biomarkers for differentiation, and they may have a significant association with the lactation process in buffalo too. The proteome dataset obtained can be used to understand the species-specific variations among other lactating animals.
Collapse
Affiliation(s)
- Shalini Jaswal
- Proteomics and Cell Biology Lab, Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, India
| | - Vijay Anand
- Department of Veterinary Physiology and Biochemistry, Veterinary College and Research Institute (TANUVAS), Orathanadu, India
| | - Syed Azmal Ali
- Proteomics and Cell Biology Lab, Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, India
| | - Manoj K Jena
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | - Sudarshan Kumar
- Proteomics and Cell Biology Lab, Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, India
| | - Jai K Kaushik
- Proteomics and Cell Biology Lab, Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, India
| | - Ashok K Mohanty
- Proteomics and Cell Biology Lab, Animal Biotechnology Centre, National Dairy Research Institute (NDRI), Karnal, India
| |
Collapse
|
4
|
Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome. Nat Microbiol 2019; 4:1798-1804. [PMID: 31332387 DOI: 10.1038/s41564-019-0514-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/13/2019] [Indexed: 12/21/2022]
Abstract
Microsporidia are eukaryotic parasites that infect essentially all animal species, including many of agricultural importance1-3, and are significant opportunistic parasites of humans4. They are characterized by having a specialized infection apparatus, an obligate intracellular lifestyle5, rudimentary mitochondria and the smallest known eukaryotic genomes5-7. Extreme genome compaction led to minimal gene sizes affecting even conserved ancient complexes such as the ribosome8-10. In the present study, the cryo-electron microscopy structure of the ribosome from the microsporidium Vairimorpha necatrix is presented, which illustrates how genome compaction has resulted in the smallest known eukaryotic cytoplasmic ribosome. Selection pressure led to the loss of two ribosomal proteins and removal of essentially all eukaryote-specific ribosomal RNA (rRNA) expansion segments, reducing the rRNA to a functionally conserved core. The structure highlights how one microsporidia-specific and several repurposed existing ribosomal proteins compensate for the extensive rRNA reduction. The microsporidian ribosome is kept in an inactive state by two previously uncharacterized dormancy factors that specifically target the functionally important E-site, P-site and polypeptide exit tunnel. The present study illustrates the distinct effects of evolutionary pressure on RNA and protein-coding genes, provides a mechanism for ribosome inhibition and can serve as a structural basis for the development of inhibitors against microsporidian parasites.
Collapse
|