1
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Quinn J, Ethier EC, Novielli A, Malone A, Ramirez CE, Salloum L, Trombetta BA, Kivisäkk P, Bremang M, Selzer S, Fournier M, Das S, Xing Y, Arnold SE, Carlyle BC. Correction to "Cerebrospinal Fluid and Brain Proteoforms of the Granin Neuropeptide Family in Alzheimer's Disease". J Am Soc Mass Spectrom 2023; 34:2435-2436. [PMID: 37581263 PMCID: PMC10557374 DOI: 10.1021/jasms.3c00265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Indexed: 08/16/2023]
Affiliation(s)
- James
P. Quinn
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Elizabeth C. Ethier
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Angelo Novielli
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Aygul Malone
- Advanced
Proteomics Facility, Department of Biochemistry, University of Oxford, Oxford, Oxfordshire OX1 3QU, United Kingdom
| | - Christopher E. Ramirez
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Lauren Salloum
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Bianca A. Trombetta
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Pia Kivisäkk
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Michael Bremang
- Proteome
Sciences LLC, Frankfurt am Main, Hessen 60438, Germany
| | - Stefan Selzer
- Proteome
Sciences LLC, Frankfurt am Main, Hessen 60438, Germany
| | - Marjorie Fournier
- Advanced
Proteomics Facility, Department of Biochemistry, University of Oxford, Oxford, Oxfordshire OX1 3QU, United Kingdom
| | - Sudeshna Das
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Yaoyi Xing
- Department
of Physiology, Anatomy & Genetics, University
of Oxford, Oxford, Oxfordshire OX1 3QU, United Kingdom
- Kavli
Institute for Nanoscience Discovery, University
of Oxford, Oxford OX1 3QU, United
Kingdom
| | - Steven E. Arnold
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Becky C. Carlyle
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
- Department
of Physiology, Anatomy & Genetics, University
of Oxford, Oxford, Oxfordshire OX1 3QU, United Kingdom
- Kavli
Institute for Nanoscience Discovery, University
of Oxford, Oxford OX1 3QU, United
Kingdom
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2
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Yip PK, Bremang M, Pike I, Ponnusamy V, Michael-Titus AT, Shah DK. Newborns with Favourable Outcomes after Perinatal Asphyxia Have Upregulated Glucose Metabolism-Related Proteins in Plasma. Biomolecules 2023; 13:1471. [PMID: 37892154 PMCID: PMC10604898 DOI: 10.3390/biom13101471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/17/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Hypoxic-ischaemic encephalopathy (HIE) is an important cause of morbidity and mortality globally. Although mild therapeutic hypothermia (TH) may improve outcomes in selected babies, the mechanism of action is not fully understood. A proteomics discovery study was carried out to analyse proteins in the plasma of newborns with HIE. Proteomic analysis of plasma from 22 newborns with moderate-severe HIE that had initially undergone TH, and relative controls including 10 newborns with mild HIE who did not warrant TH and also cord blood from 10 normal births (non-HIE) were carried out using the isobaric Tandem Mass Tag (TMT®) 10plexTM labelling with tandem mass spectrometry. A total of 7818 unique peptides were identified in all TMT10plexTM samples, translating to 3457 peptides representing 405 proteins, after applying stringent filter criteria. Apart from the unique protein signature from normal cord blood, unsupervised analysis revealed several significantly regulated proteins in the TH-treated moderate-severe HIE group. GO annotation and functional clustering revealed various proteins associated with glucose metabolism: the enzymes fructose-bisphosphate aldolase A, glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate mutase 1, phosphoglycerate kinase 1, and pyruvate kinase PKM were upregulated in newborns with favourable (sHIE+) outcomes compared to newborns with unfavourable (sHIE-) outcomes. Those with favourable outcomes had normal MR imaging or mild abnormalities not predictive of adverse outcomes. However, in comparison to mild HIE and the sHIE- groups, the sHIE+ group had the additional glucose metabolism-related enzymes upregulated, including triosephosphate isomerase, α-enolase, 6-phosphogluconate dehydrogenase, transaldolase, and mitochondrial glutathione reductase. In conclusion, our plasma proteomic study demonstrates that TH-treated newborns with favourable outcomes have an upregulation in glucose metabolism. These findings may open new avenues for more effective neuroprotective therapy.
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Affiliation(s)
- Ping K. Yip
- Centre for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK; (V.P.); (A.T.M.-T.); (D.K.S.)
| | - Michael Bremang
- Proteome Sciences PLC, Coveham House, Surrey KT11 3EP, UK (I.P.)
| | - Ian Pike
- Proteome Sciences PLC, Coveham House, Surrey KT11 3EP, UK (I.P.)
| | - Vennila Ponnusamy
- Centre for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK; (V.P.); (A.T.M.-T.); (D.K.S.)
- St. Peter’s Hospital (Ashford and St. Peter’s Hospitals NHS Foundation Trust), Chertsey KT16 0PZ, UK
| | - Adina T. Michael-Titus
- Centre for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK; (V.P.); (A.T.M.-T.); (D.K.S.)
| | - Divyen K. Shah
- Centre for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK; (V.P.); (A.T.M.-T.); (D.K.S.)
- Neonatal Unit, Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK
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3
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Quinn J, Ethier EC, Novielli A, Malone A, Ramirez CE, Salloum L, Trombetta BA, Kivisäkk P, Bremang M, Selzer S, Fournier M, Das S, Xing Y, Arnold SE, Carlyle BC. Cerebrospinal Fluid and Brain Proteoforms of the Granin Neuropeptide Family in Alzheimer's Disease. J Am Soc Mass Spectrom 2023; 34:649-667. [PMID: 36912488 PMCID: PMC10080684 DOI: 10.1021/jasms.2c00341] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/11/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The granin neuropeptide family is composed of acidic secretory signaling molecules that act throughout the nervous system to help modulate synaptic signaling and neural activity. Granin neuropeptides have been shown to be dysregulated in different forms of dementia, including Alzheimer's disease (AD). Recent studies have suggested that the granin neuropeptides and their protease-cleaved bioactive peptides (proteoforms) may act as both powerful drivers of gene expression and as a biomarker of synaptic health in AD. The complexity of granin proteoforms in human cerebrospinal fluid (CSF) and brain tissue has not been directly addressed. We developed a reliable nontryptic mass spectrometry assay to comprehensively map and quantify endogenous neuropeptide proteoforms in the brain and CSF of individuals diagnosed with mild cognitive impairment and dementia due to AD compared to healthy controls, individuals with preserved cognition despite AD pathology ("Resilient"), and those with impaired cognition but no AD or other discernible pathology ("Frail"). We drew associations between neuropeptide proteoforms, cognitive status, and AD pathology values. Decreased levels of VGF proteoforms were observed in CSF and brain tissue from individuals with AD compared to controls, while select proteoforms from chromogranin A showed the opposite effect. To address mechanisms of neuropeptide proteoform regulation, we showed that the proteases Calpain-1 and Cathepsin S can cleave chromogranin A, secretogranin-1, and VGF into proteoforms found in both the brain and CSF. We were unable to demonstrate differences in protease abundance in protein extracts from matched brains, suggesting that regulation may occur at the level of transcription.
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Affiliation(s)
- James
P. Quinn
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Elizabeth C. Ethier
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Angelo Novielli
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Aygul Malone
- Advanced
Proteomics Facility, Department of Biochemistry, University of Oxford, Oxford, Oxfordshire OX1 3QU, United Kingdom
| | - Christopher E. Ramirez
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Lauren Salloum
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Bianca A. Trombetta
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Pia Kivisäkk
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Michael Bremang
- Proteome
Sciences LLC, Frankfurt am Main, Hessen 60438, Germany
| | - Stefan Selzer
- Proteome
Sciences LLC, Frankfurt am Main, Hessen 60438, Germany
| | - Marjorie Fournier
- Advanced
Proteomics Facility, Department of Biochemistry, University of Oxford, Oxford, Oxfordshire OX1 3QU, United Kingdom
| | - Sudeshna Das
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Yaoyi Xing
- Department
of Physiology, Anatomy & Genetics, University
of Oxford, Oxford, Oxfordshire OX1 3QU, United Kingdom
- Kavli
Institute for Nanoscience Discovery, University
of Oxford, Oxford OX1 3QU, United
Kingdom
| | - Steven E. Arnold
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
| | - Becky C. Carlyle
- Massachusetts
General Hospital Department of Neurology, Harvard Medical School, Boston, Massachusetts 02129, United States
- Department
of Physiology, Anatomy & Genetics, University
of Oxford, Oxford, Oxfordshire OX1 3QU, United Kingdom
- Kavli
Institute for Nanoscience Discovery, University
of Oxford, Oxford OX1 3QU, United
Kingdom
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4
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Adiutori R, Puentes F, Bremang M, Lombardi V, Zubiri I, Leoni E, Aarum J, Sheer D, McArthur S, Pike I, Malaspina A. Analysis of circulating protein aggregates as a route of investigation into neurodegenerative disorders. Brain Commun 2021; 3:fcab148. [PMID: 34396108 PMCID: PMC8361415 DOI: 10.1093/braincomms/fcab148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 03/08/2021] [Accepted: 04/22/2021] [Indexed: 11/22/2022] Open
Abstract
Plasma proteome composition reflects the inflammatory and metabolic state of the organism and can be predictive of system-level and organ-specific pathologies. Circulating protein aggregates are enriched with neurofilament heavy chain-axonal proteins involved in brain aggregate formation and recently identified as biomarkers of the fatal neuromuscular disorder amyotrophic lateral sclerosis. Using unbiased proteomic methods, we have fully characterized the content in neuronal proteins of circulating protein aggregates from amyotrophic lateral sclerosis patients and healthy controls, with reference to brain protein aggregate composition. We also investigated circulating protein aggregate protein aggregation propensity, stability to proteolytic digestion and toxicity for neuronal and endothelial cell lines. Circulating protein aggregates separated by ultracentrifugation are visible as electron-dense macromolecular particles appearing as either large globular or as small filamentous formations. Analysis by mass spectrometry revealed that circulating protein aggregates obtained from patients are enriched with proteins involved in the proteasome system, possibly reflecting the underlying basis of dysregulated proteostasis seen in the disease, while those from healthy controls show enrichment of proteins involved in metabolism. Compared to the whole human proteome, proteins within circulating protein aggregates and brain aggregates show distinct chemical features of aggregation propensity, which appear dependent on the tissue or fluid of origin and not on the health status. Neurofilaments' two high-mass isoforms (460 and 268 kDa) showed a strong differential expression in amyotrophic lateral sclerosis compared to healthy control circulating protein aggregates, while aggregated neurofilament heavy chain was also partially resistant to enterokinase proteolysis in patients, demonstrated by immunoreactive bands at 171 and 31 kDa fragments not seen in digested healthy controls samples. Unbiased proteomics revealed that a total of 4973 proteins were commonly detected in circulating protein aggregates and brain, including 24 expressed from genes associated with amyotrophic lateral sclerosis. Interestingly, 285 circulating protein aggregate proteins (5.7%) were regulated (P < 0.05) and are present in biochemical pathways linked to disease pathogenesis and protein aggregation. Biologically, circulating protein aggregates from both patients and healthy controls had a more pronounced effect on the viability of hCMEC/D3 endothelial and PC12 neuronal cells compared to immunoglobulins extracted from the same plasma samples. Furthermore, circulating protein aggregates from patients exerted a more toxic effect than healthy control circulating protein aggregates on both cell lines at lower concentrations (P: 0.03, in both cases). This study demonstrates that circulating protein aggregates are significantly enriched with brain proteins which are representative of amyotrophic lateral sclerosis pathology and a potential source of biomarkers and therapeutic targets for this incurable disorder.
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Affiliation(s)
- Rocco Adiutori
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Fabiola Puentes
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Michael Bremang
- Proteome Sciences R&D GmbH & Co. KG, Frankfurt am Main 60438, Germany
| | - Vittoria Lombardi
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Irene Zubiri
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Emanuela Leoni
- Proteome Sciences R&D GmbH & Co. KG, Frankfurt am Main 60438, Germany
| | - Johan Aarum
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm 171 76, Sweden
| | - Denise Sheer
- Centre for Genomics and Child Health, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Simon McArthur
- Institute of Dentistry, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Ian Pike
- Proteome Sciences plc, Hamilton House, Mabledon Place, London WC1H 9BB, UK
| | - Andrea Malaspina
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
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5
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Leoni E, Bremang M, Mitra V, Zubiri I, Jung S, Lu CH, Adiutori R, Lombardi V, Russell C, Koncarevic S, Ward M, Pike I, Malaspina A. Author Correction: Combined Tissue-Fluid Proteomics to Unravel Phenotypic Variability in Amyotrophic Lateral Sclerosis. Sci Rep 2020; 10:18603. [PMID: 33097756 PMCID: PMC7584588 DOI: 10.1038/s41598-020-74974-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Emanuela Leoni
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438, Frankfurt am Main, Germany
| | - Michael Bremang
- Proteome Sciences plc, Hamilton House, Mabledon Place, London, WC1H 9BB, UK
| | - Vikram Mitra
- Proteome Sciences plc, Hamilton House, Mabledon Place, London, WC1H 9BB, UK
| | - Irene Zubiri
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Stephan Jung
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438, Frankfurt am Main, Germany
| | - Ching-Hua Lu
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Rocco Adiutori
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Vittoria Lombardi
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Claire Russell
- Proteome Sciences plc, Hamilton House, Mabledon Place, London, WC1H 9BB, UK
| | - Sasa Koncarevic
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438, Frankfurt am Main, Germany
| | - Malcolm Ward
- Proteome Sciences plc, Hamilton House, Mabledon Place, London, WC1H 9BB, UK
| | - Ian Pike
- Proteome Sciences plc, Hamilton House, Mabledon Place, London, WC1H 9BB, UK.
| | - Andrea Malaspina
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK.
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6
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Iacovella MG, Bremang M, Basha O, Giacò L, Carotenuto W, Golfieri C, Szakal B, Dal Maschio M, Infantino V, Beznoussenko GV, Joseph CR, Visintin C, Mironov AA, Visintin R, Branzei D, Ferreira-Cerca S, Yeger-Lotem E, De Wulf P. Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae. Nucleic Acids Res 2019; 46:7586-7611. [PMID: 30011030 PMCID: PMC6125641 DOI: 10.1093/nar/gky618] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/28/2018] [Indexed: 12/14/2022] Open
Abstract
The Saccharomyces cerevisiae kinase/adenosine triphosphatase Rio1 regulates rDNA transcription and segregation, pre-rRNA processing and small ribosomal subunit maturation. Other roles are unknown. When overexpressed, human ortholog RIOK1 drives tumor growth and metastasis. Likewise, RIOK1 promotes 40S ribosomal subunit biogenesis and has not been characterized globally. We show that Rio1 manages directly and via a series of regulators, an essential signaling network at the protein, chromatin and RNA levels. Rio1 orchestrates growth and division depending on resource availability, in parallel to the nutrient-activated Tor1 kinase. To define the Rio1 network, we identified its physical interactors, profiled its target genes/transcripts, mapped its chromatin-binding sites and integrated our data with yeast’s protein–protein and protein–DNA interaction catalogs using network computation. We experimentally confirmed network components and localized Rio1 also to mitochondria and vacuoles. Via its network, Rio1 commands protein synthesis (ribosomal gene expression, assembly and activity) and turnover (26S proteasome expression), and impinges on metabolic, energy-production and cell-cycle programs. We find that Rio1 activity is conserved to humans and propose that pathological RIOK1 may fuel promiscuous transcription, ribosome production, chromosomal instability, unrestrained metabolism and proliferation; established contributors to cancer. Our study will advance the understanding of numerous processes, here revealed to depend on Rio1 activity.
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Affiliation(s)
- Maria G Iacovella
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Michael Bremang
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.,Current address: Proteome Sciences Plc, Hamilton House, Mabledon Place, London, United Kingdom
| | - Omer Basha
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, POB 653, Beer-Sheva 84105, Israel
| | - Luciano Giacò
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Walter Carotenuto
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Cristina Golfieri
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Barnabas Szakal
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Marianna Dal Maschio
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Valentina Infantino
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Galina V Beznoussenko
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Chinnu R Joseph
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Clara Visintin
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Alexander A Mironov
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Rosella Visintin
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Dana Branzei
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy.,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Sébastien Ferreira-Cerca
- Lehrstuhl für Biochemie III, Universität Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Esti Yeger-Lotem
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, POB 653, Beer-Sheva 84105, Israel
| | - Peter De Wulf
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.,Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
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7
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Marttinen M, Paananen J, Neme A, Mitra V, Takalo M, Natunen T, Paldanius KMA, Mäkinen P, Bremang M, Kurki MI, Rauramaa T, Leinonen V, Soininen H, Haapasalo A, Pike I, Hiltunen M. A multiomic approach to characterize the temporal sequence in Alzheimer's disease-related pathology. Neurobiol Dis 2018; 124:454-468. [PMID: 30557660 DOI: 10.1016/j.nbd.2018.12.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/15/2018] [Accepted: 12/13/2018] [Indexed: 02/08/2023] Open
Abstract
No single-omic approach completely elucidates the multitude of alterations taking place in Alzheimer's disease (AD). Here, we coupled transcriptomic and phosphoproteomic approaches to determine the temporal sequence of changes in mRNA, protein, and phosphopeptide expression levels from human temporal cortical samples, with varying degree of AD-related pathology. This approach highlighted fluctuation in synaptic and mitochondrial function as the earliest pathological events in brain samples with AD-related pathology. Subsequently, increased expression of inflammation and extracellular matrix-associated gene products was observed. Interaction network assembly for the associated gene products, emphasized the complex interplay between these processes and the role of addressing post-translational modifications in the identification of key regulators. Additionally, we evaluate the use of decision trees and random forests in identifying potential biomarkers differentiating individuals with different degree of AD-related pathology. This multiomic and temporal sequence-based approach provides a better understanding of the sequence of events leading to AD.
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Affiliation(s)
- Mikael Marttinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Jussi Paananen
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Antonio Neme
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Vikram Mitra
- Proteome Sciences plc, Cobham, London WC1H 9BB, United Kingdom
| | - Mari Takalo
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Teemu Natunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Kaisa M A Paldanius
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Petra Mäkinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Michael Bremang
- Proteome Sciences plc, Cobham, London WC1H 9BB, United Kingdom
| | - Mitja I Kurki
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Psychiatry, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Neurosurgery of Neuro Center, Kuopio University Hospital, Kuopio 70029, Finland
| | - Tuomas Rauramaa
- Department of Pathology, Kuopio University Hospital and University of Eastern Finland, Kuopio 70029, Finland
| | - Ville Leinonen
- Neurosurgery of Neuro Center, Kuopio University Hospital, Kuopio 70029, Finland
| | - Hilkka Soininen
- Neurology of Neuro Center, Kuopio University Hospital, Kuopio 70029, Finland; Institute of Clinical Medicine/Neurology, University of Eastern Finland, Kuopio 70210, Finland
| | - Annakaisa Haapasalo
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Ian Pike
- Proteome Sciences plc, Cobham, London WC1H 9BB, United Kingdom
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland.
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8
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Zubiri I, Lombardi V, Bremang M, Mitra V, Nardo G, Adiutori R, Lu CH, Leoni E, Yip P, Yildiz O, Ward M, Greensmith L, Bendotti C, Pike I, Malaspina A. Tissue-enhanced plasma proteomic analysis for disease stratification in amyotrophic lateral sclerosis. Mol Neurodegener 2018; 13:60. [PMID: 30404656 PMCID: PMC6223075 DOI: 10.1186/s13024-018-0292-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 10/16/2018] [Indexed: 12/11/2022] Open
Abstract
Background It is unclear to what extent pre-clinical studies in genetically homogeneous animal models of amyotrophic lateral sclerosis (ALS), an invariably fatal neurodegenerative disorder, can be informative of human pathology. The disease modifying effects in animal models of most therapeutic compounds have not been reproduced in patients. To advance therapeutics in ALS, we need easily accessible disease biomarkers which can discriminate across the phenotypic variants observed in ALS patients and can bridge animal and human pathology. Peripheral blood mononuclear cells alterations reflect the rate of progression of the disease representing an ideal biological substrate for biomarkers discovery. Methods We have applied TMTcalibrator™, a novel tissue-enhanced bio fluid mass spectrometry technique, to study the plasma proteome in ALS, using peripheral blood mononuclear cells as tissue calibrator. We have tested slow and fast progressing SOD1G93A mouse models of ALS at a pre-symptomatic and symptomatic stage in parallel with fast and slow progressing ALS patients at an early and late stage of the disease. Immunoassays were used to retest the expression of relevant protein candidates. Results The biological features differentiating fast from slow progressing mouse model plasma proteomes were different from those identified in human pathology, with only processes encompassing membrane trafficking with translocation of GLUT4, innate immunity, acute phase response and cytoskeleton organization showing enrichment in both species. Biological processes associated with senescence, RNA processing, cell stress and metabolism, major histocompatibility complex-II linked immune-reactivity and apoptosis (early stage) were enriched specifically in fast progressing ALS patients. Immunodetection confirmed regulation of the immunosenescence markers Galectin-3, Integrin beta 3 and Transforming growth factor beta-1 in plasma from pre-symptomatic and symptomatic transgenic animals while Apolipoprotein E differential plasma expression provided a good separation between fast and slow progressing ALS patients. Conclusions These findings implicate immunosenescence and metabolism as novel targets for biomarkers and therapeutic discovery and suggest immunomodulation as an early intervention. The variance observed in the plasma proteomes may depend on different biological patterns of disease progression in human and animal model. Electronic supplementary material The online version of this article (10.1186/s13024-018-0292-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene Zubiri
- Neuroscience and Trauma Centre, Blizard Institute, Barts and The School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, City of London, Greater London, E1 2AT, UK. .,Proteome Sciences plc, Hamilton House, Mabledon Place, London, UK.
| | - Vittoria Lombardi
- Neuroscience and Trauma Centre, Blizard Institute, Barts and The School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, City of London, Greater London, E1 2AT, UK
| | - Michael Bremang
- Proteome Sciences plc, Hamilton House, Mabledon Place, London, UK
| | - Vikram Mitra
- Proteome Sciences plc, Hamilton House, Mabledon Place, London, UK
| | - Giovanni Nardo
- Laboratory of Molecular Neurobiology, Department of Neuroscience, IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Rocco Adiutori
- Neuroscience and Trauma Centre, Blizard Institute, Barts and The School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, City of London, Greater London, E1 2AT, UK
| | - Ching-Hua Lu
- Neuroscience and Trauma Centre, Blizard Institute, Barts and The School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, City of London, Greater London, E1 2AT, UK.,Department of Neurology, China Medical University Hospital, Taichung City, Taiwan
| | - Emanuela Leoni
- Neuroscience and Trauma Centre, Blizard Institute, Barts and The School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, City of London, Greater London, E1 2AT, UK.,Proteome Sciences plc, Hamilton House, Mabledon Place, London, UK
| | - Ping Yip
- Neuroscience and Trauma Centre, Blizard Institute, Barts and The School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, City of London, Greater London, E1 2AT, UK
| | - Ozlem Yildiz
- Neuroscience and Trauma Centre, Blizard Institute, Barts and The School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, City of London, Greater London, E1 2AT, UK
| | - Malcolm Ward
- Proteome Sciences plc, Hamilton House, Mabledon Place, London, UK
| | - Linda Greensmith
- Sobell Department of Motor Neuroscience and Movement Disorders, MRC Centre for Neuromuscular Disorders, UCL Institute of Neurology, University College London, London, UK
| | - Caterina Bendotti
- Laboratory of Molecular Neurobiology, Department of Neuroscience, IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Ian Pike
- Proteome Sciences plc, Hamilton House, Mabledon Place, London, UK
| | - Andrea Malaspina
- Neuroscience and Trauma Centre, Blizard Institute, Barts and The School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, City of London, Greater London, E1 2AT, UK.
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9
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Adiutori R, Aarum J, Zubiri I, Bremang M, Jung S, Sheer D, Pike I, Malaspina A. The proteome of neurofilament-containing protein aggregates in blood. Biochem Biophys Rep 2018; 14:168-177. [PMID: 29872749 PMCID: PMC5986704 DOI: 10.1016/j.bbrep.2018.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/15/2018] [Accepted: 04/26/2018] [Indexed: 11/24/2022] Open
Abstract
Protein aggregation in biofluids is a poorly understood phenomenon. Under normal physiological conditions, fluid-borne aggregates may contain plasma or cell proteins prone to aggregation. Recent observations suggest that neurofilaments (Nf), the building blocks of neurons and a biomarker of neurodegeneration, are included in high molecular weight complexes in circulation. The composition of these Nf-containing hetero-aggregates (NCH) may change in systemic or organ-specific pathologies, providing the basis to develop novel disease biomarkers. We have tested ultracentrifugation (UC) and a commercially available protein aggregate binder, Seprion PAD-Beads (SEP), for the enrichment of NCH from plasma of healthy individuals, and then characterised the Nf content of the aggregate fractions using gel electrophoresis and their proteome by mass spectrometry (MS). Western blot analysis of fractions obtained by UC showed that among Nf isoforms, neurofilament heavy chain (NfH) was found within SDS-stable high molecular weight aggregates. Shotgun proteomics of aggregates obtained with both extraction techniques identified mostly cell structural and to a lesser extent extra-cellular matrix proteins, while functional analysis revealed pathways involved in inflammatory response, phagosome and prion-like protein behaviour. UC aggregates were specifically enriched with proteins involved in endocrine, metabolic and cell-signalling regulation. We describe the proteome of neurofilament-containing aggregates isolated from healthy individuals biofluids using different extraction methods.
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Affiliation(s)
- Rocco Adiutori
- Centre for Neuroscience and Trauma, Queen Mary University of London, Blizard Institute, Barts and The School of Medicine and Dentistry, London, United Kingdom
| | - Johan Aarum
- Centre for Genomics and Child Health, Queen Mary University of London, Blizard Institute, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - Irene Zubiri
- Centre for Neuroscience and Trauma, Queen Mary University of London, Blizard Institute, Barts and The School of Medicine and Dentistry, London, United Kingdom
| | - Michael Bremang
- Proteome Sciences Plc, Hamilton House, Mabledon Place, London, United Kingdom
| | - Stephan Jung
- ProteomeSciencesR&DGmbH&Co.KG, Frankfurt, Germany
| | - Denise Sheer
- Centre for Genomics and Child Health, Queen Mary University of London, Blizard Institute, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - Ian Pike
- Proteome Sciences Plc, Hamilton House, Mabledon Place, London, United Kingdom
| | - Andrea Malaspina
- Centre for Neuroscience and Trauma, Queen Mary University of London, Blizard Institute, Barts and The School of Medicine and Dentistry, London, United Kingdom
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10
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Mihailovich M, Bremang M, Spadotto V, Musiani D, Vitale E, Varano G, Zambelli F, Mancuso FM, Cairns DA, Pavesi G, Casola S, Bonaldi T. miR-17-92 fine-tunes MYC expression and function to ensure optimal B cell lymphoma growth. Nat Commun 2015; 6:8725. [PMID: 26555894 PMCID: PMC4667639 DOI: 10.1038/ncomms9725] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/22/2015] [Indexed: 01/07/2023] Open
Abstract
The synergism between c-MYC and miR-17-19b, a truncated version of the miR-17-92 cluster, is well-documented during tumor initiation. However, little is known about miR-17-19b function in established cancers. Here we investigate the role of miR-17-19b in c-MYC-driven lymphomas by integrating SILAC-based quantitative proteomics, transcriptomics and 3′ untranslated region (UTR) analysis upon miR-17-19b overexpression. We identify over one hundred miR-17-19b targets, of which 40% are co-regulated by c-MYC. Downregulation of a new miR-17/20 target, checkpoint kinase 2 (Chek2), increases the recruitment of HuR to c-MYC transcripts, resulting in the inhibition of c-MYC translation and thus interfering with in vivo tumor growth. Hence, in established lymphomas, miR-17-19b fine-tunes c-MYC activity through a tight control of its function and expression, ultimately ensuring cancer cell homeostasis. Our data highlight the plasticity of miRNA function, reflecting changes in the mRNA landscape and 3′ UTR shortening at different stages of tumorigenesis. The synergism between c-MYC and miR-17-19b plays an important role in lymphoma initiation. In this study, the authors identify a panel of targets co-regulated by miR-17-19b and in MYC-driven lymphoma and unravel the molecular mechanism through which miR-17-19b inhibits MYC translation.
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Affiliation(s)
- Marija Mihailovich
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Michael Bremang
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Valeria Spadotto
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Daniele Musiani
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Elena Vitale
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Gabriele Varano
- Units of Genetics of B cells and lymphomas, IFOM, FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| | | | - Francesco M Mancuso
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - David A Cairns
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Giulio Pavesi
- Department of Biosciences, Milan University, Milan 20133, Italy
| | - Stefano Casola
- Units of Genetics of B cells and lymphomas, IFOM, FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
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11
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Soldi M, Bremang M, Bonaldi T. Biochemical systems approaches for the analysis of histone modification readout. Biochim Biophys Acta 2014; 1839:657-68. [PMID: 24681439 DOI: 10.1016/j.bbagrm.2014.03.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 03/06/2014] [Accepted: 03/18/2014] [Indexed: 11/28/2022]
Abstract
Chromatin is the macromolecular nucleoprotein complex that governs the organization of genetic material in the nucleus of eukaryotic cells. In chromatin, DNA is packed with histone proteins into nucleosomes. Core histones are prototypes of hyper-modified proteins, being decorated by a large number of site-specific reversible and irreversible post-translational modifications (PTMs), which contribute to the maintenance and modulation of chromatin plasticity, gene activation, and a variety of other biological processes and disease states. The observations of the variety, frequency and co-occurrence of histone modifications in distinct patterns at specific genomic loci have led to the idea that hPTMs can create a molecular barcode, read by effector proteins that translate it into a specific transcriptional state, or process, on the underlying DNA. However, despite the fact that this histone-code hypothesis was proposed more than 10 years ago, the molecular details of its working mechanisms are only partially characterized. In particular, two questions deserve specific investigation: how the different modifications associate and synergize into patterns and how these PTM configurations are read and translated by multi-protein complexes into a specific functional outcome on the genome. Mass spectrometry (MS) has emerged as a versatile tool to investigate chromatin biology, useful for both identifying and validating hPTMs, and to dissect the molecular determinants of histone modification readout systems. We review here the MS techniques and the proteomics methods that have been developed to address these fundamental questions in epigenetics research, emphasizing approaches based on the proteomic dissection of distinct native chromatin regions, with a critical evaluation of their present challenges and future potential. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Monica Soldi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Michael Bremang
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.
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12
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Bremang M, Cuomo A, Agresta AM, Stugiewicz M, Spadotto V, Bonaldi T. Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome. Mol Biosyst 2014; 9:2231-47. [PMID: 23748837 DOI: 10.1039/c3mb00009e] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein methylation is a post-translational modification (PTM) by which a variable number of methyl groups are transferred to lysine and arginine residues within proteins. Despite increased interest in this modification due to its reversible nature and its emerging role in a diverse set of biological pathways beyond chromatin, global identification of protein methylation has remained an unachieved goal. To characterise sites of lysine and arginine methylation beyond histones, we employed an approach that combines heavy methyl stable isotope labelling by amino acids in cell culture (hmSILAC) with high-resolution mass spectrometry-based proteomics. Through a broad evaluation of immuno-affinity enrichment and the application of two classical protein separation techniques prior to mass spectrometry, to nucleosolic and cytosolic fractions separately, we identified a total of 501 different methylation types, on 397 distinct lysine and arginine sites, present on 139 unique proteins. Our results considerably extend the number of known in vivo methylation sites and indicate their significant presence on several protein complexes involved at all stages of gene expression, from chromatin remodelling and transcription to splicing and translation. In addition, we describe the potential of the hmSILAC approach for accurate relative quantification of methylation levels between distinct functional states.
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Affiliation(s)
- Michael Bremang
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
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13
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Liger D, Quevillon-Cheruel S, Sorel I, Bremang M, Blondeau K, Aboulfath I, Janin J, van Tilbeurgh H, Leulliot N. Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily. Proteins 2006; 60:778-86. [PMID: 16021630 DOI: 10.1002/prot.20548] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In the Pseudomonas bacterial genomes, the PhzF proteins are involved in the production of phenazine derivative antibiotic and antifungal compounds. The PhzF superfamily however also encompasses proteins in all genomes from bacteria to eukaryotes, for which no function has been assigned. We have determined the three dimensional crystal structure at 2.05 A resolution of YHI9, the yeast member of the PhzF family. YHI9 has a fold similar to bacterial diaminopimelate epimerase, revealing a bimodular structure with an internal symmetry. Residue conservation identifies a putative active site at the interface between the two domains. Evolution of this protein by gene duplication, gene fusion and domain swapping from an ancestral gene containing the "hot dog" fold, identifies the protein as a "kinked double hot dog" fold.
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Affiliation(s)
- Dominique Liger
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-UMR 8619), Université Paris-Sud, Orsay, France
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14
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Leulliot N, Trésaugues L, Bremang M, Sorel I, Ulryck N, Graille M, Aboulfath I, Poupon A, Liger D, Quevillon-Cheruel S, Janin J, van Tilbeurgh H. High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all? Acta Crystallogr D Biol Crystallogr 2005; 61:664-70. [PMID: 15930617 DOI: 10.1107/s0907444905000028] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2004] [Accepted: 01/13/2005] [Indexed: 11/11/2022]
Abstract
Crystallization has long been regarded as one of the major bottlenecks in high-throughput structural determination by X-ray crystallography. Structural genomics projects have addressed this issue by using robots to set up automated crystal screens using nanodrop technology. This has moved the bottleneck from obtaining the first crystal hit to obtaining diffraction-quality crystals, as crystal optimization is a notoriously slow process that is difficult to automatize. This article describes the high-throughput optimization strategies used in the Yeast Structural Genomics project, with selected successful examples.
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Affiliation(s)
- Nicolas Leulliot
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-UMR 8619), Université Paris-Sud, Bâtiment 430, 91405 Orsay, France.
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15
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Quevillon-Cheruel S, Leulliot N, Meyer P, Graille M, Bremang M, Blondeau K, Sorel I, Poupon A, Janin J, van Tilbeurgh H. Crystal structure of the bifunctional chorismate synthase from Saccharomyces cerevisiae. J Biol Chem 2003; 279:619-25. [PMID: 14573601 DOI: 10.1074/jbc.m310380200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chorismate synthase (EC 4.2.3.5), the seventh enzyme in the shikimate pathway, catalyzes the transformation of 5-enolpyruvylshikimate 3-phosphate (EPSP) to chorismate, which is the last common precursor in the biosynthesis of numerous aromatic compounds in bacteria, fungi, and plants. The chorismate synthase reaction involves a 1,4-trans-elimination of phosphoric acid from EPSP and has an absolute requirement for reduced FMN as a cofactor. We have determined the three-dimensional x-ray structure of the yeast chorismate synthase from selenomethionine-labeled crystals at 2.2-A resolution. The structure shows a novel betaalphabetaalpha fold consisting of an alternate tight packing of two alpha-helical and two beta-sheet layers, showing no resemblance to any documented protein structure. The molecule is arranged as a tight tetramer with D2 symmetry, in accordance with its quaternary structure in solution. Electron density is missing for 23% of the amino acids, spread over sequence regions that in the three-dimensional structure converge on the surface of the protein. Many totally conserved residues are contained within these regions, and they probably form a structured but mobile domain that closes over a cleft upon substrate binding and catalysis. This hypothesis is supported by previously published spectroscopic measurements implying that the enzyme undergoes considerable structural changes upon binding of both FMN and EPSP.
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Affiliation(s)
- Sophie Quevillon-Cheruel
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire (CNRS-UMR 8619), Université Paris-Sud, Bâtiment 430, 91405 Orsay, France
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