1
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Yu X, Juraszek J, Rutten L, Bakkers MJG, Blokland S, Melchers JM, van den Broek NJF, Verwilligen AYW, Abeywickrema P, Vingerhoets J, Neefs JM, Bakhash SAM, Roychoudhury P, Greninger A, Sharma S, Langedijk JPM. Convergence of immune escape strategies highlights plasticity of SARS-CoV-2 spike. PLoS Pathog 2023; 19:e1011308. [PMID: 37126534 PMCID: PMC10174534 DOI: 10.1371/journal.ppat.1011308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 05/11/2023] [Accepted: 03/21/2023] [Indexed: 05/02/2023] Open
Abstract
The global spread of the SARS-CoV-2 virus has resulted in emergence of lineages which impact the effectiveness of immunotherapies and vaccines that are based on the early Wuhan isolate. All currently approved vaccines employ the spike protein S, as it is the target for neutralizing antibodies. Here we describe two SARS-CoV-2 isolates with unusually large deletions in the N-terminal domain (NTD) of the spike. Cryo-EM structural analysis shows that the deletions result in complete reshaping of the NTD supersite, an antigenically important region of the NTD. For both spike variants the remodeling of the NTD negatively affects binding of all tested NTD-specific antibodies in and outside of the NTD supersite. For one of the variants, we observed a P9L mediated shift of the signal peptide cleavage site resulting in the loss of a disulfide-bridge; a unique escape mechanism with high antigenic impact. Although the observed deletions and disulfide mutations are rare, similar modifications have become independently established in several other lineages, indicating a possibility to become more dominant in the future. The observed plasticity of the NTD foreshadows its broad potential for immune escape with the continued spread of SARS-CoV-2.
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Affiliation(s)
- Xiaodi Yu
- Structural & Protein Sciences, Janssen Research and Development, Spring House, Pennsylvania, United States of America
| | - Jarek Juraszek
- Janssen Vaccines & Prevention BV, Leiden, the Netherlands
| | - Lucy Rutten
- Janssen Vaccines & Prevention BV, Leiden, the Netherlands
| | | | - Sven Blokland
- Janssen Vaccines & Prevention BV, Leiden, the Netherlands
| | | | | | | | - Pravien Abeywickrema
- Structural & Protein Sciences, Janssen Research and Development, Spring House, Pennsylvania, United States of America
| | - Johan Vingerhoets
- Janssen Pharmaceutica N.V., Clinical Microbiology and Immunology, Beerse, Belgium
| | - Jean-Marc Neefs
- Janssen Pharmaceutica N.V., Discovery Sciences, Beerse, Belgium
| | - Shah A Mohamed Bakhash
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington, Seattle, Washington, United States of America
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington, Seattle, Washington, United States of America
| | - Alex Greninger
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington, Seattle, Washington, United States of America
| | - Sujata Sharma
- Structural & Protein Sciences, Janssen Research and Development, Spring House, Pennsylvania, United States of America
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2
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Grosse S, Tahri A, Raboisson P, Houpis Y, Stoops B, Jacoby E, Neefs JM, Van Loock M, Goethals O, Geluykens P, Bonfanti JF, Jonckers THM. From Oxetane to Thietane: Extending the Antiviral Spectrum of 2′-Spirocyclic Uridines by Substituting Oxygen with Sulfur. ACS Med Chem Lett 2022; 13:1879-1884. [DOI: 10.1021/acsmedchemlett.2c00372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/21/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Sandrine Grosse
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Abdellah Tahri
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Pierre Raboisson
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Yannis Houpis
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Bart Stoops
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Edgar Jacoby
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Jean-Marc Neefs
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Marnix Van Loock
- Janssen Global Public Health, R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Olivia Goethals
- Janssen Global Public Health, R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Peggy Geluykens
- Charles River, Discovery, Turnhoutseweg 30, 2340 Beerse, Belgium
| | | | - Tim H. M. Jonckers
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
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3
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De Pooter D, Van Gulck E, Chen A, Evans CF, Neefs JM, Horton H, Boden D. A Therapeutic Hepatitis B Virus DNA Vaccine Induces Specific Immune Responses in Mice and Non-Human Primates. Vaccines (Basel) 2021; 9:vaccines9090969. [PMID: 34579206 PMCID: PMC8471825 DOI: 10.3390/vaccines9090969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 05/26/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 12/25/2022] Open
Abstract
Despite the availability of an effective prophylactic vaccine for more than 30 years, nearly 300 million people worldwide are chronically infected with the hepatitis B virus (HBV), leading to 1 death every 30 s mainly from viral hepatitis-related cirrhosis and liver cancer. Chronic HBV patients exhibit weak, transient, or dysfunctional CD8+ T-cell responses to HBV, which contrasts with high CD8+ T-cell responses seen for resolvers of acute HBV infection. Therefore, a therapeutic DNA vaccine was designed, expressing both HBV core and polymerase proteins, and was sequence optimized to ensure high protein expression and secretion. Although the vaccine, administered intramuscularly via electroporation, had no effect on plasma viral parameters in a mouse model of persistent HBV infection, it did induce robust HBV-specific immune responses in healthy and adeno-associated hepatitis B virus (AAV-HBV) infected mice as well as in healthy non-human primates.
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Affiliation(s)
- Dorien De Pooter
- Janssen Infectious Diseases, Janssen Research and Development, Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium; (E.V.G.); (A.C.); (H.H.)
- Correspondence:
| | - Ellen Van Gulck
- Janssen Infectious Diseases, Janssen Research and Development, Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium; (E.V.G.); (A.C.); (H.H.)
| | - Antony Chen
- Janssen Infectious Diseases, Janssen Research and Development, Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium; (E.V.G.); (A.C.); (H.H.)
| | - Claire F. Evans
- Ichor Medical Systems Inc., 6310 Nancy Ridge Drive, Suite 107, San Diego, CA 92121, USA;
| | - Jean-Marc Neefs
- Discovery Sciences, Janssen Research and Development, Division of Janssen Pharmaceutica NV, Turn-houtseweg 30, 2340 Beerse, Belgium;
| | - Helen Horton
- Janssen Infectious Diseases, Janssen Research and Development, Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium; (E.V.G.); (A.C.); (H.H.)
| | - Daniel Boden
- Janssen Infectious Diseases, Division of Janssen Pharmaceutica NV, 260 E. Grand Avenue, South San Francisco, CA 94080, USA;
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4
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Cox MJ, Jaensch S, Van de Waeter J, Cougnaud L, Seynaeve D, Benalla S, Koo SJ, Van Den Wyngaert I, Neefs JM, Malkov D, Bittremieux M, Steemans M, Peeters PJ, Wegner JK, Ceulemans H, Gustin E, Chong YT, Göhlmann HWH. Tales of 1,008 small molecules: phenomic profiling through live-cell imaging in a panel of reporter cell lines. Sci Rep 2020; 10:13262. [PMID: 32764586 PMCID: PMC7411054 DOI: 10.1038/s41598-020-69354-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 03/14/2020] [Accepted: 07/08/2020] [Indexed: 11/09/2022] Open
Abstract
Phenomic profiles are high-dimensional sets of readouts that can comprehensively capture the biological impact of chemical and genetic perturbations in cellular assay systems. Phenomic profiling of compound libraries can be used for compound target identification or mechanism of action (MoA) prediction and other applications in drug discovery. To devise an economical set of phenomic profiling assays, we assembled a library of 1,008 approved drugs and well-characterized tool compounds manually annotated to 218 unique MoAs, and we profiled each compound at four concentrations in live-cell, high-content imaging screens against a panel of 15 reporter cell lines, which expressed a diverse set of fluorescent organelle and pathway markers in three distinct cell lineages. For 41 of 83 testable MoAs, phenomic profiles accurately ranked the reference compounds (AUC-ROC ≥ 0.9). MoAs could be better resolved by screening compounds at multiple concentrations than by including replicates at a single concentration. Screening additional cell lineages and fluorescent markers increased the number of distinguishable MoAs but this effect quickly plateaued. There remains a substantial number of MoAs that were hard to distinguish from others under the current study's conditions. We discuss ways to close this gap, which will inform the design of future phenomic profiling efforts.
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Affiliation(s)
- Michael J Cox
- Janssen Pharmaceutica N.V., Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Steffen Jaensch
- Janssen Pharmaceutica N.V., Turnhoutseweg 30, 2340, Beerse, Belgium.
| | | | | | | | | | - Seong Joo Koo
- Janssen Pharmaceutica N.V., Turnhoutseweg 30, 2340, Beerse, Belgium
| | | | - Jean-Marc Neefs
- Janssen Pharmaceutica N.V., Turnhoutseweg 30, 2340, Beerse, Belgium
| | | | - Mart Bittremieux
- Janssen Pharmaceutica N.V., Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Margino Steemans
- Janssen Pharmaceutica N.V., Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Pieter J Peeters
- Janssen Pharmaceutica N.V., Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Jörg Kurt Wegner
- Janssen Pharmaceutica N.V., Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Hugo Ceulemans
- Janssen Pharmaceutica N.V., Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Emmanuel Gustin
- Janssen Pharmaceutica N.V., Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Yolanda T Chong
- Janssen Pharmaceutica N.V., Turnhoutseweg 30, 2340, Beerse, Belgium.,Recursion, Salt Lake City, UT, USA
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5
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Verbinnen T, Tan Y, Wang G, Dehertogh P, Vergauwen K, Neefs JM, Jacoby E, Lenz O, Berke JM. Anti-HBV activity of the HBV capsid assembly modulator JNJ-56136379 across full-length genotype A–H clinical isolates and core site-directed mutants in vitro. J Antimicrob Chemother 2020; 75:2526-2534. [DOI: 10.1093/jac/dkaa179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/03/2020] [Accepted: 04/09/2020] [Indexed: 12/16/2022] Open
Abstract
Abstract
Objectives
To characterize antiviral activity of the capsid assembly modulator (CAM-N) JNJ-56136379 against HBV genotypes and variants carrying amino acid substitutions in the core protein.
Methods
Anti-HBV activity of JNJ-56136379 was investigated against a diverse panel of 53 HBV clinical isolates (genotypes A–H). The impact of core amino acid substitutions using site-directed mutants (SDMs) was assessed in a transient replication assay.
Results
JNJ-56136379 median 50% effective concentration (EC50) values across all genotypes were 10–33 nM versus 17 nM (genotype D reference). JNJ-56136379 remained active against isolates carrying nucleos(t)ide analogue resistance mutations (median EC50 2–25 nM) or basal core promoter (BCP) ± precore (PC) mutations (median EC50 13–20 nM) or PC mutations (median EC50 11 nM), representing activity against isolates from HBeAg-positive and -negative hepatitis B patients. Core amino acid substitutions in the CAM-binding pocket, when tested as SDMs at positions 23, 25, 30, 33, 37, 106, 110, 118, 124, 127 and 128, reduced JNJ-56136379 anti-HBV activity; EC50 fold increases ranged from 3.0 (S106T) to 85 (T33N). All substitutions were rare in a public database of >7600 HBV core sequences (frequencies 0.01%–0.3%). Nucleos(t)ide analogues retained full activity against these core SDMs.
Conclusions
JNJ-56136379, a potent HBV CAM-N, currently in Phase 2 clinical development, was generally fully active against an extensive panel of genotype A–H clinical isolates, regardless of the presence of nucleos(t)ide analogue resistance or BCP/PC mutations. JNJ-56136379 activity was reduced by some core amino acid substitutions in the CAM-binding pocket.
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Affiliation(s)
- Thierry Verbinnen
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Ying Tan
- Janssen China Research & Development Center, 5F North Building #1 Jinchuang Mansion, 4560 Jinke Road, Shanghai 201210, China
| | - Gengyan Wang
- Janssen China Research & Development Center, 5F North Building #1 Jinchuang Mansion, 4560 Jinke Road, Shanghai 201210, China
| | - Pascale Dehertogh
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Karen Vergauwen
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Jean-Marc Neefs
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Edgar Jacoby
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Oliver Lenz
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Jan Martin Berke
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
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6
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van Vlijmen H, Mons A, Waalkens A, Franke W, Baak A, Ruiter G, Kirkpatrick C, da Silva Santos LOB, Meerman B, Jellema R, Arts D, Kersloot M, Knijnenburg S, Lusher S, Verbeeck R, Neefs JM. The Need of Industry to Go FAIR. Data Intellegence 2020. [DOI: 10.1162/dint_a_00050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The industry sector is a very large producer and consumer of data, and many companies traditionally focused on production or manufacturing are now relying on the analysis of large amounts of data to develop new products and services. As many of the data sources needed are distributed and outside the company, FAIR data will have a major impact, both by reducing the existing internal data silos and by enabling the efficient integration with external (public and commercial) data. Many companies are still in the early phases of internal data “FAIRification”, providing opportunities for SMEs and academics to apply and develop their expertise on FAIR data in collaborations and public-private partnerships. For a global Internet of FAIR Data & Services to thrive, also involving industry, professional tools and services are essential. FAIR metrics and certifications on individuals, data, organizations, and software, must ensure that data producers and consumers have independent quality metrics on their data. In this opinion article we reflect on some industry specific challenges of FAIR implementation to be dealt with when choices are made regarding “Industry GOing FAIR”.
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Affiliation(s)
| | | | - Arne Waalkens
- Accenture, Gustav Mahlerplein 90, 1082 MA Amsterdam, The Netherlands
| | - Wouter Franke
- Zorg Instituut Nederland, Willem Dudokhof 1, 1112 ZA Diemen, The Netherlands
| | - Arie Baak
- Euretos, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Gerbrand Ruiter
- Mobiquity, Tommaso Albinonistraat 9, 1083 HM Amsterdam, The Netherlands
| | | | | | - Bert Meerman
- GO FAIR Foundation, Rijnsburgerweg 10, 2333 AA Leiden, The Netherlands
| | - Renger Jellema
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Derk Arts
- Castor, Paasheuvelweg 25, Vleugel 5D, 1105 BP Amsterdam, The Netherlands
| | - Martijn Kersloot
- Castor, Paasheuvelweg 25, Vleugel 5D, 1105 BP Amsterdam, The Netherlands
| | | | - Scott Lusher
- Janssen Pharmaceuticals, Antwerpseweg 15, 2340 Beerse, Belgium
| | - Rudi Verbeeck
- Janssen Pharmaceuticals, Antwerpseweg 15, 2340 Beerse, Belgium
| | - Jean-Marc Neefs
- Janssen Pharmaceuticals, Antwerpseweg 15, 2340 Beerse, Belgium
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7
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Jacoby E, Wroblowski B, Buyck C, Neefs JM, Meyer C, Cummings MD, van Vlijmen H. Protocols for the Design of Kinase-focused Compound Libraries. Mol Inform 2017; 37:e1700119. [PMID: 29116686 DOI: 10.1002/minf.201700119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 09/26/2017] [Accepted: 10/20/2017] [Indexed: 01/12/2023]
Abstract
Protocols for the design of kinase-focused compound libraries are presented. Kinase-focused compound libraries can be differentiated based on the design goal. Depending on whether the library should be a discovery library specific for one particular kinase, a general discovery library for multiple distinct kinase projects, or even phenotypic screening, there exists today a variety of in silico methods to design candidate compound libraries. We address the following scenarios: 1) Datamining of SAR databases and kinase focused vendor catalogues; 2) Predictions and virtual screening; 3) Structure-based design of combinatorial kinase inhibitors; 4) Design of covalent kinase inhibitors; 5) Design of macrocyclic kinase inhibitors; and 6) Design of allosteric kinase inhibitors and activators.
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Affiliation(s)
- Edgar Jacoby
- Janssen Research & Development, Turnhoutseweg 30, 2340, Beerse, Belgium
| | | | - Christophe Buyck
- Janssen Research & Development, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Jean-Marc Neefs
- Janssen Research & Development, Turnhoutseweg 30, 2340, Beerse, Belgium
| | | | - Maxwell D Cummings
- Janssen Research & Development, 1400 McKean Rd, Spring House, PA 19477, USA
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8
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Jacoby E, Tresadern G, Bembenek S, Wroblowski B, Buyck C, Neefs JM, Rassokhin D, Poncelet A, Hunt J, van Vlijmen H. Extending kinome coverage by analysis of kinase inhibitor broad profiling data. Drug Discov Today 2015; 20:652-8. [PMID: 25596550 DOI: 10.1016/j.drudis.2015.01.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/03/2014] [Accepted: 01/08/2015] [Indexed: 01/09/2023]
Abstract
The explored kinome was extended with broad profiling using the DiscoveRx and Millipore assay panels. The analysis of the profiling of 3368 selected inhibitors on 456 kinases in the DiscoveRx format delivered several insights. First, the coverage depended on the threshold of the selectivity parameter. Second, the relation between hit confirmation rates and inhibitor selectivity showed unexpectedly that higher selectivity can increase the likelihood of false positives. Third, comparing the coverage of a focused to that of a random library showed that the design based on a maximum number of scaffolds was superior to a limited number of scaffolds. Therefore, selective compounds can be used in target validation, enable the jumpstarting of new kinase drug discovery projects, and chart new biological space via phenotypic screening.
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Affiliation(s)
- Edgar Jacoby
- Janssen Research & Development, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Gary Tresadern
- Janssen Research & Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Scott Bembenek
- Janssen Research & Development, La Jolla, 3210 Merryfield Row, San Diego, CA 92121, USA
| | | | - Christophe Buyck
- Janssen Research & Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Jean-Marc Neefs
- Janssen Research & Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Dmitrii Rassokhin
- Janssen Research & Development, Spring House, 1400 McKean Road, Spring House, PA 19002, USA
| | - Alain Poncelet
- Janssen Research & Development, Val de Reuil, Campus de Maigremont, B.P. 615, 27106 Val De Reuil Cedex, France
| | - Jeremy Hunt
- KINOMEscan Division of DiscoveRx Corporation, 11180 Roselle Street, Suite D, San Diego, CA 92121, USA
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9
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Ratnam J, Zdrazil B, Digles D, Cuadrado-Rodriguez E, Neefs JM, Tipney H, Siebes R, Waagmeester A, Bradley G, Chau CH, Richter L, Brea J, Evelo CT, Jacoby E, Senger S, Loza MI, Ecker GF, Chichester C. The application of the open pharmacological concepts triple store (open PHACTS) to support drug discovery research. PLoS One 2014; 9:e115460. [PMID: 25522365 PMCID: PMC4270790 DOI: 10.1371/journal.pone.0115460] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [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: 05/16/2014] [Accepted: 10/30/2014] [Indexed: 01/08/2023] Open
Abstract
Integration of open access, curated, high-quality information from multiple disciplines in the Life and Biomedical Sciences provides a holistic understanding of the domain. Additionally, the effective linking of diverse data sources can unearth hidden relationships and guide potential research strategies. However, given the lack of consistency between descriptors and identifiers used in different resources and the absence of a simple mechanism to link them, gathering and combining relevant, comprehensive information from diverse databases remains a challenge. The Open Pharmacological Concepts Triple Store (Open PHACTS) is an Innovative Medicines Initiative project that uses semantic web technology approaches to enable scientists to easily access and process data from multiple sources to solve real-world drug discovery problems. The project draws together sources of publicly-available pharmacological, physicochemical and biomolecular data, represents it in a stable infrastructure and provides well-defined information exploration and retrieval methods. Here, we highlight the utility of this platform in conjunction with workflow tools to solve pharmacological research questions that require interoperability between target, compound, and pathway data. Use cases presented herein cover 1) the comprehensive identification of chemical matter for a dopamine receptor drug discovery program 2) the identification of compounds active against all targets in the Epidermal growth factor receptor (ErbB) signaling pathway that have a relevance to disease and 3) the evaluation of established targets in the Vitamin D metabolism pathway to aid novel Vitamin D analogue design. The example workflows presented illustrate how the Open PHACTS Discovery Platform can be used to exploit existing knowledge and generate new hypotheses in the process of drug discovery.
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Affiliation(s)
- Joseline Ratnam
- Universidade de Santiago de Compostela, Grupo BioFarma-USEF, Departamento de Farmacología, Campus Universitario Sur s/n, 15782 Santiago de Compostela, Spain
- * E-mail:
| | - Barbara Zdrazil
- University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria
| | - Daniela Digles
- University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria
| | - Emiliano Cuadrado-Rodriguez
- Universidade de Santiago de Compostela, Grupo BioFarma-USEF, Departamento de Farmacología, Campus Universitario Sur s/n, 15782 Santiago de Compostela, Spain
| | - Jean-Marc Neefs
- Janssen Research & Development, Turnhoutseweg 30, Beerse, Belgium
| | - Hannah Tipney
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
| | - Ronald Siebes
- Vrije Universiteit, Faculty of Sciences, division of Math. and Computer Science, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands
| | - Andra Waagmeester
- Department of Bioinformatics – BiGCaT, Maastricht University, Maastricht, The Netherlands
| | - Glyn Bradley
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
| | - Chau Han Chau
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
| | - Lars Richter
- University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria
| | - Jose Brea
- Universidade de Santiago de Compostela, Grupo BioFarma-USEF, Departamento de Farmacología, Campus Universitario Sur s/n, 15782 Santiago de Compostela, Spain
| | - Chris T. Evelo
- Department of Bioinformatics – BiGCaT, Maastricht University, Maastricht, The Netherlands
| | - Edgar Jacoby
- Janssen Research & Development, Turnhoutseweg 30, Beerse, Belgium
| | - Stefan Senger
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
| | - Maria Isabel Loza
- Universidade de Santiago de Compostela, Grupo BioFarma-USEF, Departamento de Farmacología, Campus Universitario Sur s/n, 15782 Santiago de Compostela, Spain
| | - Gerhard F. Ecker
- University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria
| | - Christine Chichester
- Swiss Institute of Bioinformatics, CALIPHO Group, CMU – Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
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10
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Koul A, Vranckx L, Dhar N, Göhlmann HWH, Özdemir E, Neefs JM, Schulz M, Lu P, Mørtz E, McKinney JD, Andries K, Bald D. Delayed bactericidal response of Mycobacterium tuberculosis to bedaquiline involves remodelling of bacterial metabolism. Nat Commun 2014; 5:3369. [PMID: 24569628 PMCID: PMC3948051 DOI: 10.1038/ncomms4369] [Citation(s) in RCA: 185] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 02/03/2014] [Indexed: 01/07/2023] Open
Abstract
Bedaquiline (BDQ), an ATP synthase inhibitor, is the first drug to be approved for treatment of multidrug-resistant tuberculosis in decades. Though BDQ has shown excellent efficacy in clinical trials, its early bactericidal activity during the first week of chemotherapy is minimal. Here, using microfluidic devices and time-lapse microscopy of Mycobacterium tuberculosis, we confirm the absence of significant bacteriolytic activity during the first 3-4 days of exposure to BDQ. BDQ-induced inhibition of ATP synthesis leads to bacteriostasis within hours after drug addition. Transcriptional and proteomic analyses reveal that M. tuberculosis responds to BDQ by induction of the dormancy regulon and activation of ATP-generating pathways, thereby maintaining bacterial viability during initial drug exposure. BDQ-induced bacterial killing is significantly enhanced when the mycobacteria are grown on non-fermentable energy sources such as lipids (impeding ATP synthesis via glycolysis). Our results show that BDQ exposure triggers a metabolic remodelling in mycobacteria, thereby enabling transient bacterial survival.
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Affiliation(s)
- Anil Koul
- Infectious diseases and vaccines therapeutic area, Janssen Research & Development, Johnson & Johnson Pharmaceuticals, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Luc Vranckx
- Infectious diseases and vaccines therapeutic area, Janssen Research & Development, Johnson & Johnson Pharmaceuticals, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Neeraj Dhar
- Swiss Federal Institute of Technology in Lausanne (EPFL), School of Life Sciences, 1015 Lausanne, Switzerland
| | - Hinrich W H Göhlmann
- CREATe, Janssen Research & Development, Johnson & Johnson Pharmaceuticals, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Emre Özdemir
- Swiss Federal Institute of Technology in Lausanne (EPFL), School of Life Sciences, 1015 Lausanne, Switzerland
| | - Jean-Marc Neefs
- CREATe, Janssen Research & Development, Johnson & Johnson Pharmaceuticals, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Melanie Schulz
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Ping Lu
- Department of Molecular Cell Biology, AIMMS, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Ejvind Mørtz
- Alphalyse A/S, Unsbjergvej 4, DK-5220 Odense SØ, Denmark
| | - John D McKinney
- Swiss Federal Institute of Technology in Lausanne (EPFL), School of Life Sciences, 1015 Lausanne, Switzerland
| | - Koen Andries
- Infectious diseases and vaccines therapeutic area, Janssen Research & Development, Johnson & Johnson Pharmaceuticals, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Dirk Bald
- Department of Molecular Cell Biology, AIMMS, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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11
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12
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Abstract
Despite the apparent homology in the protein kinase C (PKC) family, it has become clear that slight structural differences are sufficient to have unique signalling properties for each individual isoform. For PKCepsilon in depth investigation of these aspects revealed unique actions in the CNS and lead to development of specific modulators with clinical perspective. In this review, we describe to which extent PKCepsilon is distinct from other isoforms on the level of tissue expression and protein structure. As this kinase is highly expressed in the brain, we outline three main aspects of PKCepsilon signalling in the CNS. First, its ability to alter the permeability of N-type Ca2+ channels in dorsal root ganglia has been shown to enhance nociception. Secondly, PKCepsilon increases anxiety by diminishing GABA(A)R-induced inhibitory post-synaptic currents in the prefrontal cortex. Another important aspect of the latter inhibition is the reduced sensitivity of GABA(A) receptors to ethanol, a mechanism potentially contributing to abuse. A third signalling cascade improves cognitive functions by facilitating cholinergic signalling in the hippocampus. Collectively, these findings point to a physical and behavioural sensitising role for this kinase.
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Affiliation(s)
- Kristof Van Kolen
- CNS Research, Johnson & Johnson Pharmaceutical Research and Development, Beerse, Belgium.
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13
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Wouters MM, Neefs JM, Kerchove d'Exaerde AD, Vanderwinden JM, Smans KA. Downregulation of two novel genes in Sl/Sld and W(LacZ)/Wv mouse jejunum. Biochem Biophys Res Commun 2006; 346:491-500. [PMID: 16765319 DOI: 10.1016/j.bbrc.2006.05.132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Accepted: 05/22/2006] [Indexed: 11/22/2022]
Abstract
Interstitial cells of Cajal (ICC) are the so-called pacemaker cells of the gut. W(LacZ)/Wv and Sl/Sld mice lack ICC surrounding the myenteric plexus (MP) in the jejunum. We compared the gene expression profile of wild type (WT) and W(LacZ)/Wv and Sl/Sld mice using suppression subtractive hybridization (SSH), generating a cDNA library of 1303 clones from which 48 unique sequences were differentially expressed with Southern blot. Among them, we identified heme oxygenase2, TROY, and phospholamban in ICC using immunohistochemistry. Using RT-qPCR, c-Kit and two new transcripts Dithp and prenylcysteine oxidase1 were significantly lower expressed in Sl/Sld and W(LacZ)/Wv versus WT. Prenylcysteine oxidase1 appeared cytotoxic for COS-7 cells and was highly expressed in liver while Dithp was mainly expressed in small intestine. The combination of SSH, Southern blot, RT-qPCR, and immunohistochemistry turned out to be a useful approach to identify rarely expressed genes and genes with small differences in expression.
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Affiliation(s)
- Mira M Wouters
- Department of Internal Medicine, Johnson and Johnson, Pharmaceutical Research and Development, A Subdivision of Janssen Pharmaceutics, Beerse, Belgium
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14
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Andries K, Verhasselt P, Guillemont J, Göhlmann HWH, Neefs JM, Winkler H, Van Gestel J, Timmerman P, Zhu M, Lee E, Williams P, de Chaffoy D, Huitric E, Hoffner S, Cambau E, Truffot-Pernot C, Lounis N, Jarlier V. A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis. Science 2005; 307:223-7. [PMID: 15591164 DOI: 10.1126/science.1106753] [Citation(s) in RCA: 1526] [Impact Index Per Article: 80.3] [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: 12/23/2022]
Abstract
The incidence of tuberculosis has been increasing substantially on a worldwide basis over the past decade, but no tuberculosis-specific drugs have been discovered in 40 years. We identified a diarylquinoline, R207910, that potently inhibits both drug-sensitive and drug-resistant Mycobacterium tuberculosis in vitro (minimum inhibitory concentration 0.06 mug/ml). In mice, R207910 exceeded the bactericidal activities of isoniazid and rifampin by at least 1 log unit. Substitution of drugs included in the World Health Organization's first-line tuberculosis treatment regimen (rifampin, isoniazid, and pyrazinamide) with R207910 accelerated bactericidal activity, leading to complete culture conversion after 2 months of treatment in some combinations. A single dose of R207910 inhibited mycobacterial growth for 1 week. Plasma levels associated with efficacy in mice were well tolerated in healthy human volunteers. Mutants selected in vitro suggest that the drug targets the proton pump of adenosine triphosphate (ATP) synthase.
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Affiliation(s)
- Koen Andries
- Johnson & Johnson Pharmaceutical Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium.
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15
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Claeskens A, Ongenae N, Neefs JM, Cheyns P, Kaijen P, Cools M, Kutoh E. Hevin is down-regulated in many cancers and is a negative regulator of cell growth and proliferation. Br J Cancer 2000; 82:1123-30. [PMID: 10735494 PMCID: PMC2363342 DOI: 10.1054/bjoc.1999.1051] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have cloned a human Hevin cDNA from omental adipose tissue of different patients by reverse transcription polymerase chain reaction and shown a sequence variation due to a possible polymorphism at amino acid position 161 (E/G). Hevin protein expressed in vitro showed molecular weights of approximately 75 kDa and 150 kDa, suggesting that Hevin may form a homodimer in vitro. Using Northern blots and a human expressed sequence tAg database analysis, Hevin was shown to be widely expressed in human normal or non-neoplastic diseased tissues with various levels. In contrast to this, its expression was strongly down-regulated in most neoplastic cells or tissues tested. However, neither the mechanism nor the physiological meaning of this down-regulation is known. As an initial step towards investigating the functional role of Hevin in cell growth and differentiation, we transiently or stably expressed this gene in cancer cells (HeLa 3S) that are devoid of endogenous Hevin and measured DNA synthesis (cell proliferation) by 5-bromo-2'-deoxyuridine incorporation. Hevin was shown to be a negative regulator of cell proliferation. Furthermore, we have shown that Hevin can inhibit progression of cells from G1 to S phase or prolong G1 phase. This is the first report which describes the function of Hevin in cell growth and proliferation. Through database analysis, Hevin was found to be located on chromosome 4 which contains loss of heterozygosity of many tumour suppressor genes. Taken together, these results suggest that Hevin may be a candidate for a tumour suppressor gene and a potential target for cancer diagnosis/therapy.
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Affiliation(s)
- A Claeskens
- Department of Biochemistry, Janssen Research Foundation, Beerse, Belgium
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16
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Pangalos MN, Neefs JM, Somers M, Verhasselt P, Bekkers M, van der Helm L, Fraiponts E, Ashton D, Gordon RD. Isolation and expression of novel human glutamate carboxypeptidases with N-acetylated alpha-linked acidic dipeptidase and dipeptidyl peptidase IV activity. J Biol Chem 1999; 274:8470-83. [PMID: 10085079 DOI: 10.1074/jbc.274.13.8470] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.0] [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
Hydrolysis of the neuropeptide N-acetyl-L-aspartyl-L-glutamate (NAAG) by N-acetylated alpha-linked acidic dipeptidase (NAALADase) to release glutamate may be important in a number of neurodegenerative disorders in which excitotoxic mechanisms are implicated. The gene coding for human prostate-specific membrane antigen, a marker of prostatic carcinomas, and its rat homologue glutamate carboxypeptidase II have recently been shown to possess such NAALADase activity. In contrast, a closely related member of this gene family, rat ileal 100-kDa protein, possesses a dipeptidyl peptidase IV activity. Here, we describe the cloning of human ileal 100-kDa protein, which we have called a NAALADase- "like" (NAALADase L) peptidase based on its sequence similarity to other members of this gene family, and its inability to hydrolyze NAAG in transient transfection experiments. Furthermore, we describe the cloning of a third novel member of this gene family, NAALADase II, which codes for a type II integral membrane protein and which we have localized to chromosome 11 by fluorescent in situ hybridization analysis. Transient transfection of NAALADase II cDNA confers both NAALADase and dipeptidyl peptidase IV activity to COS cells. Expression studies using reverse transcription-polymerase chain reaction and Northern blot hybridization show that NAALADase II is highly expressed in ovary and testis as well as within discrete brain areas.
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Affiliation(s)
- M N Pangalos
- Janssen Research Foundation, B2340 Beerse, Belgium.
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17
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Abstract
Histamine H1 receptor expression has been reported to change in disorders such as allergic rhinitis, autoimmune myocarditis, rheumatoid arthritis and atherosclerosis. Here we report the isolation and characterization of genomic clones containing the 5' flanking (regulatory) region of the human histamine H1 receptor gene. An intron of approx. 5.8 kb was identified in the 5' untranslated region, which suggests that an entire subfamily of G-protein-coupled receptors may contain an intron immediately upstream of the start codon. The transcription initiation site was mapped by 5' rapid amplification of cDNA ends to a region 6.2 kb upstream of the start codon. Immediately upstream of the transcription start site a fragment of 1.85 kb was identified that showed promoter activity when placed upstream of a luciferase reporter gene and transiently transfected into cells expressing the histamine H1 receptor. The promoter sequence shares a number of characteristics with the promoter sequences of other G-protein-coupled receptor encoding genes, including binding sites for several transcription factors, and the absence of TATA and CAAT sequences at the appropriate locations. The promoter sequence described here differs from that reported previously [Fukui, Fujimoto, Mizuguchi, Sakamoto, Horio, Takai, Yamada and Ito (1994) Biochem. Biophys. Res. Commun. 201, 894-901] because the reported genomic clone was chimaeric. Furthermore our study provides evidence that the 3' untranslated region of the H1 receptor mRNA is much longer than previously accepted. Together, these findings provide a complete view of the structure of the human histamine H1 receptor gene. Both the coding region of the H1 receptor gene and its promoter region were independently mapped to chromosome 3p25.
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Affiliation(s)
- M D De Backer
- Department of Experimental Molecular Biology, Janssen Research Foundation, Turnhoutseweg 30, B2340 Beerse, Belgium.
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Wilmotte A, Neefs JM, De Wachter R. Evolutionary affiliation of the marine nitrogen-fixing cyanobacterium Trichodesmium sp. strain NIBB 1067, derived by 16S ribosomal RNA sequence analysis. Microbiology (Reading) 1994; 140 ( Pt 8):2159-64. [PMID: 7522848 DOI: 10.1099/13500872-140-8-2159] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The 16S rRNA sequence of Trichodesmium sp. strain NIBB 1067 was determined and used for the construction of a distance tree and bootstrap analysis. The tree shows that, among the available cyanobacterial 16S rRNA sequences, Trichodesmium NIBB 1067 has Oscillatoria PCC 7515 as its closest relative, presenting 94.9% of sequence similarity with the latter strain. This is in contrast to a difference of 9 mol% G+C in mean genomic DNA base composition between the two organisms. Nevertheless, the genotypic heterogeneity presented by a number of strains assigned to the genus Oscillatoria hinders a taxonomic decision on the separate existence of the genera Trichodesmium and Oscillatoria. The sequence of the internal transcribed spacer (ITS) between the 16S and 23S rRNA genes was also determined, as a possible marker to study inter- and intraspecific variability. The ITS contains the genes coding for tRNA(Ile) and tRNA(Ala) and its total length is 547 nucleotides. In six out of eight sequenced clones, there is a duplication of 29 nucleotides, surrounding the 5' end of the tRNA(Ile).
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Affiliation(s)
- A Wilmotte
- Department of Biochemistry, University of Antwerp (UIA), Belgium
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19
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Nelissen B, Wilmotte A, Neefs JM, De Wachter R. Phylogenetic Relationships Among Filamentous Helical Cyanobacteria Investigated on the Basis of 16S Ribosomal RNA Gene Sequence Analysis. Syst Appl Microbiol 1994. [DOI: 10.1016/s0723-2020(11)80009-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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20
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van de Peer Y, Neefs JM, de Rijk P, de Vos P, de Wachter R. About the Order of Divergence of the Major Bacterial Taxa During Evolution. Syst Appl Microbiol 1994. [DOI: 10.1016/s0723-2020(11)80028-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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21
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Wilmotte A, Van De Peer Y, Goris A, Chapelle S, De Baere R, Nelissen B, Neefs JM, Hennebert GL, De Wachter R. Evolutionary Relationships Among Higher Fungi Inferred from Small Ribosomal Subunit RNA Sequence Analysis. Syst Appl Microbiol 1993. [DOI: 10.1016/s0723-2020(11)80277-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Van de Peer Y, Neefs JM, De Rijk P, De Wachter R. Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: calibration of the molecular clock. J Mol Evol 1993; 37:221-32. [PMID: 8411212 DOI: 10.1007/bf02407359] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.6] [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: 01/30/2023]
Abstract
The detailed descriptions now available for the secondary structure of small-ribosomal-subunit RNA, including areas of highly variable primary structure, facilitate the alignment of nucleotide sequences. However, for optimal exploitation of the information contained in the alignment, a method must be available that takes into account the local sequence variability in the computation of evolutionary distance. A quantitative definition for the variability of an alignment position is proposed in this study. It is a parameter in an equation which expresses the probability that the alignment position contains a different nucleotide in two sequences, as a function of the distance separating these sequences, i.e., the number of substitutions per nucleotide that occurred during their divergence. This parameter can be estimated from the distance matrix resulting from the conversion of pairwise sequence dissimilarities into pairwise distances. Alignment positions can then be subdivided into a number of sets of matching variability, and the average variability of each set can be derived. Next, the conversion of dissimilarity into distance can be recalculated for each set of alignment positions separately, using a modified version of the equation that corrects for multiple substitutions and changing for each set the parameter that reflects its average variability. The distances computed for each set are finally averaged, giving a more precise distance estimation. Trees constructed by the algorithm based on variability calibration have a topology markedly different from that of trees constructed from the same alignments in the absence of calibration. This is illustrated by means of trees constructed from small-ribosomal-subunit RNA sequences of Metazoa. A reconstruction of vertebrate evolution based on calibrated alignments matches the consensus view of paleontologists, contrary to trees based on uncalibrated alignments. In trees derived from sequences covering several metazoan phyla, artefacts in topology that are probably due to a high clock rate in certain lineages are avoided.
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Affiliation(s)
- Y Van de Peer
- Department Biochemie, Universiteit Antwerpen (UIA), Belgium
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23
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Abstract
The database on small ribosomal subunit RNA structure contained 1804 nucleotide sequences on April 23, 1993. This number comprises 365 eukaryotic, 65 archaeal, 1260 bacterial, 30 plastidial, and 84 mitochondrial sequences. These are stored in the form of an alignment in order to facilitate the use of the database as input for comparative studies on higher-order structure and for reconstruction of phylogenetic trees. The elements of the postulated secondary structure for each molecule are indicated by special symbols. The database is available on-line directly from the authors by ftp and can also be obtained from the EMBL nucleotide sequence library by electronic mail, ftp, and on CD ROM disk.
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Affiliation(s)
- J M Neefs
- Departement Biochemie, Universiteit Antwerpen (UIA), Belgium
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24
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25
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Affiliation(s)
- P De Rijk
- Departement Biochemie, Universiteit Antwerpen, Belgium
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26
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De Wachter R, Neefs JM, Goris A, Van de Peer Y. The gene coding for small ribosomal subunit RNA in the basidiomycete Ustilago maydis contains a group I intron. Nucleic Acids Res 1992; 20:1251-7. [PMID: 1561081 PMCID: PMC312166 DOI: 10.1093/nar/20.6.1251] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.8] [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: 12/27/2022] Open
Abstract
The nucleotide sequence of the gene coding for small ribosomal subunit RNA in the basidiomycete Ustilago maydis was determined. It revealed the presence of a group I intron with a length of 411 nucleotides. This is the third occurrence of such an intron discovered in a small subunit rRNA gene encoded by a eukaryotic nuclear genome. The other two occurrences are in Pneumocystis carinii, a fungus of uncertain taxonomic status, and Ankistrodesmus stipitatus, a green alga. The nucleotides of the conserved core structure of 101 group I intron sequences present in different genes and genome types were aligned and their evolutionary relatedness was examined. This revealed a cluster including all group I introns hitherto found in eukaryotic nuclear genes coding for small and large subunit rRNAs. A secondary structure model was designed for the area of the Ustilago maydis small ribosomal subunit RNA precursor where the intron is situated. It shows that the internal guide sequence pairing with the intron boundaries fits between two helices of the small subunit rRNA, and that minimal rearrangement of base pairs suffices to achieve the definitive secondary structure of the 18S rRNA upon splicing.
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Affiliation(s)
- R De Wachter
- Departement Biochemie, Universiteit Antwerpen (UIA), Belgium
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27
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Hendriks L, Goris A, Van De Peer Y, Neefs JM, Vancanneyt M, Kersters K, Berny JF, Hennebert GL, De Wachter R. Phylogenetic Relationships among Ascomycetes and Ascomycete-like Yeasts as Deduced from Small Ribosomal Subunit RNA Sequences. Syst Appl Microbiol 1992. [DOI: 10.1016/s0723-2020(11)80145-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Hendriks L, Goris A, Van de Peer Y, Neefs JM, Vancanneyt M, Kersters K, Hennebert GL, De Wachter R. Phylogenetic analysis of five medically important Candida species as deduced on the basis of small ribosomal subunit RNA sequences. J Gen Microbiol 1991; 137:1223-30. [PMID: 1865186 DOI: 10.1099/00221287-137-5-1223] [Citation(s) in RCA: 35] [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] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The classification of species belonging to the genus Candida Berkhout is problematic. Therefore, we have determined the small ribosomal subunit RNA (srRNA) sequences of the type strains of three human pathogenic Candida species; Candida krusei, C. lusitaniae and C. tropicalis. The srRNA sequences were aligned with published eukaryotic srRNA sequences and evolutionary trees were inferred using a matrix optimization method. An evolutionary tree comprising all available eukaryotic srRNA sequences, including two other pathogenic Candida species, C. albicans and C. glabrata, showed that the yeasts diverge rather late in the course of eukaryote evolution, namely at the same depth as green plants, ciliates and some smaller taxa. The cluster of the higher fungi consists of 10 ascomycetes and ascomycete-like species with the first branches leading to Neurospora crassa, Pneumocystis carinii, Candida lusitaniae and C. krusei, in that order. Next there is a dichotomous divergence leading to a group consisting of Torulaspora delbrueckii, Saccharomyces cerevisiae, C. glabrata and Kluyveromyces lactis and a smaller group comprising C. tropicalis and C. albicans. The divergence pattern obtained on the basis of srRNA sequence data is also compared to various other chemotaxonomic data.
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Affiliation(s)
- L Hendriks
- Departement Biochemie, Universiteit Antwerpen (UIA), Belgium
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29
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Affiliation(s)
- J M Neefs
- Departement Biochemie, Universiteit Antwerpen, UIA, Belgium
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30
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Neefs JM, De Wachter R. A proposal for the secondary structure of a variable area of eukaryotic small ribosomal subunit RNA involving the existence of a pseudoknot. Nucleic Acids Res 1990; 18:5695-704. [PMID: 2170942 PMCID: PMC332302 DOI: 10.1093/nar/18.19.5695] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.2] [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: 12/30/2022] Open
Abstract
Eukaryotic small ribosomal subunit RNAs contain an area of variable structure, V4, which comprises about 250 nucleotides in most species, whereas the corresponding area in bacterial small ribosomal subunit RNAs consists of about 64 nucleotides folded into a single hairpin. There is no consensus on the secondary structure of area V4 in eukaryotes, about 10 different models having been proposed. The prediction of a model on a comparative basis poses special problems because, due to the variability of the area in length as well as sequence, a dependable alignment is very difficult to achieve. A new model was derived by systematic examination of all combinations of helices that have been hitherto proposed, plus some new ones. The following properties of the helices were examined: transposability to all presently known sequences, presence of compensating substitutions, and thermodynamic stability. A model was selected by ranking all possible combinations of transposable helices according to the number of compensating substitutions scored. The optimal model comprises a pseudoknot and four hairpin structures. Certain species contain additional hairpins inserted between these structural elements, while in others the structure is partially or entirely deleted.
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Affiliation(s)
- J M Neefs
- Department Biochimie, Universiteit Antwerpen (UIA), Belgium
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31
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Hendriks L, Van de Peer Y, Van Herck M, Neefs JM, De Wachter R. The 18S ribosomal RNA sequence of the sea anemone Anemonia sulcata and its evolutionary position among other eukaryotes. FEBS Lett 1990; 269:445-9. [PMID: 1976100 DOI: 10.1016/0014-5793(90)81212-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Evolutionary trees based on partial small ribosomal subunit RNA sequences of 22 metazoa species have been published [(1988) Science 239, 748-753]. In these trees, cnidarians (Radiata) seemed to have evolved independently from the Bilateria, which is in contradiction with the general evolutionary view. In order to further investigate this problem, the complete srRNA sequence of the sea anemone Anemonia sulcata was determined and evolutionary trees were constructed using a matrix optimization method. In the tree thus obtained the sea anemone and Bilateria together form a monophyletic cluster, with the sea anemone forming the first line of the metazoan group.
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Affiliation(s)
- L Hendriks
- Department Biochemie, Universiteit Antwerpen, (UIA), Belgium
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32
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Van de Peer Y, Neefs JM, De Wachter R. Small ribosomal subunit RNA sequences, evolutionary relationships among different life forms, and mitochondrial origins. J Mol Evol 1990; 30:463-76. [PMID: 2111858 DOI: 10.1007/bf02101118] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [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: 12/30/2022]
Abstract
A tree was constructed from a structurally conserved area in an alignment of 83 small ribosomal subunit sequences of eukaryotic, archaebacterial, eubacterial, plastidial, and mitochondrial origin. The algorithm involved computation and optimization of a dissimilarity matrix. According to the tree, only plant mitochondria belong to the eubacterial primary kingdom, whereas animal, fungal, algal, and ciliate mitochondria branch off from an internal node situated between the tree primary kingdoms. This result is at variance with a parsimony tree of similar size published by Cedergren et al. (J Mol Evol 28:98-112, 1988), which postulates the mitochondria to be monophyletic and to belong to the eubacterial primary kingdom. The discrepancy does not follow from the use of conflicting sequence alignments, hence it must be due to the use of different treeing algorithms. We tested our algorithm on a set of sequences resulting from a simulated evolution and found it capable of faithfully reconstructing a branching topology that involved very unequal evolutionary rates. The use of more limited or more extended areas of the complete sequence alignment, comprising only very conserved or also more variable portions of the small ribosomal subunit structure, does have some influence on the tree topology. In all cases, however, the nonplant mitochondria seem to branch off before the emergence of eubacteria, and the differences are limited to the branching pattern among different types of mitochondria.
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Affiliation(s)
- Y Van de Peer
- Departement Biochemie, Universiteit Antwerpen, Belgium
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33
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Affiliation(s)
- J M Neefs
- Departement Biochemie, Universiteit Antwerpen, Belgium
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34
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Dams E, Hendriks L, Van de Peer Y, Neefs JM, Smits G, Vandenbempt I, De Wachter R. Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res 1988; 16 Suppl:r87-173. [PMID: 2453029 PMCID: PMC340911 DOI: 10.1093/nar/16.suppl.r87] [Citation(s) in RCA: 218] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- E Dams
- Departement Biochemie, Universiteit Antwerpen (UIA), Belgium
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