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Liao TW, Huang L, Wilson TJ, Ganser LR, Lilley DMJ, Ha T. Linking folding dynamics and function of SAM/SAH riboswitches at the single molecule level. Nucleic Acids Res 2023; 51:8957-8969. [PMID: 37522343 PMCID: PMC10516623 DOI: 10.1093/nar/gkad633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/27/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023] Open
Abstract
Riboswitches are regulatory elements found in bacterial mRNAs that control downstream gene expression through ligand-induced conformational changes. Here, we used single-molecule FRET to map the conformational landscape of the translational SAM/SAH riboswitch and probe how co-transcriptional ligand-induced conformational changes affect its translation regulation function. Riboswitch folding is highly heterogeneous, suggesting a rugged conformational landscape that allows for sampling of the ligand-bound conformation even in the absence of ligand. The addition of ligand shifts the landscape, favoring the ligand-bound conformation. Mutation studies identified a key structural element, the pseudoknot helix, that is crucial for determining ligand-free conformations and their ligand responsiveness. We also investigated ribosomal binding site accessibility under two scenarios: pre-folding and co-transcriptional folding. The regulatory function of the SAM/SAH riboswitch involves kinetically favoring ligand binding, but co-transcriptional folding reduces this preference with a less compact initial conformation that exposes the Shine-Dalgarno sequence and takes min to redistribute to more compact conformations of the pre-folded riboswitch. Such slow equilibration decreases the effective ligand affinity. Overall, our study provides a deeper understanding of the complex folding process and how the riboswitch adapts its folding pattern in response to ligand, modulates ribosome accessibility and the role of co-transcriptional folding in these processes.
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Affiliation(s)
- Ting-Wei Liao
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Timothy J Wilson
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Laura R Ganser
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - David M J Lilley
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
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2
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Li M, Deng J, Peng X, Wang J, Wilson TJ, Huang L, Lilley DMJ. Structure and ion-dependent folding of k-junctions. RNA 2023; 29:1411-1422. [PMID: 37311599 PMCID: PMC10573300 DOI: 10.1261/rna.079678.123] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/22/2023] [Indexed: 06/15/2023]
Abstract
k-Junctions are elaborated forms of kink turns with an additional helix on the nonbulged strand, thus forming a three-way helical junction. Two were originally identified in the structures of Arabidopsis and Escherichia coli thiamine pyrophosphate (TPP) riboswitches, and another called DUF-3268 was tentatively identified from sequence information. In this work we show that the Arabidopsis and E. coli riboswitch k-junctions fold in response to the addition of magnesium or sodium ions, and that atomic mutations that should disrupt key hydrogen bonding interactions greatly impair folding. Using X-ray crystallography, we have determined the structure of the DUF-3268 RNA and thus confirmed that it is a k-junction. It also folds upon the addition of metal ions, though requiring a 40-fold lower concentration of either divalent or monovalent ions. The key difference between the DUF-3268 and riboswitch k-junctions is the lack of nucleotides inserted between G1b and A2b in the former. We show that this insertion is primarily responsible for the difference in folding properties. Finally, we show that the DUF-3268 can functionally substitute for the k-junction in the E. coli TPP riboswitch such that the chimera can bind the TPP ligand, although less avidly.
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Affiliation(s)
- Mengxiao Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Jie Deng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Xuemei Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Jia Wang
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
| | - Timothy J Wilson
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - David M J Lilley
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
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3
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Islam A, Actis LA, Wilson TJ. Natural Antibodies Mediate Protection Against Acinetobacter baumannii Respiratory Infections. J Infect Dis 2023; 228:353-363. [PMID: 36951192 PMCID: PMC10420402 DOI: 10.1093/infdis/jiad069] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 02/22/2023] [Accepted: 03/21/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Acinetobacter baumannii causes a wide range of dangerous infections due to the emergence of pandrug-resistant strains. Therefore, there is a need for alternative therapeutics to treat these infections, including those targeting the host immune responses. However, immune responses, especially the humoral response against this pathogen, are poorly understood. METHODS This study investigated the lymphocyte-mediated innate immune resistance to A. baumannii AB5075 pulmonary infection using B- and T-cell-deficient (Rag2-/-) mice, the protective effect of natural antibodies (NAbs), and the expression of complement-mediated responses using a mouse pneumonia model. RESULTS Our results showed that intranasally infected Rag2-/- mice are impaired in clearing bacteria from lung, liver, and spleen at 24 hours postinfection compared to wildtype mice. Animal pretreatment with normal mouse serum or purified antibodies from naive mice rescued Rag2-/- mice from infection. Analysis of C3 complement protein binding demonstrated that NAbs increased C3 protein deposition on A. baumannii cells, indicating the activation of the classical complement pathway by NAbs. CONCLUSIONS Overall, our study shows that NAbs mediate innate immune resistance against A. baumannii, a finding that may lead to the development of effective therapies against human infections caused by this antibiotic-resistant A. baumannii.
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Freeman ADJ, Déclais AC, Wilson TJ, Lilley DJ. Biochemical and mechanistic analysis of the cleavage of branched DNA by human ANKLE1. Nucleic Acids Res 2023; 51:5743-5754. [PMID: 37216589 PMCID: PMC10287932 DOI: 10.1093/nar/gkad416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/28/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023] Open
Abstract
ANKLE1 is a nuclease that provides a final opportunity to process unresolved junctions in DNA that would otherwise create chromosomal linkages blocking cell division. It is a GIY-YIG nuclease. We have expressed an active domain of human ANKLE1 containing the GIY-YIG nuclease domain in bacteria, that is monomeric in solution and when bound to a DNA Y-junction, and unilaterally cleaves a cruciform junction. Using an AlphaFold model of the enzyme we identify the key active residues, and show that mutation of each leads to impairment of activity. There are two components in the catalytic mechanism. Cleavage rate is pH dependent, corresponding to a pKa of 6.9, suggesting an involvement of the conserved histidine in proton transfer. The reaction rate depends on the nature of the divalent cation, likely bound by glutamate and asparagine side chains, and is log-linear with the metal ion pKa. We propose that the reaction is subject to general acid-base catalysis, using a combination of tyrosine and histidine acting as general base and water directly coordinated to the metal ion as general acid. The reaction is temperature dependent; activation energy Ea = 37 kcal mol-1, suggesting that cleavage is coupled to opening of DNA in the transition state.
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Affiliation(s)
- Alasdair D J Freeman
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Anne-Cécile Déclais
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Timothy J Wilson
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David M J Lilley
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
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McCarthy E, Ekesan Ş, Giese TJ, Wilson TJ, Deng J, Huang L, Lilley DJ, York DM. Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology. Nucleic Acids Res 2023; 51:4508-4518. [PMID: 37070188 PMCID: PMC10201425 DOI: 10.1093/nar/gkad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/09/2023] [Accepted: 04/10/2023] [Indexed: 04/19/2023] Open
Abstract
A methyltransferase ribozyme (MTR1) was selected in vitro to catalyze alkyl transfer from exogenous O6-methylguanine (O6mG) to a target adenine N1, and recently, high-resolution crystal structures have become available. We use a combination of classical molecular dynamics, ab initio quantum mechanical/molecular mechanical (QM/MM) and alchemical free energy (AFE) simulations to elucidate the atomic-level solution mechanism of MTR1. Simulations identify an active reactant state involving protonation of C10 that hydrogen bonds with O6mG:N1. The deduced mechanism involves a stepwise mechanism with two transition states corresponding to proton transfer from C10:N3 to O6mG:N1 and rate-controlling methyl transfer (19.4 kcal·mol-1 barrier). AFE simulations predict the pKa for C10 to be 6.3, close to the experimental apparent pKa of 6.2, further implicating it as a critical general acid. The intrinsic rate derived from QM/MM simulations, together with pKa calculations, enables us to predict an activity-pH profile that agrees well with experiment. The insights gained provide further support for a putative RNA world and establish new design principles for RNA-based biochemical tools.
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Affiliation(s)
- Erika McCarthy
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Timothy J Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Timothy J Wilson
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Jie Deng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong–Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong–Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - David M J Lilley
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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6
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Schwab NR, Young NE, Nzenwata DU, Toh E, Mikulin JA, Wilson TJ, Nelson DE, Balish MF. Characterization of Virulence-Associated Traits in Mycoplasma penetrans Strains Acting as Likely Etiological Agents of Idiopathic Nongonococcal Urethritis. J Infect Dis 2023; 227:1050-1058. [PMID: 36588346 PMCID: PMC10319971 DOI: 10.1093/infdis/jiac505] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023] Open
Abstract
Mycoplasma penetrans is an emerging pathogen with a reduced genome. This bacterium has only previously been cultured from individuals with chronic immunodeficiencies. Here we report the characteristics of 4 M. penetrans isolates from the urine of immunocompetent males with nongonococcal urethritis, in comparison with strain HF-2 from an immunocompromised patient. Several features exhibited distinct differences between these isolates and HF-2. Unlike HF-2, all 4 were resistant to azithromycin. They exhibited greater sialic acid-dependent binding to erythrocytes, gliding motility speed, and H2O2 production than HF-2. All new isolates produced thinner capsules than HF-2. Invasiveness varied, with some isolates being more invasive than HF-2 and some less invasive. Cytotoxicity to HeLa cells was similar to HF-2, and all strains could clear extracellular traps produced by innate immune cells. We conclude that subtle differences among M. penetrans strains may be critical for this organism to establish an infection in an otherwise healthy individual.
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Affiliation(s)
- Nathan R Schwab
- Department of Microbiology, Miami University, Oxford, Ohio, USA
| | - Natalie E Young
- Department of Microbiology, Miami University, Oxford, Ohio, USA
| | | | - Evelyn Toh
- Department of Microbiology and Immunology, School of Medicine, Indiana University, Indianapolis, Indiana, USA
| | | | | | - David E Nelson
- Department of Microbiology and Immunology, School of Medicine, Indiana University, Indianapolis, Indiana, USA
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7
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Deng J, Wilson TJ, Wang J, Peng X, Li M, Lin X, Liao W, Lilley DMJ, Huang L. Author Correction: Structure and mechanism of a methyltransferase ribozyme. Nat Chem Biol 2022; 18:792. [PMID: 35668192 PMCID: PMC9236900 DOI: 10.1038/s41589-022-01073-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jie Deng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
| | - Jia Wang
- College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xuemei Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Mengxiao Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiaowei Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Wenjian Liao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK.
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
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8
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Deng J, Wilson TJ, Wang J, Peng X, Li M, Lin X, Liao W, Lilley DMJ, Huang L. Structure and mechanism of a methyltransferase ribozyme. Nat Chem Biol 2022; 18:556-564. [PMID: 35301479 PMCID: PMC9050513 DOI: 10.1038/s41589-022-00982-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 09/15/2021] [Accepted: 01/26/2022] [Indexed: 11/09/2022]
Abstract
Known ribozymes in contemporary biology perform a limited range of chemical catalysis, but in vitro selection has generated species that catalyze a broader range of chemistry; yet, there have been few structural and mechanistic studies of selected ribozymes. A ribozyme has recently been selected that can catalyze a site-specific methyl transfer reaction. We have solved the crystal structure of this ribozyme at a resolution of 2.3 Å, showing how the RNA folds to generate a very specific binding site for the methyl donor substrate. The structure immediately suggests a catalytic mechanism involving a combination of proximity and orientation and nucleobase-mediated general acid catalysis. The mechanism is supported by the pH dependence of the rate of catalysis. A selected methyltransferase ribozyme can thus use a relatively sophisticated catalytic mechanism, broadening the range of known RNA-catalyzed chemistry. ![]()
The authors present the crystal structure of the MTR1 ribozyme that transfers the methyl group from O6-methylguanine to an adenine N1 in the target RNA and propose a catalytic mechanism based upon proximity, orientation and general acid catalysis.
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Affiliation(s)
- Jie Deng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
| | - Jia Wang
- College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xuemei Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Mengxiao Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiaowei Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Wenjian Liao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK.
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China. .,Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
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9
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Rainey A, Pierce A, Deng X, Actis LA, Smith P, Kiss AJ, Wilson TJ. Validation and deployment of a direct saliva real-time RT-PCR test on pooled samples for COVID-19 surveillance testing. PLoS One 2021; 16:e0261956. [PMID: 34969053 PMCID: PMC8718011 DOI: 10.1371/journal.pone.0261956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/15/2021] [Indexed: 02/07/2023] Open
Abstract
A direct, real-time reverse transcriptase PCR test on pooled saliva was validated in 2,786 participants against oropharyngeal swabs. Among asymptomatic/pre-symptomatic participants, the test was found to be in 99.21% agreement and 45% more sensitive than contemporaneous oropharyngeal swabs. The test was then used for surveillance testing on 44,242 saliva samples from asymptomatic participants. Those whose saliva showed evidence of SARS-CoV-2 within 50 cycles of amplification were referred for confirmatory testing, with 87% of those tested by nasal swab within 72 hours receiving a positive diagnostic result on Abbott ID NOW or real-time PCR platforms. Median Ct values on the saliva PCR for those with a positive and negative confirmatory tests was 30.67 and 35.92 respectively, however, binary logistic regression analysis of the saliva Ct values indicates that Ct thresholds as high as 47 may be useful in a surveillance setting. Overall, data indicate that direct RT-PCR testing of pooled saliva samples is an effective method of SARS-CoV-2 surveillance.
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Affiliation(s)
- Amanda Rainey
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Austin Pierce
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Xiaoyun Deng
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Luis A. Actis
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
| | - Philip Smith
- Department of Kinesiology, Nutrition, and Health, Miami University, Oxford, Ohio, United States of America
| | - Andor J. Kiss
- Center for Bioinformatics and Functional Genomics, Miami University, Oxford, Ohio, United States of America
| | - Timothy J. Wilson
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
- * E-mail:
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10
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Mikulin JA, Bates BL, Wilson TJ. A simplified method for separating renal MPCs using SLAMF9. Cytometry A 2021; 99:1209-1217. [PMID: 34092043 PMCID: PMC9930532 DOI: 10.1002/cyto.a.24469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 01/13/2021] [Revised: 04/01/2021] [Accepted: 05/31/2021] [Indexed: 12/23/2022]
Abstract
Mononuclear phagocytes comprise an array of tissue-resident and monocyte-derived cells with important roles in tissue homeostasis and resistance to infection. Their diverse phenotypes make functional characterization within tissues challenging, because multiple surface markers are typically required for subset identification and isolation by cell sorting methods. Analysis of SLAMF9 expression within renal mononuclear phagocyte populations by multi-parametric flow cytometry indicates that SLAMF9 is a specific marker for identification of kidney-resident CD45+ CD11c+ MHC-II+ cells corresponding to prominent tissue-resident MPC populations derived from dendritic cell progenitors in adult mice. High SLAMF9 expression was sufficient to identify and sort these cells from disaggregated tissue using a user-operated cell sorter. The population can be further subdivided according to expression of CD11b and CD14 to identify IRF8high cDC1 cells and cleanly separate the CD11bhigh F4/80low and CD11bint F4/80high CD11c+ MPC subsets. Therefore, SLAMF9 expression allows for the identification and sorting of kidney-resident CD11b+ CD11c+ CD64+ F4/80+ CX3 CR1+ MHC-II+ MPCs without the need for complex antibody panels or reporter mice, simplifying isolation of these cells for study ex vivo.
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11
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DeLuca JM, Murphy MK, Wang X, Wilson TJ. FCRL1 Regulates B Cell Receptor-Induced ERK Activation through GRB2. J Immunol 2021; 207:2688-2698. [PMID: 34697226 DOI: 10.4049/jimmunol.2100218] [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] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/17/2021] [Indexed: 11/19/2022]
Abstract
Regulation of BCR signaling has important consequences for generating effective Ab responses to pathogens and preventing production of autoreactive B cells during development. Currently defined functions of Fc receptor-like (FCRL) 1 include positive regulation of BCR-induced calcium flux, proliferation, and Ab production; however, the mechanistic basis of FCRL1 signaling and its contributions to B cell development remain undefined. Molecular characterization of FCRL1 signaling shows phosphotyrosine-dependent associations with GRB2, GRAP, SHIP-1, and SOS1, all of which can profoundly influence MAPK signaling. In contrast with previous characterizations of FCRL1 as a strictly activating receptor, we discover a role for FCRL1 in suppressing ERK activation under homeostatic and BCR-stimulated conditions in a GRB2-dependent manner. Our analysis of B cells in Fcrl1 -/- mice shows that ERK suppression by FCRL1 is associated with a restriction in the number of cells surviving splenic maturation in vivo. The capacity of FCRL1 to modulate ERK activation presents a potential for FCRL1 to be a regulator of peripheral B cell tolerance, homeostasis, and activation.
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Affiliation(s)
- Jenna M DeLuca
- Department of Microbiology, Miami University, Oxford, OH
| | | | - Xin Wang
- Department of Microbiology, Miami University, Oxford, OH
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12
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Wilson TJ, Lilley DMJ. The potential versatility of RNA catalysis. Wiley Interdiscip Rev RNA 2021; 12:e1651. [PMID: 33949113 DOI: 10.1002/wrna.1651] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 01/21/2023]
Abstract
It is commonly thought that in the early development of life on this planet RNA would have acted both as a store of genetic information and as a catalyst. While a number of RNA enzymes are known in contemporary cells, they are largely confined to phosphoryl transfer reactions, whereas an RNA based metabolism would have required a much greater chemical diversity of catalysis. Here we discuss how RNA might catalyze a wider variety of chemistries, and particularly how information gleaned from riboswitches could suggest how ribozymes might recruit coenzymes to expand their chemical range. We ask how we might seek such activities in modern biology. This article is categorized under: RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions Regulatory RNAs/RNAi/Riboswitches > Riboswitches RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry.
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Affiliation(s)
- Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
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Huang L, Liao X, Li M, Wang J, Peng X, Wilson TJ, Lilley DMJ. Structure and folding of four putative kink turns identified in structured RNA species in a test of structural prediction rules. Nucleic Acids Res 2021; 49:5916-5924. [PMID: 33978763 PMCID: PMC8191799 DOI: 10.1093/nar/gkab333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/13/2021] [Accepted: 05/09/2021] [Indexed: 01/25/2023] Open
Abstract
k-Turns are widespread key architectural elements that occur in many classes of RNA molecules. We have shown previously that their folding properties (whether or not they fold into their tightly kinked structure on addition of metal ions) and conformation depend on their local sequence, and we have elucidated a series of rules for prediction of these properties from sequence. In this work, we have expanded the rules for prediction of folding properties, and then applied the full set to predict the folding and conformation of four probable k-turns we have identified amongst 224 structured RNA species found in bacterial intergenenic regions by the Breaker lab (1). We have analyzed the ion-dependence of folding of the four k-turns using fluorescence resonance energy transfer, and determined the conformation of two of them using X-ray crystallography. We find that the experimental data fully conform to both the predicted folding and conformational properties. We conclude that our folding rules are robust, and can be applied to new k-turns of unknown characteristics with confidence.
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Affiliation(s)
- Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, PR China
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Xinli Liao
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Mengxiao Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, PR China
| | - Jia Wang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Xuemei Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, PR China
| | - Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
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DeLuca JM, Murphy MK, Wilson TJ. FCRL1 inhibits ERK: Implications on B cell homeostasis and humoral immunity. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.98.32] [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] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Abstract
FCRL1 is a tyrosine-phosphorylated receptor found on the surface of B cells and some dendritic cells. FCRL1 co-localizes with BCR signaling complexes following BCR engagement and augments BCR-induced calcium flux. By examination of phosphotyrosine-dependent interactions of FCRL1 with intracellular signaling partners, we have identified interactions between FCRL1-Tyr281 and GRAP, GRB2, SHIP-1, and SOS1, with a requirement for GRB2 to mediate binding of FCRL1 to SHIP-1 and SOS1. Examination of MAP kinase signaling downstream of FCRL1 revealed that FCRL1 suppresses ERK phosphorylation in B cells at a resting state and following BCR engagement. In vivo, naïve FCRL1 knockout mice accumulate more B cells in the spleen, including immature, follicular and marginal zone cells, implicating a potential role for FCRL1 in B cell selection and maturation. By contrast, after immunization with thymus-dependent and independent antigens, FCRL1 knockout mice show impaired production of antigen-specific antibodies indicating an essential role for FCRL1 in humoral immune responses.
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Murphy MK, Moon JT, Skolaris AT, Mikulin JA, Wilson TJ. Evidence for the loss and recovery of SLAMF9 during human evolution: implications on Dollo's law. Immunogenetics 2021; 73:243-251. [PMID: 33616677 PMCID: PMC7898023 DOI: 10.1007/s00251-021-01208-7] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/05/2021] [Indexed: 11/04/2022]
Abstract
Signaling lymphocyte activation molecule family member 9 (SLAMF9) is a cell surface protein of the CD2/SLAM family of leukocyte surface receptors. It is conserved throughout mammals and has roles in the initiation of inflammatory responses and regulation of plasmacytoid dendritic cell function. Through comparison of reference sequences encoding SLAMF9 in human, mouse, and primate sequences, we have determined that the SLAMF9 gene underwent successive mutation events, resulting in the loss of the protein and subsequent recovery of a less stable version. The mutations included a single base pair deletion in the second exon and a change in the splice acceptor site of that same exon. These changes would have had the effect of creating and later repairing a frameshift in the coding sequence. These events took place since the divergence of the human lineage from the chimpanzee-human last common ancestor and represent the first known case of the functional loss and recovery of a gene within the human lineage.
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Affiliation(s)
- Maegan K Murphy
- Department of Microbiology, Miami University, 700 E. High Street, Oxford, OH, 45056, USA
| | - Justin T Moon
- Department of Microbiology, Miami University, 700 E. High Street, Oxford, OH, 45056, USA
| | - Alexis T Skolaris
- Department of Microbiology, Miami University, 700 E. High Street, Oxford, OH, 45056, USA
| | - Joseph A Mikulin
- Department of Microbiology, Miami University, 700 E. High Street, Oxford, OH, 45056, USA
| | - Timothy J Wilson
- Department of Microbiology, Miami University, 700 E. High Street, Oxford, OH, 45056, USA.
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Davis AA, Iams WT, Chan D, Oh MS, Lentz RW, Peterman N, Robertson A, Shah A, Srivas R, Wilson TJ, Lambert NJ, George PS, Wong B, Wood HW, Close JC, Tezcan A, Nesmith K, Tezcan H, Chae YK. Early Assessment of Molecular Progression and Response by Whole-genome Circulating Tumor DNA in Advanced Solid Tumors. Mol Cancer Ther 2020; 19:1486-1496. [PMID: 32371589 DOI: 10.1158/1535-7163.mct-19-1060] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/07/2020] [Accepted: 04/24/2020] [Indexed: 12/22/2022]
Abstract
Treatment response assessment for patients with advanced solid tumors is complex and existing methods require greater precision. Current guidelines rely on imaging, which has known limitations, including the time required to show a deterministic change in target lesions. Serial changes in whole-genome (WG) circulating tumor DNA (ctDNA) were used to assess response or resistance to treatment early in the treatment course. Ninety-six patients with advanced cancer were prospectively enrolled (91 analyzed and 5 excluded), and blood was collected before and after initiation of a new, systemic treatment. Plasma cell-free DNA libraries were prepared for either WG or WG bisulfite sequencing. Longitudinal changes in the fraction of ctDNA were quantified to retrospectively identify molecular progression (MP) or major molecular response (MMR). Study endpoints were concordance with first follow-up imaging (FFUI) and stratification of progression-free survival (PFS) and overall survival (OS). Patients with MP (n = 13) had significantly shorter PFS (median 62 days vs. 310 days) and OS (255 days vs. not reached). Sensitivity for MP to identify clinical progression was 54% and specificity was 100%. MP calls were from samples taken a median of 28 days into treatment and 39 days before FFUI. Patients with MMR (n = 27) had significantly longer PFS and OS compared with those with neither call (n = 51). These results demonstrated that ctDNA changes early after treatment initiation inform response to treatment and correlate with long-term clinical outcomes. Once validated, molecular response assessment can enable early treatment change minimizing side effects and costs associated with additional cycles of ineffective treatment.
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Affiliation(s)
- Andrew A Davis
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Wade T Iams
- Vanderbilt University Medical Center, Nashville, Tennessee
| | - David Chan
- Cancer Care Associates TMPN, Redondo Beach, California
| | - Michael S Oh
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Robert W Lentz
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Neil Peterman
- Lexent Bio, Inc., San Francisco and San Diego, California
| | - Alex Robertson
- Lexent Bio, Inc., San Francisco and San Diego, California
| | - Abhik Shah
- Lexent Bio, Inc., San Francisco and San Diego, California
| | - Rohith Srivas
- Lexent Bio, Inc., San Francisco and San Diego, California
| | | | | | - Peter S George
- Lexent Bio, Inc., San Francisco and San Diego, California
| | - Becky Wong
- Lexent Bio, Inc., San Francisco and San Diego, California
| | - Haleigh W Wood
- Lexent Bio, Inc., San Francisco and San Diego, California
| | - Jason C Close
- Lexent Bio, Inc., San Francisco and San Diego, California
| | - Ayse Tezcan
- Lexent Bio, Inc., San Francisco and San Diego, California
| | - Ken Nesmith
- Lexent Bio, Inc., San Francisco and San Diego, California
| | - Haluk Tezcan
- Lexent Bio, Inc., San Francisco and San Diego, California.
| | - Young Kwang Chae
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois.
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
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Bates BL, Mikulin JA, Wilson TJ. A single-marker method of renal cDC2 isolation. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.159.42] [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] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Because of their ability to present antigens, respond to inflammatory signals, and produce critical acute-phase cytokines, renal dendritic cells are of particular interest to those studying various disease states of the kidney. Markers such as CD11c, MHC-II, CX3CR1, and CD11b have historically been used in the murine system to isolate renal dendritic cells from the various parenchymal cells among which they’re embedded. In this study, we have determined that signaling lymphocyte activation molecule family member 9 (SLAMF9) is sufficient to mark the population of CD11b+ MHCIIhi CX3CR1+ CD11c+ F4/80+ cells in the murine kidney under homeostatic conditions. Using SLAMF9, we have devised a single-marker method of renal cDC2 isolation via fluorescence-activated cell sorting (FACS). This method will allow isolation of mouse CD11b+ dendritic cells with minimal surface receptor interference.
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Wilson TJ, Clare S, Mikulin J, Johnson CM, Harcourt K, Lyons PA, Dougan G, Smith KGC. Signalling lymphocyte activation molecule family member 9 is found on select subsets of antigen-presenting cells and promotes resistance to Salmonella infection. Immunology 2020; 159:393-403. [PMID: 31880316 PMCID: PMC7078004 DOI: 10.1111/imm.13169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 09/16/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022] Open
Abstract
Signalling lymphocyte activation molecule family member 9 (SLAMF9) is an orphan receptor of the CD2/SLAM family of leucocyte surface proteins. Examination of SLAMF9 expression and function indicates that SLAMF9 promotes inflammation by specialized subsets of antigen‐presenting cells. Within healthy liver and circulating mouse peripheral blood mononuclear cells, SLAMF9 is expressed on CD11b+, Ly6C−, CD11clow, F4/80low, MHC‐II+, CX3CR1+ mononuclear phagocytes as well as plasmacytoid dendritic cells. In addition, SLAMF9 can be found on peritoneal B1 cells and small (F4/80low), but not large (F4/80high), peritoneal macrophages. Upon systemic challenge with Salmonella enterica Typhimurium, Slamf9−/− mice were impaired in their ability to clear the infection from the liver. In humans, SLAMF9 is up‐regulated upon differentiation of monocytes into macrophages, and lipopolysaccharide stimulation of PMA‐differentiated, SLAMF9 knockdown THP‐1 cells showed an essential role of SLAMF9 in production of granulocyte–macrophage colony‐stimulating factor, tumour necrosis factor‐α, and interleukin‐1β. Taken together, these data implicate SLAMF9 in the initiation of inflammation and clearance of bacterial infection.
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Affiliation(s)
- Timothy J Wilson
- Department of Microbiology, Miami University, Oxford, OH, USA.,Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Simon Clare
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Joseph Mikulin
- Department of Microbiology, Miami University, Oxford, OH, USA
| | | | | | - Paul A Lyons
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.,Cambridge Institute for Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,Cambridge Institute for Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kenneth G C Smith
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.,Cambridge Institute for Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, UK
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19
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Mikulin JA, Wilson TJ. Distribution and phenotypes of SLAMF9+ myeloid cells in mouse tissues. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.126.29] [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] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
SLAM family receptors are critical mediators of immune function, whose expression varies across tissue and cell type. However, the expression of SLAM Family Member 9 (SLAMF9), the most recently discovered protein in the family, has yet to be investigated in mouse or human tissues. In this study, we sought to discover in what tissues and the degree to which SLAMF9 is expressed in the mouse model, as well as determine whether the cells expressing SLAMF9 belong to either a known or a novel subset. We discovered that, within the non-classical monocyte subset (CD45+CD11b+Ly6c-), two broad groups emerged based on SLAMF9 expression. The SLAMF9+ cells in this subset appear to constitute a homogenous group in both the kidney and liver. Renal SLAMF9+ cells also demonstrate higher expression of MHC-II, CX3CR1, and CD11c than their SLAMF9-counterparts, as well as low F4/80 expression and no CD103 expression. However, a cell type with largely similar marker expression and lower frequency appears in the hepatic non-classical monocyte gate, indicating that the cell type may be conserved across tissues. Therefore, SLAMF9 marks a subset of CD103−, CD172a+ classical dendritic cells and may designate a specialized subset of these cells with similar functions in both the liver and kidneys.
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20
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Huang L, Wang J, Wilson TJ, Lilley DMJ. Structure-guided design of a high-affinity ligand for a riboswitch. RNA 2019; 25:423-430. [PMID: 30609994 PMCID: PMC6426286 DOI: 10.1261/rna.069567.118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 12/28/2018] [Indexed: 06/09/2023]
Abstract
We have designed structure-based ligands for the guanidine-II riboswitch that bind with enhanced affinity, exploiting the twin binding sites created by loop-loop interaction. We synthesized diguanidine species, comprising two guanidino groups covalently connected by Cn linkers where n = 4 or 5. Calorimetric and fluorescent analysis shows that these ligands bind with a 10-fold higher affinity to the riboswitch compared to guanidine. We determined X-ray crystal structures of the riboswitch bound to the new ligands, showing that the guanidino groups are bound to both nucleobases and backbone within the binding pockets, analogously to guanidine binding. The connecting chain passes through side openings in the binding pocket and traverses the minor groove of the RNA. The combination of the riboswitch loop-loop interaction and our novel ligands has potential applications in chemical biology.
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Affiliation(s)
- Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Jia Wang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
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21
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Sng CCT, O'Byrne S, Prigozhin DM, Bauer MR, Harvey JC, Ruhle M, Challis BG, Lear S, Roberts LD, Workman S, Janowitz T, Magiera L, Doffinger R, Buckland MS, Jodrell DJ, Semple RK, Wilson TJ, Modis Y, Thaventhiran JED. A type III complement factor D deficiency: Structural insights for inhibition of the alternative pathway. J Allergy Clin Immunol 2018; 142:311-314.e6. [PMID: 29522842 PMCID: PMC6034011 DOI: 10.1016/j.jaci.2018.01.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/02/2018] [Accepted: 01/16/2018] [Indexed: 01/24/2023]
Affiliation(s)
| | - Sorcha O'Byrne
- Department of Clinical Immunology, Cambridge University Hospitals National Health Service Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Daniil M Prigozhin
- Molecular Immunity Unit, Department of Medicine, Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Matthias R Bauer
- Division of Structural Studies, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Jennifer C Harvey
- Department of Immunology, Royal Free London National Health Service Foundation Trust, London, United Kingdom
| | - Michelle Ruhle
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Ben G Challis
- Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Sara Lear
- Department of Clinical Immunology, Cambridge University Hospitals National Health Service Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Lee D Roberts
- Leeds Institute of Cardiovascular and Metabolic Medicine, Leeds Institute of Genetics, Health and Therapeutics (LIGHT) Laboratories, University of Leeds, Leeds, United Kingdom
| | - Sarita Workman
- Department of Immunology, Royal Free London National Health Service Foundation Trust, London, United Kingdom
| | - Tobias Janowitz
- Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Lukasz Magiera
- Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Rainer Doffinger
- Department of Clinical Immunology, Cambridge University Hospitals National Health Service Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Matthew S Buckland
- Department of Immunology, Royal Free London National Health Service Foundation Trust, London, United Kingdom
| | - Duncan J Jodrell
- Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Robert K Semple
- Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, United Kingdom; University of Edinburgh Centre for Cardiovascular Sciences, Queen's Medical Research Institute, Little France Crescent, Edinburgh, United Kingdom
| | | | - Yorgo Modis
- Molecular Immunity Unit, Department of Medicine, Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - James E D Thaventhiran
- Cancer Research UK Cambridge Institute, Cambridge, United Kingdom; Department of Clinical Immunology, Cambridge University Hospitals National Health Service Trust, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; MRC Toxicology Unit, University of Leicester, Leicester, United Kingdom.
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22
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Abstract
Riboswitches are structural elements found in mRNA molecules that couple small-molecule binding to regulation of gene expression, usually by controlling transcription or translation. We have determined high-resolution crystal structures of the ykkC guanidine III riboswitch from Thermobifida fusca. The riboswitch forms a classic H-type pseudoknot that includes a triple helix that is continuous with a central core of conserved nucleotides. These form a left-handed helical ramp of inter-nucleotide interactions, generating the guanidinium cation binding site. The ligand is hydrogen bonded to the Hoogsteen edges of two guanine bases. The binding pocket has a side opening that can accommodate a small side chain, shown by structures with bound methylguanidine, aminoguanidine, ethylguanidine, and agmatine. Comparison of the new structure with those of the guanidine I and II riboswitches reveals that evolution generated three different structural solutions for guanidine binding and subsequent gene regulation, although with some common elements.
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Affiliation(s)
- Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Jia Wang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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23
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Abstract
The TS ribozyme (originally called "twister sister") is a catalytic RNA. We present a crystal structure of the ribozyme in a pre-reactive conformation. Two co-axial helical stacks are organized by a three-way junction and two tertiary contacts. Five divalent metal ions are directly coordinated to RNA ligands, making important contributions to the RNA architecture. The scissile phosphate lies in a quasihelical loop region that is organized by a network of hydrogen bonding. A divalent metal ion is directly bound to the nucleobase 5' to the scissile phosphate, with an inner-sphere water molecule positioned to interact with the O2' nucleophile. The rate of ribozyme cleavage correlated in a log-linear manner with divalent metal ion pKa, consistent with proton transfer in the transition state, and we propose that the bound metal ion is a likely general base for the cleavage reaction. Our data indicate that the TS ribozyme functions predominantly as a metalloenzyme.
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Affiliation(s)
- Yijin Liu
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Timothy J. Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - David M.J. Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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24
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Lilley DM, Wilson TJ, Liu Y. The Structural and Mechanistic Origins of Catalysis in Nucleolytic Ribozymes. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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25
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Abstract
We describe the multifactorial origins of catalysis by the twister ribozyme. We provide evidence that the adenine immediately 3' to the scissile phosphate (A1) acts as a general acid. Substitution of ring nitrogen atoms indicates that very unusually the N3 of A1 is the proton donor to the oxyanion leaving group. A1 is accommodated in a specific binding pocket that raises its pKa toward neutrality, juxtaposes its N3 with the O5' to be protonated, and helps create the in-line trajectory required for nucleophilic attack. A1 performs general acid catalysis while G33 acts as a general base. A 100-fold stereospecific phosphorothioate effect at the scissile phosphate is consistent with a significant stabilization of the transition state by the ribozyme, and functional group substitution at G33 indicates that its exocyclic N2 interacts directly with the scissile phosphate. A model of the ribozyme active site is proposed that accommodates these catalytic strategies.
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Affiliation(s)
- Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee , Dow Street, Dundee DD1 5EH, U.K
| | - Yijin Liu
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee , Dow Street, Dundee DD1 5EH, U.K
| | - Christof Domnick
- Life and Medical Sciences Institute, University of Bonn , Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Stephanie Kath-Schorr
- Life and Medical Sciences Institute, University of Bonn , Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee , Dow Street, Dundee DD1 5EH, U.K
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26
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Martin JS, Kephart WC, Mobley CB, Wilson TJ, Goodlett MD, Roberts MD. A single 60-min bout of peristaltic pulse external pneumatic compression transiently upregulates phosphorylated ribosomal protein s6. Clin Physiol Funct Imaging 2016; 37:602-609. [PMID: 26769680 DOI: 10.1111/cpf.12343] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 07/01/2015] [Accepted: 12/09/2015] [Indexed: 11/28/2022]
Abstract
We investigated whether a single 60-min bout of whole leg, peristaltic pulse external pneumatic compression (EPC) altered select growth factor-related mRNAs and/or various phospho(p)-proteins related to cell growth, proliferation, inflammation and apoptosis signalling (e.g. Akt-mTOR, Jak-Stat). Ten participants (8 males, 2 females; aged 22·2 ± 0·4 years) reported to the laboratory 4 h post-prandial, and vastus lateralis muscle biopsies were obtained prior to (PRE), 1 h and 4 h post-EPC treatment. mRNA expression was analysed using real-time RT-PCR and phosphophorylated and cleaved proteins were analysed using an antibody array. No changes in selected growth factor-related mRNAs were observed following EPC. All p-proteins significantly altered by EPC decreased, except for p-rps6 (Ser235/236) which increased 31% 1 h post-EPC compared to PRE levels (P = 0·016). Notable decreases also included p-BAD (Ser112; -28%, P = 0·004) at 4 h post-EPC compared to PRE levels. In summary, an acute bout of EPC transiently upregulates p-rps6 as well as affecting other markers in the Akt-mTOR signalling cascade. Future research should characterize whether chronic EPC application promotes alterations in lower-limb musculature and/or enhances exercise-induced training adaptations.
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Affiliation(s)
- J S Martin
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine - Auburn Campus, Auburn, AL, USA.,School of Kinesiology, Auburn University, Auburn, AL, USA
| | - W C Kephart
- School of Kinesiology, Auburn University, Auburn, AL, USA
| | - C B Mobley
- School of Kinesiology, Auburn University, Auburn, AL, USA
| | | | - M D Goodlett
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine - Auburn Campus, Auburn, AL, USA.,Athletics Department, Auburn University, Auburn, AL, USA
| | - M D Roberts
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine - Auburn Campus, Auburn, AL, USA.,School of Kinesiology, Auburn University, Auburn, AL, USA
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27
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Liu Y, Freeman ADJ, Déclais AC, Wilson TJ, Gartner A, Lilley DMJ. Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA. Cell Rep 2015; 13:2565-2575. [PMID: 26686639 PMCID: PMC4695337 DOI: 10.1016/j.celrep.2015.11.042] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [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: 07/30/2015] [Revised: 10/04/2015] [Accepted: 11/11/2015] [Indexed: 11/25/2022] Open
Abstract
We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 Å resolution. The structure of the GEN1 protein reveals it to have an elaborated FEN-XPG family fold that is modified for its role in four-way junction resolution. The functional unit in the crystal is a monomer of active GEN1 bound to the product of resolution cleavage, with an extensive DNA binding interface for both helical arms. Within the crystal lattice, a GEN1 dimer interface juxtaposes two products, whereby they can be reconnected into a four-way junction, the structure of which agrees with that determined in solution. The reconnection requires some opening of the DNA structure at the center, in agreement with permanganate probing and 2-aminopurine fluorescence. The structure shows that a relaxation of the DNA structure accompanies cleavage, suggesting how second-strand cleavage is accelerated to ensure productive resolution of the junction. GEN1 crystallized with a resolution product containing two perpendicular DNA helices GEN1 shares the FEN1 superfamily fold, with a two-metal ion-containing active site GEN1 forms a dimer that juxtaposes two products in a substrate-like complex A resulting model of a GEN1-junction complex is supported by solution experiments
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Affiliation(s)
- Yijin Liu
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Alasdair D J Freeman
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Anne-Cécile Déclais
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Anton Gartner
- Center for Gene Regulation and Expression, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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28
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Margraf S, Garner LI, Wilson TJ, Brown MH. A polymorphism in a phosphotyrosine signalling motif of CD229 (Ly9, SLAMF3) alters SH2 domain binding and T-cell activation. Immunology 2015. [PMID: 26221972 PMCID: PMC4610628 DOI: 10.1111/imm.12513] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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] [Indexed: 01/15/2023] Open
Abstract
Signalling lymphocyte activation molecule (SLAM) family members regulate activation and inhibition in the innate and adaptive immune systems. Genome‐wide association studies identified their genetic locus (1q23) as highly polymorphic and associated with susceptibility to systemic lupus erythematosus (SLE). Here we show that the Val602 variant of the non‐synonymous single nucleotide polymorphism (SNP) rs509749 in the SLAM family member CD229 (Ly9, SLAMF3) has a two‐fold lower affinity compared with the SLE‐associated Met602 variant for the small adaptor protein SAP. Comparison of the two variants in T‐cell lines revealed the Val602 variant to be significantly more highly expressed than CD229 Met602. Activation was diminished in cells expressing CD229 Val602 compared with CD229 Met602 as measured by up‐regulation of CD69. There was no correlation between homozygosity at rs509749 and activation in peripheral blood mononuclear cells from healthy donors. These findings identify potential mechanisms by which a single SNP can perturb fine‐tuning in the immune system with significant functional consequences.
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Affiliation(s)
- Stefanie Margraf
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Lee I Garner
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Timothy J Wilson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Marion H Brown
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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29
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Lilley DM, Liu Y, Wilson TJ. 84 The crystal structure and catalytic mechanism of the twister ribozyme. J Biomol Struct Dyn 2015. [DOI: 10.1080/07391102.2015.1032701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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30
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Czajkowsky DM, Andersen JT, Fuchs A, Wilson TJ, Mekhaiel D, Colonna M, He J, Shao Z, Mitchell DA, Wu G, Dell A, Haslam S, Lloyd KA, Moore SC, Sandlie I, Blundell PA, Pleass RJ. Developing the IVIG biomimetic, hexa-Fc, for drug and vaccine applications. Sci Rep 2015; 5:9526. [PMID: 25912958 PMCID: PMC5224519 DOI: 10.1038/srep09526] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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: 10/29/2014] [Accepted: 02/26/2015] [Indexed: 12/20/2022] Open
Abstract
The remarkable clinical success of Fc-fusion proteins has driven intense investigation for even more potent replacements. Using quality-by-design (QbD) approaches, we generated hexameric-Fc (hexa-Fc), a ~20 nm oligomeric Fc-based scaffold that we here show binds low-affinity inhibitory receptors (FcRL5, FcγRIIb, and DC-SIGN) with high avidity and specificity, whilst eliminating significant clinical limitations of monomeric Fc-fusions for vaccine and/or cancer therapies, in particular their poor ability to activate complement. Mass spectroscopy of hexa-Fc reveals high-mannose, low-sialic acid content, suggesting that interactions with these receptors are influenced by the mannose-containing Fc. Molecular dynamics (MD) simulations provides insight into the mechanisms of hexa-Fc interaction with these receptors and reveals an unexpected orientation of high-mannose glycans on the human Fc that provides greater accessibility to potential binding partners. Finally, we show that this biosynthetic nanoparticle can be engineered to enhance interactions with the human neonatal Fc receptor (FcRn) without loss of the oligomeric structure, a crucial modification for these molecules in therapy and/or vaccine strategies where a long plasma half-life is critical.
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Affiliation(s)
- Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240 P. R. China
| | - Jan Terje Andersen
- Centre for Immune Regulation (CIR) and Department of Immunology, Oslo University Hospital Rikshospitalet, P.O. Box 4956, Oslo N-0424, Norway
| | - Anja Fuchs
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Timothy J Wilson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David Mekhaiel
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jianfeng He
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240 P. R. China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240 P. R. China
| | - Daniel A Mitchell
- Clinical Sciences Research Laboratories, Warwick Medical School, University of Warwick, Coventry CV2 2DX, UK
| | - Gang Wu
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7
| | - Anne Dell
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7
| | - Stuart Haslam
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7
| | - Katy A Lloyd
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Shona C Moore
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Inger Sandlie
- 1] Centre for Immune Regulation (CIR) and Department of Immunology, Oslo University Hospital Rikshospitalet, P.O. Box 4956, Oslo N-0424, Norway [2] CIR and Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Patricia A Blundell
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Richard J Pleass
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
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31
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Affiliation(s)
- Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
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Griauzde J, Gemmete JJ, Chaudhary N, Wilson TJ, Pandey AS. Large-volume blood patch to multiple sites in the epidural space through a single-catheter access site for treatment of spontaneous intracranial hypotension. AJNR Am J Neuroradiol 2014; 35:1841-6. [PMID: 24788127 DOI: 10.3174/ajnr.a3945] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Spontaneous intracranial hypotension can be a therapeutic challenge to the treating physician. In this study, we present our experience with the administration of a large-volume blood patch to multiple sites in the epidural space through a single-catheter access site. MATERIALS AND METHODS A retrospective review was conducted of patients with spontaneous intracranial hypotension who underwent a large-volume blood patch to multiple sites in the epidural space through a single-catheter access site from 2010 to 2012. Patient demographic data, clinical charts, indications for treatment, radiographic images, procedure notes, and postprocedure hospital course were reviewed. RESULTS Overall, 9 patients were identified who underwent 20 blood patch procedures. Patients were selected to undergo the large-volume procedure either because they had a failed site-directed epidural blood patch or if imaging demonstrated multiple possible leak sites. There were 6 women and 3 men, with an average age of 33.5 years. The mean volume of blood injected per procedure was 54.1 mL (median=55 mL; range=38-70 mL). All patients had an orthostatic headache as one of their presenting symptoms; 22% also presented with neurocognitive decline and behavioral changes; 89% of patients had improvement or resolution of their symptoms; and 80% of patients who had a previously failed site-directed epidural blood or fibrin glue patch improved with a large volume catheter-directed blood patch. CONCLUSIONS Our experience supports the use of a large-volume blood patch to multiple sites in the epidural space through a single-catheter access site for the treatment of spontaneous intracranial hypotension. Additionally, our results indicate a role for this procedure in refractory cases of spontaneous intracranial hypotension.
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Affiliation(s)
- J Griauzde
- From the Departments of Radiology (J.G., J.J.G., N.C.)
| | - J J Gemmete
- From the Departments of Radiology (J.G., J.J.G., N.C.) Neurosurgery (J.J.G., N.C., T.J.W., A.S.P.) Otolaryngology (J.J.G.), University of Michigan Hospitals, Ann Arbor, Michigan.
| | - N Chaudhary
- From the Departments of Radiology (J.G., J.J.G., N.C.) Neurosurgery (J.J.G., N.C., T.J.W., A.S.P.)
| | - T J Wilson
- Neurosurgery (J.J.G., N.C., T.J.W., A.S.P.)
| | - A S Pandey
- Neurosurgery (J.J.G., N.C., T.J.W., A.S.P.)
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33
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Wilson TJ, Garner LI, Metcalfe C, King E, Margraf S, Brown MH. Fine specificity and molecular competition in SLAM family receptor signalling. PLoS One 2014; 9:e92184. [PMID: 24642916 PMCID: PMC3958483 DOI: 10.1371/journal.pone.0092184] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 02/20/2014] [Indexed: 01/24/2023] Open
Abstract
SLAM family receptors regulate activation and inhibition in immunity through recruitment of activating and inhibitory SH2 domain containing proteins to immunoreceptor tyrosine based switch motifs (ITSMs). Binding of the adaptors, SAP and EAT-2 to ITSMs in the cytoplasmic regions of SLAM family receptors is important for activation. We analysed the fine specificity of SLAM family receptor phosphorylated ITSMs and the conserved tyrosine motif in EAT-2 for SH2 domain containing signalling proteins. Consistent with the literature describing dependence of CRACC (SLAMF7) on EAT-2, CRACC bound EAT-2 (KD = 0.003 μM) with approximately 2 orders of magnitude greater affinity than SAP (KD = 0.44 μM). RNA interference in cytotoxicity assays in NK92 cells showed dependence of CRACC on SAP in addition to EAT-2, indicating selectivity of SAP and EAT-2 may depend on the relative concentrations of the two adaptors. The concentration of SAP was four fold higher than EAT-2 in NK92 cells. Compared with SAP, the significance of EAT-2 recruitment and its downstream effectors are not well characterised. We identified PLCγ1 and PLCγ2 as principal binding partners for the EAT-2 tail. Both PLCγ1 and PLCγ2 are functionally important for cytotoxicity in NK92 cells through CD244 (SLAMF4), NTB-A (SLAMF6) and CRACC. Comparison of the specificity of SH2 domains from activating and inhibitory signalling mediators revealed a hierarchy of affinities for CD244 (SLAMF4) ITSMs. While binding of phosphatase SH2 domains to individual ITSMs of CD244 was weak compared with SAP or EAT-2, binding of tandem SH2 domains of SHP-2 to longer peptides containing tandem phosphorylated ITSMs in human CD244 increased the affinity ten fold. The concentration of the tyrosine phosphatase, SHP-2 was in the order of a magnitude higher than the adaptors, SAP and EAT-2. These data demonstrate a mechanism for direct recruitment of phosphatases in inhibitory signalling by ITSMs, while explaining competitive dominance of SAP and EAT-2.
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MESH Headings
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Binding Sites
- Binding, Competitive
- Cell Line
- Gene Expression Regulation
- Humans
- Immunity, Innate
- Immunoreceptor Tyrosine-Based Activation Motif
- Immunoreceptor Tyrosine-Based Inhibition Motif
- Killer Cells, Natural/cytology
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Molecular Sequence Data
- Phospholipase C gamma/genetics
- Phospholipase C gamma/metabolism
- Protein Binding
- Protein Structure, Tertiary
- Protein Tyrosine Phosphatase, Non-Receptor Type 11/genetics
- Protein Tyrosine Phosphatase, Non-Receptor Type 11/metabolism
- Receptor-Like Protein Tyrosine Phosphatases, Class 3/genetics
- Receptor-Like Protein Tyrosine Phosphatases, Class 3/metabolism
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Signal Transduction/genetics
- Signaling Lymphocytic Activation Molecule Family
- Signaling Lymphocytic Activation Molecule Family Member 1
- Transcription Factors/genetics
- Transcription Factors/metabolism
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Affiliation(s)
- Timothy J. Wilson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Lee I. Garner
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Clive Metcalfe
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Elliott King
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Stefanie Margraf
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Marion H. Brown
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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34
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Wilson TJ, Davis M, Pandey AS, Stetler W, Chaudhary N, Gemmete J, Thompson BG. Abstract WP75: Dual Antiplatelet Therapy in Addition to Post-Operative Heparin and Dextran Reduces Clinically Symptomatic Thromboembolic Events During Elective Aneurysm Coiling. Stroke 2013. [DOI: 10.1161/str.44.suppl_1.awp75] [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] [Indexed: 11/16/2022]
Abstract
BACKGROUND:
Thromboembolism is a feared complication of coiling a cerebral aneurysm. The purpose of this study was to compare the thromboembolic events between cerebral aneurysms coiled with an anti-thromboembolic regimen versus those with no regimen.
METHODS:
This retrospective cohort study included all adult patients who underwent elective coiling of an intracranial aneurysm between January 1, 2005 and February 1, 2012. All aneurysms were treated with conventional coiling. Patients were started on aspirin and clopidogrel for seven days prior to treatment with aspirin continued indefinitely and clopidogrel for 4 weeks post-coiling. During the coiling procedure patients were given heparin to maintain an activated clotting time 2.5x baseline. Additionally, dextran-40 and heparin were infused for 24 hours post coil placement. The primary endpoint was the presence of a clinically significant thromboembolic event as determine by physical exam and/or MRI diffusion weighted imaging. Each variable was analyzed for its independent association with the occurrence of an embolic event.
RESULTS:
312 aneurysms were electively treated. 261 of 312 aneurysms received our anti-thromboembolic regimen versus 51 who did not. There were a total of 6 (1.9%) embolic events. Patients who received the anti-thromboembolic regimen had 3 (1.1%) embolic events versus 3 (5.9%) in those not receiving the regimen (
p
= 0.024). Patients receiving the anti-thromboembolic regimen had significantly more active tobacco use but the two groups did not differ in age, sex, or the presence of obesity, diabetes, or hypercoagulable state. There was no difference in the occurrence of central nervous system or systemic hemorrhages between the two groups. In univariate analysis, the presence of a hypercoagulable state (
p
= 0.014) and the lack of anti-embolic regimen (
p
= 0.043) were associated with the occurrence of an embolic event. Both remained significant in multivariate analysis (
p
= 0.016 and
p
= 0.048, respectively).
CONCLUSION:
An anti-thromboembolic regimen consisting of dual antiplatelet therapy plus post-operative heparin and dextran reduced the risk of embolic events during elective aneurysm coiling. This regimen was safe, with no observed increase in hemorrhagic complications.
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35
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Wilson TJ, Lilley DM. A Mechanistic Comparison of the Varkud Satellite and Hairpin Ribozymes. Progress in Molecular Biology and Translational Science 2013; 120:93-121. [DOI: 10.1016/b978-0-12-381286-5.00003-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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36
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Kath-Schorr S, Wilson TJ, Li NS, Lu J, Piccirilli JA, Lilley DMJ. General acid-base catalysis mediated by nucleobases in the hairpin ribozyme. J Am Chem Soc 2012; 134:16717-24. [PMID: 22958171 DOI: 10.1021/ja3067429] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The catalytic mechanism by which the hairpin ribozyme accelerates cleavage or ligation of the phosphodiester backbone of RNA has been incompletely understood. There is experimental evidence for an important role for an adenine (A38) and a guanine (G8), and it has been proposed that these act in general acid-base catalysis. In this work we show that a large reduction in cleavage rate on substitution of A38 by purine (A38P) can be reversed by replacement of the 5'-oxygen atom at the scissile phosphate by sulfur (5'-PS), which is a much better leaving group. This is consistent with A38 acting as the general acid in the unmodified ribozyme. The rate of cleavage of the 5'-PS substrate by the A38P ribozyme increases with pH log-linearly, indicative of a requirement for a deprotonated base with a relatively high pK(a). On substitution of G8 by diaminopurine, the 5'-PS substrate cleavage rate at first increases with pH and then remains at a plateau, exhibiting an apparent pK(a) consistent with this nucleotide acting in general base catalysis. Alternative explanations for the pH dependence of hairpin ribozyme reactivity are discussed, from which we conclude that general acid-base catalysis by A38 and G8 is the simplest and most probable explanation consistent with all the experimental data.
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Affiliation(s)
- Stephanie Kath-Schorr
- Cancer Research UK, Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Abstract
Fc receptor-like (FcRL) proteins are a family of cellular receptors homologous to FcγRI and are predominantly expressed by B cells. They function to costimulate or inhibit BCR signaling through consensus ITAMs and ITIMs; however, the extracellular ligands of these receptors remain unknown or controversial. In this study, we tested the ability of human FcRL proteins to bind Igs and found FcRL4 and FcRL5 to be bona fide Fc receptors. In cellular binding assays, FcRL4 bound efficiently to IgA and FcRL5 binds all IgG isotypes with varied efficiency. Additionally, we generated mAbs capable of specifically blocking these interactions. Given their expression on activated B cells and potential for inhibitory signaling, FcRL4 and FcRL5 are likely to be important for immune complex-dependent human B cell regulation, and they represent novel therapeutic targets for receptor blockade therapies.
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Affiliation(s)
- Timothy J Wilson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
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38
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Ouellet J, Schorr S, Iqbal A, Wilson TJ, Lilley DMJ. Orientation of cyanine fluorophores terminally attached to DNA via long, flexible tethers. Biophys J 2011; 101:1148-54. [PMID: 21889452 DOI: 10.1016/j.bpj.2011.07.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 07/04/2011] [Accepted: 07/11/2011] [Indexed: 11/15/2022] Open
Abstract
Cyanine fluorophores are commonly used in single-molecule FRET experiments with nucleic acids. We have previously shown that indocarbocyanine fluorophores attached to the 5'-termini of DNA and RNA via three-carbon atom linkers stack on the ends of the helix, orienting their transition moments. We now investigate the orientation of sulfoindocarbocyanine fluorophores tethered to the 5'-termini of DNA via 13-atom linkers. Fluorescence lifetime measurements of sulfoindocarbocyanine 3 attached to double-stranded DNA indicate that the fluorophore is extensively stacked onto the terminal basepair at 15 °C, with properties that depend on the terminal sequence. In single molecules of duplex DNA, FRET efficiency between sulfoindocarbocyanine 3 and 5 attached in this manner is modulated with helix length, indicative of fluorophore orientation and consistent with stacked fluorophores that can undergo lateral motion. We conclude that terminal stacking is an intrinsic property of the cyanine fluorophores irrespective of the length of the tether and the presence or absence of sulfonyl groups. However, compared to short-tether indocarbocyanine, the mean rotational relationship between the two fluorophores is changed by ∼60° for the long-tether sulfoindocarbocyanine fluorophores. This is consistent with the transition moments becoming approximately aligned with the long axis of the terminal basepair for the long-linker species.
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Affiliation(s)
- Jonathan Ouellet
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
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39
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Wilson TJ, Lilley DMJ. Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data. RNA 2011; 17:213-21. [PMID: 21173201 PMCID: PMC3022271 DOI: 10.1261/rna.2473711] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The active centers of the hairpin and VS ribozymes are both generated by the interaction of two internal loops, and both ribozymes use guanine and adenine nucleobases to accelerate cleavage and ligation reactions. The centers are topologically equivalent and the relative positioning of key elements the same. There is good evidence that the cleavage reaction of the VS ribozyme is catalyzed by the guanine (G638) acting as general base and the adenine (A756) as general acid. We now critically evaluate the experimental mechanistic evidence for the hairpin ribozyme. We conclude that all the available data are fully consistent with a major contribution to catalysis by general acid-base catalysis involving the adenine (A38) and guanine (G8). It appears that the two ribozymes are mechanistically equivalent.
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Affiliation(s)
- Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD15EH, United Kingdom
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Li NS, Frederiksen JK, Koo SC, Lu J, Wilson TJ, Lilley DMJ, Piccirilli JA. A general and efficient approach for the construction of RNA oligonucleotides containing a 5'-phosphorothiolate linkage. Nucleic Acids Res 2010; 39:e31. [PMID: 21148150 PMCID: PMC3061073 DOI: 10.1093/nar/gkq1265] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [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] [Indexed: 11/17/2022] Open
Abstract
Oligoribonucleotides containing a 5′-phosphorothiolate linkage have provided effective tools to study the mechanisms of RNA catalysis, allowing resolution of kinetic ambiguity associated with mechanistic dissection and providing a strategy to establish linkage between catalysis and specific functional groups. However, challenges associated with their synthesis have limited wider application of these modified nucleic acids. Here, we describe a general semisynthetic strategy to obtain these oligoribonucleotides reliably and relatively efficiently. The approach begins with the chemical synthesis of an RNA dinucleotide containing the 5′-phosphorothiolate linkage, with the adjacent 2′-hydroxyl group protected as the photolabile 2′-O-o-nitrobenzyl or 2′-O-α-methyl-o-nitrobenzyl derivative. Enzymatic ligation of the 2′-protected dinucleotide to transcribed or chemically synthesized 5′ and 3′ flanking RNAs yields the full-length oligoribonucleotide. The photolabile protecting group increases the chemical stability of these highly activated oligoribonucleotides during synthesis and long-term storage but is easily removed with UV irradiation under neutral conditions, allowing immediate use of the modified RNA in biochemical experiments.
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Affiliation(s)
- Nan-Sheng Li
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57th Street, Room W406, Chicago, IL 60637, USA.
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Jobim M, Chagastelles P, Salim PH, Portela P, Wilson TJ, Curti AG, Jobim MR, João DA, Nardi NB, Tschiedel B, Jobim LF, Roesler R, Schwartsmann G. Association of killer cell immunoglobulin-like receptors and human leukocyte antigen–C genotypes in South Brazilian with type 1 diabetes. Hum Immunol 2010; 71:799-803. [DOI: 10.1016/j.humimm.2010.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 02/19/2010] [Accepted: 05/12/2010] [Indexed: 01/04/2023]
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Wilson TJ, Gilfillan S, Colonna M. Fc Receptor-Like A Associates with Intracellular IgG and IgM but Is Dispensable for Antigen-Specific Immune Responses. J I 2010; 185:2960-7. [DOI: 10.4049/jimmunol.1001428] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Swanson CL, Wilson TJ, Strauch P, Colonna M, Pelanda R, Torres RM. Type I IFN enhances follicular B cell contribution to the T cell-independent antibody response. ACTA ACUST UNITED AC 2010; 207:1485-500. [PMID: 20566717 PMCID: PMC2901065 DOI: 10.1084/jem.20092695] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [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] [Indexed: 12/24/2022]
Abstract
Humoral immunity to viruses and encapsulated bacteria is comprised of T cell-independent type 2 (TI-2) antibody responses that are characterized by rapid antibody production by marginal zone and B1 B cells. We demonstrate that toll-like receptor (TLR) ligands influence the TI-2 antibody response not only by enhancing the overall magnitude but also by skewing this response to one that is dominated by IgG isotypes. Importantly, TLR ligands facilitate this response by inducing type I interferon (IFN), which in turn elicits rapid and significant amounts of antigen-specific IgG2c predominantly from FO (follicular) B cells. Furthermore, we show that although the IgG2c antibody response requires B cell-autonomous IFN-alpha receptor signaling, it is independent of B cell-intrinsic TLR signaling. Thus, innate signals have the capacity to enhance TI-2 antibody responses by promoting participation of FO B cells, which then elaborate effective IgG anti-pathogen antibodies.
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Affiliation(s)
- Cristina L Swanson
- Integrated Department of Immunology, University of Colorado, Denver, CO 80206, USA
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Jobim M, Salim PH, Portela P, Wilson TJ, Fraportti J, Baronio D, Gil B, Penna LS, Roesler R, Jobim LF, Schwartsmann G. Killer cell immunoglobulin-like receptor gene diversity in a Caucasian population of Southern Brazil. Int J Immunogenet 2010; 37:83-9. [PMID: 20082646 DOI: 10.1111/j.1744-313x.2009.00894.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- M Jobim
- Department of Immunology, Hospital de Clínicas, Porto Alegre, Brazil.
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Boles KS, Vermi W, Facchetti F, Fuchs A, Wilson TJ, Diacovo TG, Cella M, Colonna M. A novel molecular interaction for the adhesion of follicular CD4 T cells to follicular DC. Eur J Immunol 2009; 39:695-703. [PMID: 19197944 DOI: 10.1002/eji.200839116] [Citation(s) in RCA: 187] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nectins and Nectin-like molecules (Necl) play a critical role in cell polarity within epithelia and in the nervous and reproductive systems. Recently, immune receptors specific for Nectins/Necl have been described. Since the expression and distribution of Nectins/Necl is often subverted during tumorigenesis, it has been suggested that the immune system may use these receptors to recognize and eliminate tumors. Here we describe a novel immunoreceptor, Washington University Cell Adhesion Molecule, which is expressed on human follicular B helper T cells (TFH) and binds a Nectin/Necl family member, the poliovirus receptor (PVR), under both static and flow conditions. Furthermore, we demonstrate that PVR is abundantly expressed by follicular DC (FDC) within the germinal center. These results reveal a novel molecular interaction that mediates adhesion of TFH to FDC and provide the first evidence that immune receptors for Nectins/Necl may be involved the generation of T cell-dependent antibody responses.
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Affiliation(s)
- Kent S Boles
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
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Araki L, Morita K, Yamaguchi M, Zhao ZY, Wilson TJ, Lilley DMJ, Harusawa S. Synthesis of Novel C4-Linked C2-Imidazole Ribonucleoside Phosphoramidite and Its Application to Probing the Catalytic Mechanism of a Ribozyme. J Org Chem 2009; 74:2350-6. [DOI: 10.1021/jo802556s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lisa Araki
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan, School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dundee DDI 5EH, U.K
| | - Keiji Morita
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan, School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dundee DDI 5EH, U.K
| | - Maho Yamaguchi
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan, School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dundee DDI 5EH, U.K
| | - Zheng-yun Zhao
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan, School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dundee DDI 5EH, U.K
| | - Timothy J. Wilson
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan, School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dundee DDI 5EH, U.K
| | - David M. J. Lilley
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan, School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dundee DDI 5EH, U.K
| | - Shinya Harusawa
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan, School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dundee DDI 5EH, U.K
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Jobim M, Jobim LFJ, Salim PH, Cestari TF, Toresan R, Gil BC, Jobim MR, Wilson TJ, Kruger M, Schlottfeldt J, Schwartsmann G. A study of the killer cell immunoglobulin-like receptor gene KIR2DS1 in a Caucasoid Brazilian population with psoriasis vulgaris. ACTA ACUST UNITED AC 2008; 72:392-6. [PMID: 18643961 DOI: 10.1111/j.1399-0039.2008.01096.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Psoriasis is a chronic inflammatory skin disease whose pathogenesis and genetic background remain unclear. Considering that previous studies have suggested an association of psoriasis vulgaris (PV) and killer cell immunoglobulin-like receptors (KIRs), we typed 15 KIR genes and human leukocyte antigen (HLA)-Cw in 79 Brazilian Caucasoid patients with PV and 110 healthy controls by polymerase chain reaction (PCR) using sequence-specific oligonucleotides and sequence-specific primers. We did not observe a relevant increase in the frequency of the activating KIR2DS1 gene in the PV group [KIR2DS1, 46 of 79 cases (58.2%) vs 40 of 110 controls (36.4%)]. However, an association of KIR2DS1 with Cw*0602+ in 26.5% of PV patients was observed, while it was present in only 5.4% of controls. These results suggest that activating KIR2DS1 gene may not confer susceptibility to PV, and an association of KIR2DS1 gene with the HLA-Cw*0602+ was observed in these patients.
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Affiliation(s)
- M Jobim
- Department of Immunology, Hospital de Clínicas, Porto Alegre, Brazil.
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Abstract
A guanine (G638) within the substrate loop of the VS ribozyme plays a critical role in the cleavage reaction. Replacement by any other nucleotide results in severe impairment of cleavage, yet folding of the substrate is not perturbed, and the variant substrates bind the ribozyme with similar affinity, acting as competitive inhibitors. Functional group substitution shows that the imino proton on the N1 is critical, suggesting a possible role in general acid-base catalysis, and this in accord with the pH dependence of the reaction rate for the natural and modified substrates. We propose a chemical mechanism for the ribozyme that involves general acid-base catalysis by the combination of the nucleobases of guanine 638 and adenine 756. This is closely similar to the probable mechanism of the hairpin ribozyme, and the active site arrangements for the two ribozymes appear topologically equivalent. This has probably arisen by convergent evolution.
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Affiliation(s)
- Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
| | - Aileen C McLeod
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK. Tel.: +44 1382 384243; Fax: +44 1382 385893; E-mail:
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Wilson TJ, Presti RM, Tassi I, Overton ET, Cella M, Colonna M. FcRL6, a new ITIM-bearing receptor on cytolytic cells, is broadly expressed by lymphocytes following HIV-1 infection. Blood 2007; 109:3786-93. [PMID: 17213291 DOI: 10.1182/blood-2006-06-030023] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Fc receptor–like proteins (FcRLs) are a growing family of molecules homologous to FcγRI. Whereas all 7 previously reported Fc receptor homologs are expressed by B cells, here we report a new receptor, FcRL6, that is expressed by cytolytic cells including natural killer (NK) cells and effector and effector-memory CD8+ T cells. FcRL6 contains a novel cytoplasmic cysteine-rich motif and recruits SHP-2 through a phosphorylated ITIM, indicating a potential signaling function in effector lymphocytes. In vitro, FcRL6 does not greatly influence NK-cell or CD8+ T-cell–mediated cytotoxicity and has minimal impact on cytokine secretion. However, FcRL6 expression among T lymphocytes is greatly expanded in human immunodeficiency virus type 1 (HIV-1)–infected individuals, and includes not only effector and effector-memory CD8+ T cells but also populations of CD4+ T cells. Expansion of FcRL6-positive lymphocytes is not related to viral load, but is indicative of the dysregulated expansion of terminally differentiated effector lymphocyte populations in response to chronic HIV-1 infection and may serve as an important marker for chronic immune activation and for tracking the generation of effector cells following immune stimulation.
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Affiliation(s)
- Timothy J Wilson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
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Wilson TJ, Nahas M, Araki L, Harusawa S, Ha T, Lilley DMJ. RNA folding and the origins of catalytic activity in the hairpin ribozyme. Blood Cells Mol Dis 2006; 38:8-14. [PMID: 17150385 DOI: 10.1016/j.bcmd.2006.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2006] [Accepted: 10/10/2006] [Indexed: 11/26/2022]
Abstract
The nucleolytic ribozymes catalyse site-specific phosphodiester cleavage and ligation transesterification reactions in RNA. The hairpin ribozyme folds to generate an intimate loop-loop interaction to create the local environment in which catalysis can proceed. We have studied the ion-induced folding using single-molecule FRET experiments, showing that the four-way helical junction accelerates the folding 500-fold by introducing a discrete intermediate that juxtaposes the loops. Using FRET we can observe individual hairpin ribozyme molecules as they undergo multiple cycles of cleavage and ligation, and measure the rates of the internal reactions, free of uncertainties in the contributions of docking and substrate dissociation processes. On average, the cleaved ribozyme undergoes several docking-undocking events before a ligation reaction occurs. On the basis of these experiments, we have explored the role of the nucleobases G8 and A38 in the catalysis. Both cleavage and ligation reactions are pH dependent, corresponding to the titration of a group with pKa=6.2. We have used a novel ribonucleoside in which these bases are replaced by imidazole to investigate the role of acid-base catalysis in this ribozyme. We observe significant rates of cleavage and ligation, and a bell-shaped pH dependence for both.
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Affiliation(s)
- Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, UK
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