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Senn KA, Lipinski KA, Zeps NJ, Griffin AF, Wilkinson ME, Hoskins AA. Control of 3' splice site selection by the yeast splicing factor Fyv6. bioRxiv 2024:2024.05.04.592262. [PMID: 38746449 PMCID: PMC11092753 DOI: 10.1101/2024.05.04.592262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Pre-mRNA splicing is catalyzed in two steps: 5' splice site (SS) cleavage and exon ligation. A number of proteins transiently associate with spliceosomes to specifically impact these steps (1 st and 2 nd step factors). We recently identified Fyv6 (FAM192A in humans) as a 2 nd step factor in S. cerevisiae ; however, we did not determine how widespread Fyv6's impact is on the transcriptome. To answer this question, we have used RNA-Seq to analyze changes in splicing. These results show that loss of Fyv6 results in activation of non-consensus, branch point (BP) proximal 3' SS transcriptome-wide. To identify the molecular basis of these observations, we determined a high-resolution cryo-EM structure of a yeast product complex spliceosome containing Fyv6 at 2.3 Å. The structure reveals that Fyv6 is the only 2 nd step factor that contacts the Prp22 ATPase and that Fyv6 binding is mutually exclusive with that of the 1 st step factor Yju2. We then use this structure to dissect Fyv6 functional domains and interpret results of a genetic screen for fyv6Δ suppressor mutations. The combined transcriptomic, structural, and genetic studies allow us to propose a model in which Yju2/Fyv6 exchange facilitates exon ligation and Fyv6 promotes usage of Prp22-dependent, BP distal 3' SS.
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Madigan V, Zhang Y, Raghavan R, Wilkinson ME, Faure G, Puccio E, Segel M, Lash B, Macrae RK, Zhang F. Human paraneoplastic antigen Ma2 (PNMA2) forms icosahedral capsids that can be engineered for mRNA delivery. Proc Natl Acad Sci U S A 2024; 121:e2307812120. [PMID: 38437549 PMCID: PMC10945824 DOI: 10.1073/pnas.2307812120] [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: 06/07/2023] [Accepted: 10/20/2023] [Indexed: 03/06/2024] Open
Abstract
A number of endogenous genes in the human genome encode retroviral gag-like proteins, which were domesticated from ancient retroelements. The paraneoplastic Ma antigen (PNMA) family members encode a gag-like capsid domain, but their ability to assemble as capsids and traffic between cells remains mostly uncharacterized. Here, we systematically investigate human PNMA proteins and find that a number of PNMAs are secreted by human cells. We determine that PNMA2 forms icosahedral capsids efficiently but does not naturally encapsidate nucleic acids. We resolve the cryoelectron microscopy (cryo-EM) structure of PNMA2 and leverage the structure to design engineered PNMA2 (ePNMA2) particles with RNA packaging abilities. Recombinantly purified ePNMA2 proteins package mRNA molecules into icosahedral capsids and can function as delivery vehicles in mammalian cell lines, demonstrating the potential for engineered endogenous capsids as a nucleic acid therapy delivery modality.
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Affiliation(s)
- Victoria Madigan
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- McGovern Institute for Brain Research at Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- HHMI, Cambridge, MA02139
| | - Yugang Zhang
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- McGovern Institute for Brain Research at Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- HHMI, Cambridge, MA02139
| | - Rumya Raghavan
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- McGovern Institute for Brain Research at Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- HHMI, Cambridge, MA02139
| | - Max E. Wilkinson
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- McGovern Institute for Brain Research at Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- HHMI, Cambridge, MA02139
| | - Guilhem Faure
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- McGovern Institute for Brain Research at Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- HHMI, Cambridge, MA02139
| | - Elena Puccio
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- McGovern Institute for Brain Research at Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- HHMI, Cambridge, MA02139
| | - Michael Segel
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- McGovern Institute for Brain Research at Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- HHMI, Cambridge, MA02139
| | - Blake Lash
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- McGovern Institute for Brain Research at Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- HHMI, Cambridge, MA02139
| | - Rhiannon K. Macrae
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- McGovern Institute for Brain Research at Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- HHMI, Cambridge, MA02139
| | - Feng Zhang
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- McGovern Institute for Brain Research at Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- HHMI, Cambridge, MA02139
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Wilkinson ME, Frangieh CJ, Macrae RK, Zhang F. Structure of the R2 non-LTR retrotransposon initiating target-primed reverse transcription. Science 2023; 380:301-308. [PMID: 37023171 PMCID: PMC10499050 DOI: 10.1126/science.adg7883] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [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: 01/20/2023] [Accepted: 03/21/2023] [Indexed: 04/08/2023]
Abstract
Non-long terminal repeat (non-LTR) retrotransposons, or long interspersed nuclear elements (LINEs), are an abundant class of eukaryotic transposons that insert into genomes by target-primed reverse transcription (TPRT). During TPRT, a target DNA sequence is nicked and primes reverse transcription of the retrotransposon RNA. Here, we report the cryo-electron microscopy structure of the Bombyx mori R2 non-LTR retrotransposon initiating TPRT at its ribosomal DNA target. The target DNA sequence is unwound at the insertion site and recognized by an upstream motif. An extension of the reverse transcriptase (RT) domain recognizes the retrotransposon RNA and guides the 3' end into the RT active site to template reverse transcription. We used Cas9 to retarget R2 in vitro to non-native sequences, suggesting future use as a reprogrammable RNA-based gene-insertion tool.
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Affiliation(s)
- Max E. Wilkinson
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Chris J. Frangieh
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Rhiannon K. Macrae
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Feng Zhang
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
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Strecker J, Demircioglu FE, Li D, Faure G, Wilkinson ME, Gootenberg JS, Abudayyeh OO, Nishimasu H, Macrae RK, Zhang F. RNA-activated protein cleavage with a CRISPR-associated endopeptidase. Science 2022; 378:874-881. [PMID: 36423276 PMCID: PMC10028731 DOI: 10.1126/science.add7450] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 11/06/2022]
Abstract
In prokaryotes, CRISPR-Cas systems provide adaptive immune responses against foreign genetic elements through RNA-guided nuclease activity. Recently, additional genes with non-nuclease functions have been found in genetic association with CRISPR systems, suggesting that there may be other RNA-guided non-nucleolytic enzymes. One such gene from Desulfonema ishimotonii encodes the TPR-CHAT protease Csx29, which is associated with the CRISPR effector Cas7-11. Here, we demonstrate that this CRISPR-associated protease (CASP) exhibits programmable RNA-activated endopeptidase activity against a sigma factor inhibitor to regulate a transcriptional response. Cryo-electron microscopy of an active and substrate-bound CASP complex reveals an allosteric activation mechanism that reorganizes Csx29 catalytic residues upon target RNA binding. This work reveals an RNA-guided function in nature that can be leveraged for RNA-sensing applications in vitro and in human cells.
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Affiliation(s)
- Jonathan Strecker
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, Cambridge, MA 02139, USA
- Department of Biological Engineering, Cambridge, MA 02139, USA
| | - F. Esra Demircioglu
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, Cambridge, MA 02139, USA
- Department of Biological Engineering, Cambridge, MA 02139, USA
| | - David Li
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, Cambridge, MA 02139, USA
- Department of Biological Engineering, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Guilhem Faure
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, Cambridge, MA 02139, USA
- Department of Biological Engineering, Cambridge, MA 02139, USA
| | - Max E. Wilkinson
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, Cambridge, MA 02139, USA
- Department of Biological Engineering, Cambridge, MA 02139, USA
| | | | | | - Hiroshi Nishimasu
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Inamori Research Institute for Science, 620 Suiginya-cho, Kyoto 600-8411, Japan
| | - Rhiannon K. Macrae
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, Cambridge, MA 02139, USA
- Department of Biological Engineering, Cambridge, MA 02139, USA
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, Cambridge, MA 02139, USA
- Department of Biological Engineering, Cambridge, MA 02139, USA
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5
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Hirano S, Kappel K, Altae-Tran H, Faure G, Wilkinson ME, Kannan S, Demircioglu FE, Yan R, Shiozaki M, Yu Z, Makarova KS, Koonin EV, Macrae RK, Zhang F. Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA. Nature 2022; 610:575-581. [PMID: 36224386 PMCID: PMC9581776 DOI: 10.1038/s41586-022-05324-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 09/06/2022] [Indexed: 11/09/2022]
Abstract
RNA-guided systems, such as CRISPR-Cas, combine programmable substrate recognition with enzymatic function, a combination that has been used advantageously to develop powerful molecular technologies1,2. Structural studies of these systems have illuminated how the RNA and protein jointly recognize and cleave their substrates, guiding rational engineering for further technology development3. Recent work identified a new class of RNA-guided systems, termed OMEGA, which include IscB, the likely ancestor of Cas9, and the nickase IsrB, a homologue of IscB lacking the HNH nuclease domain4. IsrB consists of only around 350 amino acids, but its small size is counterbalanced by a relatively large RNA guide (roughly 300-nt ωRNA). Here, we report the cryogenic-electron microscopy structure of Desulfovirgula thermocuniculi IsrB (DtIsrB) in complex with its cognate ωRNA and a target DNA. We find the overall structure of the IsrB protein shares a common scaffold with Cas9. In contrast to Cas9, however, which uses a recognition (REC) lobe to facilitate target selection, IsrB relies on its ωRNA, part of which forms an intricate ternary structure positioned analogously to REC. Structural analyses of IsrB and its ωRNA as well as comparisons to other RNA-guided systems highlight the functional interplay between protein and RNA, advancing our understanding of the biology and evolution of these diverse systems.
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Affiliation(s)
- Seiichi Hirano
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Kalli Kappel
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Han Altae-Tran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Max E Wilkinson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Soumya Kannan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - F Esra Demircioglu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Rui Yan
- CryoEM Shared Resources, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
| | - Momoko Shiozaki
- CryoEM Shared Resources, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
| | - Zhiheng Yu
- CryoEM Shared Resources, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Rhiannon K Macrae
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
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Gao LA, Wilkinson ME, Strecker J, Makarova KS, Macrae RK, Koonin EV, Zhang F. Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Science 2022; 377:eabm4096. [PMID: 35951700 PMCID: PMC10028730 DOI: 10.1126/science.abm4096] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [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: 01/13/2023]
Abstract
Many organisms have evolved specialized immune pattern-recognition receptors, including nucleotide-binding oligomerization domain-like receptors (NLRs) of the STAND superfamily that are ubiquitous in plants, animals, and fungi. Although the roles of NLRs in eukaryotic immunity are well established, it is unknown whether prokaryotes use similar defense mechanisms. Here, we show that antiviral STAND (Avs) homologs in bacteria and archaea detect hallmark viral proteins, triggering Avs tetramerization and the activation of diverse N-terminal effector domains, including DNA endonucleases, to abrogate infection. Cryo-electron microscopy reveals that Avs sensor domains recognize conserved folds, active-site residues, and enzyme ligands, allowing a single Avs receptor to detect a wide variety of viruses. These findings extend the paradigm of pattern recognition of pathogen-specific proteins across all three domains of life.
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Affiliation(s)
- Linyi Alex Gao
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research
- Department of Brain and Cognitive Sciences
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Society of Fellows, Harvard University, Cambridge, MA 02138, USA
- Correspondence: (F.Z.) or (L.A.G.)
| | - Max E. Wilkinson
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research
- Department of Brain and Cognitive Sciences
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jonathan Strecker
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research
- Department of Brain and Cognitive Sciences
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Rhiannon K. Macrae
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research
- Department of Brain and Cognitive Sciences
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research
- Department of Brain and Cognitive Sciences
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Correspondence: (F.Z.) or (L.A.G.)
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Iball GR, Tolan D, Avery GR, Cope LH, Hoare T, Lambie H, Lowe A, de Noronha RJ, Roberts CL, Wilkinson ME, Woolfall P. Improving practice in radiology: a quality-improvement project examining CT colonography patient dose and scanning technique. Clin Radiol 2021; 76:626.e13-626.e21. [PMID: 33714540 DOI: 10.1016/j.crad.2021.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/05/2021] [Indexed: 11/26/2022]
Abstract
AIM To audit scanning technique and patient doses for computed tomography (CT) colonography (CTC) examinations in a large UK region and to identify opportunities for quality improvement. MATERIALS AND METHODS Scanning technique and patient dose data were gathered for both contrast-enhanced and unenhanced CTC examinations from 33 imaging protocols across 27 scanners. Measurements of patient weight and effective diameter were also obtained. Imaging protocols were compared to identify technique differences between similar scanners. Scanner average doses were calculated and combined to generate regional diagnostic reference limits (DRLs) for both examinations. RESULTS The regional DRLs for contrast-enhanced examinations were volume CT dose index (CTDIvol) of 11 and 5 mGy for the two scan phases (contrast-enhanced and either delayed phase or non-contrast enhanced respectively), and dose-length product (DLP) of 740 mGy·cm. For unenhanced examinations, these were 5 mGy and 450 mGy·cm. These are notably lower than the national DRLs of 11 mGy and 950 mGy·cm. Substantial differences in scan technique and doses on similar scanners were identified as areas for quality-improvement action. CONCLUSION A regional CTC dose audit has demonstrated compliance with national DRLs but marked variation in practice between sites for the dose delivered to patients, notably when scanners of the same type were compared for the same indication. This study demonstrates that the national DRL is too high for current scanner technology and should be revised.
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Affiliation(s)
- G R Iball
- Department of Medical Physics, Old Medical School, Leeds General Infirmary, Leeds, LS1 3EX, UK.
| | - D Tolan
- Radiology Department, St James' University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - G R Avery
- Department of Radiology, Hull and East Yorkshire Hospitals NHS Trust Castle Hill Hospital, Cottingham, Hull, HU16 5JQ, UK
| | - L H Cope
- Radiology Department, South Tyneside NHS FT, Harton Lane South Shields, Tyne and Wear, NE34 0PL, UK
| | - T Hoare
- Radiology Department, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Trust, Queen Victoria Road, Newcastle upon Tyne, NE1 4LP, UK
| | - H Lambie
- Radiology Department, St James' University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - A Lowe
- Radiology Department, Bradford Royal Infirmary, Duckworth Lane, Bradford, BD9 6RJ, UK
| | - R J de Noronha
- Radiology Department, Sheffield Teaching Hospital Trust, Herries Road, Sheffield, S5 7AU, UK
| | - C L Roberts
- Radiology, Calderdale and Huddersfield NHS Trust, Huddersfield, West Yorkshire, HD3 3EA, UK
| | - M E Wilkinson
- Northumbria Healthcare NHS Foundation Trust, Wansbeck General Hospital, Woodhorn Lane, Ashington, Norhumberland, NE 63 9JJ, UK
| | - P Woolfall
- Radiology Department, University Hospital of North Tees, Stockton on Tees, TS19 8PE, UK
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8
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Wilkinson ME, Fica SM, Galej WP, Nagai K. Structural basis for conformational equilibrium of the catalytic spliceosome. Mol Cell 2021; 81:1439-1452.e9. [PMID: 33705709 PMCID: PMC8022279 DOI: 10.1016/j.molcel.2021.02.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/14/2020] [Accepted: 02/11/2021] [Indexed: 12/21/2022]
Abstract
The ATPase Prp16 governs equilibrium between the branching (B∗/C) and exon ligation (C∗/P) conformations of the spliceosome. Here, we present the electron cryomicroscopy reconstruction of the Saccharomyces cerevisiae C-complex spliceosome at 2.8 Å resolution and identify a novel C-complex intermediate (Ci) that elucidates the molecular basis for this equilibrium. The exon-ligation factors Prp18 and Slu7 bind to Ci before ATP hydrolysis by Prp16 can destabilize the branching conformation. Biochemical assays suggest that these pre-bound factors prime the C complex for conversion to C∗ by Prp16. A complete model of the Prp19 complex (NTC) reveals how the branching factors Yju2 and Isy1 are recruited by the NTC before branching. Prp16 remodels Yju2 binding after branching, allowing Yju2 to remain tethered to the NTC in the C∗ complex to promote exon ligation. Our results explain how Prp16 action modulates the dynamic binding of step-specific factors to alternatively stabilize the C or C∗ conformation and establish equilibrium of the catalytic spliceosome. Cryo-EM reveals new Ci spliceosome intermediate between branching and exon ligation Binding of branching and exon-ligation factors to Ci governs spliceosome equilibrium Exon-ligation factors Slu7 and Prp18 bind Ci weakly before Prp16 action After Prp16 action, pre-bound Slu7 and Prp18 bind strongly to promote exon ligation
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Affiliation(s)
- Max E Wilkinson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
| | - Sebastian M Fica
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
| | - Wojciech P Galej
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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9
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Abstract
The spliceosome removes introns from messenger RNA precursors (pre-mRNA). Decades of biochemistry and genetics combined with recent structural studies of the spliceosome have produced a detailed view of the mechanism of splicing. In this review, we aim to make this mechanism understandable and provide several videos of the spliceosome in action to illustrate the intricate choreography of splicing. The U1 and U2 small nuclear ribonucleoproteins (snRNPs) mark an intron and recruit the U4/U6.U5 tri-snRNP. Transfer of the 5' splice site (5'SS) from U1 to U6 snRNA triggers unwinding of U6 snRNA from U4 snRNA. U6 folds with U2 snRNA into an RNA-based active site that positions the 5'SS at two catalytic metal ions. The branch point (BP) adenosine attacks the 5'SS, producing a free 5' exon. Removal of the BP adenosine from the active site allows the 3'SS to bind, so that the 5' exon attacks the 3'SS to produce mature mRNA and an excised lariat intron.
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Affiliation(s)
- Max E Wilkinson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; ,
| | - Clément Charenton
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; ,
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; ,
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10
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Abstract
Recent developments have resulted in electron cryo-microscopy (cryo-EM) becoming a useful tool for the structure determination of biological macromolecules. For samples containing inherent flexibility, heterogeneity or preferred orientation, the collection of extensive cryo-EM data using several conditions and microscopes is often required. In such a scenario, merging cryo-EM data sets is advantageous because it allows improved three-dimensional reconstructions to be obtained. Since data sets are not always collected with the same pixel size, merging data can be challenging. Here, two methods to combine cryo-EM data are described. Both involve the calculation of a rescaling factor from independent data sets. The effects of errors in the scaling factor on the results of data merging are also estimated. The methods described here provide a guideline for cryo-EM users who wish to combine data sets from the same type of microscope and detector.
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Affiliation(s)
- Max E. Wilkinson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Ananthanarayanan Kumar
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Ana Casañal
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
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11
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Charenton C, Wilkinson ME, Nagai K. Mechanism of 5' splice site transfer for human spliceosome activation. Science 2019; 364:362-367. [PMID: 30975767 DOI: 10.1126/science.aax3289] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/02/2019] [Indexed: 12/11/2022]
Abstract
The prespliceosome, comprising U1 and U2 small nuclear ribonucleoproteins (snRNPs) bound to the precursor messenger RNA 5' splice site (5'SS) and branch point sequence, associates with the U4/U6.U5 tri-snRNP to form the fully assembled precatalytic pre-B spliceosome. Here, we report cryo-electron microscopy structures of the human pre-B complex captured before U1 snRNP dissociation at 3.3-angstrom core resolution and the human tri-snRNP at 2.9-angstrom resolution. U1 snRNP inserts the 5'SS-U1 snRNA helix between the two RecA domains of the Prp28 DEAD-box helicase. Adenosine 5'-triphosphate-dependent closure of the Prp28 RecA domains releases the 5'SS to pair with the nearby U6 ACAGAGA-box sequence presented as a mobile loop. The structures suggest that formation of the 5'SS-ACAGAGA helix triggers remodeling of an intricate protein-RNA network to induce Brr2 helicase relocation to its loading sequence in U4 snRNA, enabling Brr2 to unwind the U4/U6 snRNA duplex to allow U6 snRNA to form the catalytic center of the spliceosome.
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Affiliation(s)
| | | | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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12
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Fica SM, Oubridge C, Wilkinson ME, Newman AJ, Nagai K. A human postcatalytic spliceosome structure reveals essential roles of metazoan factors for exon ligation. Science 2019; 363:710-714. [PMID: 30705154 DOI: 10.1126/science.aaw5569] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 01/21/2019] [Indexed: 12/11/2022]
Abstract
During exon ligation, the Saccharomyces cerevisiae spliceosome recognizes the 3'-splice site (3'SS) of precursor messenger RNA (pre-mRNA) through non-Watson-Crick pairing with the 5'SS and the branch adenosine, in a conformation stabilized by Prp18 and Prp8. Here we present the 3.3-angstrom cryo-electron microscopy structure of a human postcatalytic spliceosome just after exon ligation. The 3'SS docks at the active site through conserved RNA interactions in the absence of Prp18. Unexpectedly, the metazoan-specific FAM32A directly bridges the 5'-exon and intron 3'SS of pre-mRNA and promotes exon ligation, as shown by functional assays. CACTIN, SDE2, and NKAP-factors implicated in alternative splicing-further stabilize the catalytic conformation of the spliceosome during exon ligation. Together these four proteins act as exon ligation factors. Our study reveals how the human spliceosome has co-opted additional proteins to modulate a conserved RNA-based mechanism for 3'SS selection and to potentially fine-tune alternative splicing at the exon ligation stage.
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Affiliation(s)
- Sebastian M Fica
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Chris Oubridge
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Max E Wilkinson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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13
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Abstract
The removal of noncoding introns from pre-messenger RNA (pre-mRNA) is an essential step in eukaryotic gene expression and is catalyzed by a dynamic multi-megadalton ribonucleoprotein complex called the spliceosome. The spliceosome assembles on pre-mRNA substrates by the stepwise addition of small nuclear ribonucleoprotein particles and numerous protein factors. Extensive remodeling is required to form the RNA-based active site and to mediate the pre-mRNA branching and ligation reactions. In the past two years, cryo-electron microscopy (cryo-EM) structures of spliceosomes captured in different assembly and catalytic states have greatly advanced our understanding of its mechanism. This was made possible by long-standing efforts in the purification of spliceosome intermediates as well as recent developments in cryo-EM imaging and computational methodology. The resulting high-resolution densities allow for de novo model building in core regions of the complexes. In peripheral and less ordered regions, the combination of cross-linking, bioinformatics, biochemical, and genetic data is essential for accurate modeling. Here, we summarize these achievements and highlight the critical steps in obtaining near-atomic resolution structures of the spliceosome.
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Affiliation(s)
- Max E Wilkinson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; , , ,
| | - Pei-Chun Lin
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; , , ,
| | - Clemens Plaschka
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; , , ,
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; , , ,
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14
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Wilkinson ME, Fica SM, Galej WP, Norman CM, Newman AJ, Nagai K. Postcatalytic spliceosome structure reveals mechanism of 3'-splice site selection. Science 2017; 358:1283-1288. [PMID: 29146871 DOI: 10.1126/science.aar3729] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 11/09/2017] [Indexed: 12/27/2022]
Abstract
Introns are removed from eukaryotic messenger RNA precursors by the spliceosome in two transesterification reactions-branching and exon ligation. The mechanism of 3'-splice site recognition during exon ligation has remained unclear. Here we present the 3.7-angstrom cryo-electron microscopy structure of the yeast P-complex spliceosome immediately after exon ligation. The 3'-splice site AG dinucleotide is recognized through non-Watson-Crick pairing with the 5' splice site and the branch-point adenosine. After the branching reaction, protein factors work together to remodel the spliceosome and stabilize a conformation competent for 3'-splice site docking, thereby promoting exon ligation. The structure accounts for the strict conservation of the GU and AG dinucleotides at the 5' and 3' ends of introns and provides insight into the catalytic mechanism of exon ligation.
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Affiliation(s)
- Max E Wilkinson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Sebastian M Fica
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | | | | | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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15
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Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ, Nagai K. Structure of a spliceosome remodelled for exon ligation. Nature 2017; 542:377-380. [PMID: 28076345 PMCID: PMC5321579 DOI: 10.1038/nature21078] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [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: 11/15/2016] [Accepted: 01/04/2017] [Indexed: 12/11/2022]
Abstract
The spliceosome excises introns from pre-mRNAs in two sequential transesterifications – branching and exon ligation1 – catalysed at a single catalytic metal site in U6 snRNA2,3. The recent structures of the spliceosomal C complex4,5 with the cleaved 5’-exon and lariat—3’-exon bound to the catalytic centre revealed that branching-specific factors such as Cwc25 lock the branch helix into position for nucleophilic attack of the branch adenosine at the 5’-splice site. Furthermore, the ATPase Prp16 is positioned to bind and translocate the intron downstream of the branch point to destabilize branching-specific factors and release the branch helix from the active site4. Here we present the 3.8Å cryo-EM structure of a Saccharomyces cerevisiae spliceosome stalled after Prp16-mediated remodelling but prior to exon ligation. While the U6 snRNA catalytic core remains firmly held in the active site cavity of Prp8 by proteins common to both steps, the branch helix has rotated by 75 degrees compared to complex C and is stabilized into a new position by Prp17, Cef1, and the reoriented Prp8 RNaseH domain. This rotation of the branch helix removes the branch adenosine from the catalytic core, creates a space for 3’-exon docking, and restructures the pairing of the 5’-splice site with the U6 snRNA ACAGAGA region. Slu7 and Prp18, which promote exon ligation, bind together to the Prp8 RNaseH domain. The ATPase Prp22, bound to Prp8 in place of Prp16, could interact with the 3’-exon, suggesting a possible basis for mRNA release after exon ligation6,7. Together with the C complex structure4, our new C* complex structure reveals the two major conformations of the spliceosome during the catalytic stages of splicing.
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Affiliation(s)
- Sebastian M Fica
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Chris Oubridge
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Wojciech P Galej
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Max E Wilkinson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Xiao-Chen Bai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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16
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Wilkinson ME, Mackay E, Quinn PF, Stutter M, Beven KJ, MacLeod CJA, Macklin MG, Elkhatib Y, Percy B, Vitolo C, Haygarth PM. A cloud based tool for knowledge exchange on local scale flood risk. J Environ Manage 2015; 161:38-50. [PMID: 26143084 DOI: 10.1016/j.jenvman.2015.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 05/13/2015] [Accepted: 06/05/2015] [Indexed: 06/04/2023]
Abstract
There is an emerging and urgent need for new approaches for the management of environmental challenges such as flood hazard in the broad context of sustainability. This requires a new way of working which bridges disciplines and organisations, and that breaks down science-culture boundaries. With this, there is growing recognition that the appropriate involvement of local communities in catchment management decisions can result in multiple benefits. However, new tools are required to connect organisations and communities. The growth of cloud based technologies offers a novel way to facilitate this process of exchange of information in environmental science and management; however, stakeholders need to be engaged with as part of the development process from the beginning rather than being presented with a final product at the end. Here we present the development of a pilot Local Environmental Virtual Observatory Flooding Tool. The aim was to develop a cloud based learning platform for stakeholders, bringing together fragmented data, models and visualisation tools that will enable these stakeholders to make scientifically informed environmental management decisions at the local scale. It has been developed by engaging with different stakeholder groups in three catchment case studies in the UK and a panel of national experts in relevant topic areas. However, these case study catchments are typical of many northern latitude catchments. The tool was designed to communicate flood risk in locally impacted communities whilst engaging with landowners/farmers about the risk of runoff from the farmed landscape. It has been developed iteratively to reflect the needs, interests and capabilities of a wide range of stakeholders. The pilot tool combines cloud based services, local catchment datasets, a hydrological model and bespoke visualisation tools to explore real time hydrometric data and the impact of flood risk caused by future land use changes. The novel aspects of the pilot tool are; the co-evolution of tools on a cloud based platform with stakeholders, policy and scientists; encouraging different science disciplines to work together; a wealth of information that is accessible and understandable to a range of stakeholders; and provides a framework for how to approach the development of such a cloud based tool in the future. Above all, stakeholders saw the tool and the potential of cloud technologies as an effective means to taking a whole systems approach to solving environmental issues. This sense of community ownership is essential in order to facilitate future appropriate and acceptable land use management decisions to be co-developed by local catchment communities. The development processes and the resulting pilot tool could be applied to local catchments globally to facilitate bottom up catchment management approaches.
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Affiliation(s)
| | - E Mackay
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom; Centre for Ecology and Hydrology, Lancaster, United Kingdom
| | - P F Quinn
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - M Stutter
- James Hutton Institute, Aberdeen, United Kingdom
| | - K J Beven
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom; Department of Earth Sciences, Uppsala University, Uppsala, Sweden
| | | | - M G Macklin
- Department of Geography and Earth Sciences, Aberystwyth University, United Kingdom; Institute of Agriculture and Environment, Massey University, New Zealand
| | - Y Elkhatib
- School of Computing and Communications, Lancaster University, Lancaster, United Kingdom
| | - B Percy
- Reading e-Science Centre, University of Reading, Reading, United Kingdom
| | - C Vitolo
- Department of Civil and Environmental Engineering, Imperial College London, London, United Kingdom
| | - P M Haygarth
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
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Wilkinson ME, Quinn PF, Barber NJ, Jonczyk J. A framework for managing runoff and pollution in the rural landscape using a Catchment Systems Engineering approach. Sci Total Environ 2014; 468-469:1245-1254. [PMID: 23968737 DOI: 10.1016/j.scitotenv.2013.07.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 05/24/2013] [Accepted: 07/13/2013] [Indexed: 06/02/2023]
Abstract
Intense farming plays a key role in increasing local scale runoff and erosion rates, resulting in water quality issues and flooding problems. There is potential for agricultural management to become a major part of improved strategies for controlling runoff. Here, a Catchment Systems Engineering (CSE) approach has been explored to solve the above problem. CSE is an interventionist approach to altering the catchment scale runoff regime through the manipulation of hydrological flow pathways throughout the catchment. By targeting hydrological flow pathways at source, such as overland flow, field drain and ditch function, a significant component of the runoff generation can be managed in turn reducing soil nutrient losses. The Belford catchment (5.7 km(2)) is a catchment scale study for which a CSE approach has been used to tackle a number of environmental issues. A variety of Runoff Attenuation Features (RAFs) have been implemented throughout the catchment to address diffuse pollution and flooding issues. The RAFs include bunds disconnecting flow pathways, diversion structures in ditches to spill and store high flows, large wood debris structure within the channel, and riparian zone management. Here a framework for applying a CSE approach to the catchment is shown in a step by step guide to implementing mitigation measures in the Belford Burn catchment. The framework is based around engagement with catchment stakeholders and uses evidence arising from field science. Using the framework, the flooding issue has been addressed at the catchment scale by altering the runoff regime. Initial findings suggest that RAFs have functioned as designed to reduce/attenuate runoff locally. However, evidence suggested that some RAFs needed modification and new RAFs be created to address diffuse pollution issues during storm events. Initial findings from these modified RAFs are showing improvements in sediment trapping capacities and reductions in phosphorus, nitrate and suspended sediment losses during storm events.
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Affiliation(s)
- M E Wilkinson
- The James Hutton Institute, Craigiebuckler, Aberdeen, AB15 8QH, UK; School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
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18
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Wilkinson ME. Ceroid lipofuscinosis, neuronal 3, Juvenile-Batten disease: case report and literature review. Optometry 2001; 72:724-8. [PMID: 12363260] [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] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
BACKGROUND Ocularly, Batten disease is characterized by a rapid deterioration of vision, progressing to blindness within a few years. Onset typically occurs at between 5 and 10 years of age. The fundus shows a bull's eye maculopathy, diffuse pigmentary degeneration, arteriolar attenuation and optic atrophy, and an extinguished ERG. CASE REPORT AND LITERATURE REVIEW The visual acuity and ocular health findings of a 7-year-old child, eventually diagnosed with Batten disease, are reviewed. Additionally, a review of the literature concerning the ocular and systemic manifestations of the various ceroid lipofuscinoses is presented. CONCLUSION Batten disease is the most likely of the ceroid lipofuscinoses to be manifested in an ophthalmic practitioner's office before the diagnosis of the underlying condition. Although there currently is no treatment for this condition, making the correct diagnosis is important for appropriate low-vision management, educational planning, and genetic counseling.
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Affiliation(s)
- M E Wilkinson
- Department of Ophthalmology and Visual Sciences, University of Iowa Hospital and Clinics, Iowa City 52242-1091, USA.
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Wilkinson ME, Stewart IW, Trantham CS. Iowa's pediatric low-vision services. Optometry 2000; 71:40-8. [PMID: 10680417] [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] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
BACKGROUND Reports in the literature concerning best practice for the evaluation and management of children with visual impairments are limited, with a resulting lack of information concerning the potential for optimizing vision to enhance general development and assist with the educational needs of this population. METHOD The development of a multidisciplinary approach to provide low-vision services for children with visual impairment has occurred over the past 18 years in Iowa. In that time, 1,348 children from around the state of Iowa have been evaluated through an itinerant low-vision service program, coordinated by the Iowa Braille School. RESULTS A low-vision clinic model--designed to provide services (primarily) for academic students--was not meeting the needs of the pediatric low-vision population in the state. After a statewide review of the program, changes were made that have resulted in low-vision services being provided to a greater and more diverse number of students. The roles of the various members of the multidisciplinary team will be reviewed. Changes in large-print orders and use by special education teachers in the state as a direct result of the low-vision services will also be discussed. CONCLUSION Ongoing, comprehensive multidisciplinary low-vision services--including optometric low-vision care as a key component--are necessary to help children with visual impairments meet their educational, vocational, and avocational needs. With ongoing low-vision services, unnecessary costs such as those associated with large-print materials can be reduced, thereby creating significant savings to local, state, and federal special educational services.
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Affiliation(s)
- M E Wilkinson
- Department of Ophthalmology and Visual Sciences, University of Iowa Hospital and Clinics, Iowa City, USA
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Abstract
Driving is a highly prized activity for individuals of all ages. The decision to continue driving after a decrease in central acuity or visual field can be a source of anxiety for the individual and his or her family, as well as the ophthalmic practitioner. Although a great deal of research has been done concerning vision and driving, much controversy still surrounds this subject. This article reviews the literature concerning visual impairment and driving and makes suggestions for what should be considered when determining who should and should not continue to drive.
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Affiliation(s)
- M E Wilkinson
- Low Vision Service, University of Iowa Center for Macular Degeneration, USA
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Wilkinson ME, Stewart IW. Iowa's pediatric low vision services. J Am Optom Assoc 1996; 67:397-402. [PMID: 8888865] [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] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Reports in the literature concerning the evaluation and low vision management of visually impaired children are limited, resulting in a lack of information about the characteristics and needs of this population. METHODS A review was performed of 762 children evaluated over a 14-year period in a low vision clinic program coordinated by the Iowa Braille and Sight Saving School. RESULTS The age, sex, ocular condition, best corrected visual acuity, habitual near point working distance, and optical devices recommended for use by these children were analyzed. CONCLUSIONS Ongoing, comprehensive multidisciplinary low vision services are necessary to help children with visual impairments meet their educational, vocational and avocational needs. With ongoing low vision care unnecessary costs-such as those for large print material-can be avoided, therefore creating a significant savings to local or state educational services.
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Affiliation(s)
- M E Wilkinson
- Vision Rehabilitation Institute, Genesis Medical Center, Davenport, IA 52804, USA
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Yudkin J, Norman DH, Wilkinson ME, Berry WT. Absence of response of some tongue conditions in children to administration of vitamins. Proc Nutr Soc 1970; 29:Suppl:8A-9A. [PMID: 4248950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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