1
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Towle Z, Cruickshank F, Mackay CL, Clarke DJ, Horsfall LE. Utilising Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to track the oxidation of lignin by an alkaliphilic laccase. Analyst 2024; 149:2399-2411. [PMID: 38477231 PMCID: PMC11018093 DOI: 10.1039/d4an00124a] [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: 01/24/2024] [Accepted: 03/07/2024] [Indexed: 03/14/2024]
Abstract
Lignin is a complex heteroaromatic polymer which is one of the most abundant and diverse biopolymers on the planet. It comprises approximately one third of all woody plant matter, making it an attractive candidate as an alternative, renewable feedstock to petrochemicals to produce fine chemicals. However, the inherent complexity of lignin makes it difficult to analyse and characterise using common analytical techniques, proving a hindrance to the utilisation of lignin as a green chemical feedstock. Herein we outline the tracking of lignin degradation by an alkaliphilic laccase in a semi-quantitative manner using a combined chemical analysis approach using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to characterise shifts in chemical diversity and relative abundance of ions, and NMR to highlight changes in the structure of lignin. Specifically, an alkaliphilic laccase was used to degrade an industrially relevant lignin, with compounds such as syringaresinol being almost wholly removed (95%) after 24 hours of treatment. Structural analyses reinforced these findings, indicating a >50% loss of NMR signal relating to β-β linkages, of which syringaresinol is representative. Ultimately, this work underlines a combined analytical approach that can be used to gain a broader semi-quantitative understanding of the enzymatic activity of laccases within a complex, non-model mixture.
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Affiliation(s)
- Zak Towle
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Roger Land Building, King's Buildings, Edinburgh, EH9 3FF, UK.
| | - Faye Cruickshank
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK.
| | - C Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK.
| | - David J Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK.
| | - Louise E Horsfall
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Roger Land Building, King's Buildings, Edinburgh, EH9 3FF, UK.
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2
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Chen A, Re RN, Davis TD, Tran K, Moriuchi YW, Wu S, La Clair JJ, Louie GV, Bowman ME, Clarke DJ, Mackay CL, Campopiano DJ, Noel JP, Burkart MD. Visualizing the Interface of Biotin and Fatty Acid Biosynthesis through SuFEx Probes. J Am Chem Soc 2024; 146:1388-1395. [PMID: 38176024 DOI: 10.1021/jacs.3c10181] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Site-specific covalent conjugation offers a powerful tool to identify and understand protein-protein interactions. In this study, we discover that sulfur fluoride exchange (SuFEx) warheads effectively crosslink the Escherichia coli acyl carrier protein (AcpP) with its partner BioF, a key pyridoxal 5'-phosphate (PLP)-dependent enzyme in the early steps of biotin biosynthesis by targeting a tyrosine residue proximal to the active site. We identify the site of crosslink by MS/MS analysis of the peptide originating from both partners. We further evaluate the BioF-AcpP interface through protein crystallography and mutational studies. Among the AcpP-interacting BioF surface residues, three critical arginine residues appear to be involved in AcpP recognition so that pimeloyl-AcpP can serve as the acyl donor for PLP-mediated catalysis. These findings validate an evolutionary gain-of-function for BioF, allowing the organism to build biotin directly from fatty acid biosynthesis through surface modifications selective for salt bridge formation with acidic AcpP residues.
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Affiliation(s)
- Aochiu Chen
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Rebecca N Re
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Tony D Davis
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Kelley Tran
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Yuta W Moriuchi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Sitong Wu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Gordon V Louie
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, San Diego, California 92037, United States
| | - Marianne E Bowman
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, San Diego, California 92037, United States
| | - David J Clarke
- EaSTCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Rd, Edinburgh EH9 3FJ, U.K
| | - C Logan Mackay
- EaSTCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Rd, Edinburgh EH9 3FJ, U.K
| | - Dominic J Campopiano
- EaSTCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Rd, Edinburgh EH9 3FJ, U.K
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, San Diego, California 92037, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
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3
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Saleeb RS, Leighton C, Lee JE, O’Shaughnessy J, Jeacock K, Chappard A, Cumberland R, Zhao T, Ball SR, Sunde M, Clarke DJ, Piché K, McPhail JA, Louwrier A, Angers R, Gandhi S, Downey P, Kunath T, Horrocks MH. Two-color coincidence single-molecule pulldown for the specific detection of disease-associated protein aggregates. Sci Adv 2023; 9:eadi7359. [PMID: 37967183 PMCID: PMC10651132 DOI: 10.1126/sciadv.adi7359] [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] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/16/2023] [Indexed: 11/17/2023]
Abstract
Protein misfolding and aggregation is a characteristic of many neurodegenerative disorders, including Alzheimer's and Parkinson's disease. The oligomers generated during aggregation are likely involved in disease pathogenesis and present promising biomarker candidates. However, owing to their small size and low concentration, specific tools to quantify and characterize aggregates in complex biological samples are still lacking. Here, we present single-molecule two-color aggregate pulldown (STAPull), which overcomes this challenge by probing immobilized proteins using orthogonally labeled detection antibodies. By analyzing colocalized signals, we can eliminate monomeric protein and specifically quantify aggregated proteins. Using the aggregation-prone alpha-synuclein protein as a model, we demonstrate that this approach can specifically detect aggregates with a limit of detection of 5 picomolar. Furthermore, we show that STAPull can be used in a range of samples, including human biofluids. STAPull is applicable to protein aggregates from a variety of disorders and will aid in the identification of biomarkers that are crucial in the effort to diagnose these diseases.
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Affiliation(s)
- Rebecca S. Saleeb
- EaStCHEM School of Chemistry, The University of Edinburgh, Edinburgh EH9 3FJ, UK
- IRR Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Craig Leighton
- EaStCHEM School of Chemistry, The University of Edinburgh, Edinburgh EH9 3FJ, UK
- IRR Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Ji-Eun Lee
- EaStCHEM School of Chemistry, The University of Edinburgh, Edinburgh EH9 3FJ, UK
- IRR Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Judi O’Shaughnessy
- EaStCHEM School of Chemistry, The University of Edinburgh, Edinburgh EH9 3FJ, UK
- IRR Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Kiani Jeacock
- EaStCHEM School of Chemistry, The University of Edinburgh, Edinburgh EH9 3FJ, UK
| | - Alexandre Chappard
- EaStCHEM School of Chemistry, The University of Edinburgh, Edinburgh EH9 3FJ, UK
- IRR Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Robyn Cumberland
- EaStCHEM School of Chemistry, The University of Edinburgh, Edinburgh EH9 3FJ, UK
| | - Tianxiao Zhao
- EaStCHEM School of Chemistry, The University of Edinburgh, Edinburgh EH9 3FJ, UK
- IRR Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Sarah R. Ball
- School of Medical Sciences, Faculty of Medicine and Health, and Sydney Nano, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - David J. Clarke
- EaStCHEM School of Chemistry, The University of Edinburgh, Edinburgh EH9 3FJ, UK
| | - Kristin Piché
- Stressmarq Biosciences Inc., Suite 117-1537 Hillside Ave, Victoria, V8T 2C1 BC, Canada
| | - Jacob A. McPhail
- Stressmarq Biosciences Inc., Suite 117-1537 Hillside Ave, Victoria, V8T 2C1 BC, Canada
| | - Ariel Louwrier
- Stressmarq Biosciences Inc., Suite 117-1537 Hillside Ave, Victoria, V8T 2C1 BC, Canada
| | | | - Sonia Gandhi
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | | | - Tilo Kunath
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, The University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Mathew H. Horrocks
- EaStCHEM School of Chemistry, The University of Edinburgh, Edinburgh EH9 3FJ, UK
- IRR Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh EH16 4UU, UK
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4
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Feng X, Zhang Q, Clarke DJ, Deng H, O’Hagan D. 3'- O-β-Glucosyl-4',5'-didehydro-5'-deoxyadenosine Is a Natural Product of the Nucleocidin Producers Streptomyces virens and Streptomyces calvus. J Nat Prod 2023; 86:2326-2332. [PMID: 37748016 PMCID: PMC10616807 DOI: 10.1021/acs.jnatprod.3c00521] [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] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Indexed: 09/27/2023]
Abstract
3'-O-β-Glucosyl-4',5'-didehydro-5'-deoxyadenosine 13 is identified as a natural product of Streptomyces calvus and Streptomyces virens. It is also generated in vitro by direct β-glucosylation of 4',5'-didehydro-5'-deoxyadenosine 12 with the enzyme NucGT. The intact incorporation of oxygen-18 and deuterium isotopes from (±)[1-18O,1-2H2]-glycerol 14 into C-5' of nucleocidin 1 and its related metabolites precludes 3'-O-β-glucosyl-4',5'-didehydro-5'-deoxyadenosine 13 as a biosynthetic precursor to nucleocidin 1.
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Affiliation(s)
- Xuan Feng
- School
of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, U.K.
| | - Qingzhi Zhang
- School
of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, U.K.
| | - David J. Clarke
- EaStChem
School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh, EH9 3FJ, U.K.
| | - Hai Deng
- Department
of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, U.K.
| | - David O’Hagan
- School
of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, U.K.
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5
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Johansson JF, Shannon R, Mossabir R, Airlie J, Ozer S, Moreau LA, Farrin A, Mead G, English C, Fitzsimons CF, Clarke DJ, Forster A. Intervention to reduce sedentary behaviour and improve outcomes after stroke (Get Set Go): a study protocol for the process evaluation of a pilot cluster randomised controlled trial (RECREATE). BMJ Open 2023; 13:e075363. [PMID: 37699629 PMCID: PMC10503356 DOI: 10.1136/bmjopen-2023-075363] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/16/2023] [Indexed: 09/14/2023] Open
Abstract
INTRODUCTION Stroke survivors spend long periods of time engaging in sedentary behaviour (SB) even when their functional recovery is good. In the RECREATE programme, an intervention aimed at reducing SB ('Get Set Go') will be implemented and evaluated in a pragmatic external pilot cluster randomised controlled trial with embedded process and economic evaluations. We report the protocol for the process evaluation which will address the following objectives: (1) describe and clarify causal assumptions about the intervention, and its mechanisms of impact; (2) assess implementation fidelity; (3) explore views, perceptions and acceptability of the intervention to staff, stroke survivors and their carers; (4) establish the contextual factors that influence implementation, intervention mechanisms and outcomes. METHODS AND ANALYSIS This pilot trial will be conducted in 15 UK-based National Health Service stroke services. This process evaluation study, underpinned by the Medical Research Council guidance, will be undertaken in six of the randomised services (four intervention, two control). Data collection includes the following: observations of staff training sessions, non-participant observations in inpatient and community settings, semi-structured interviews with staff, patients and carers, and documentary analysis of key intervention components. Additional quantitative implementation data will be collected in all sites. Training observations and documentary analysis data will be summarised, with other observational and interview data analysed using thematic analysis. Relevant theories will be used to interpret the findings, including the theoretical domains framework, normalisation process theory and the theoretical framework of acceptability. Anticipated outputs include the following: recommendations for intervention refinements (both content and implementation); a revised implementation plan and a refined logic model. ETHICS AND DISSEMINATION The study was approved by Yorkshire & The Humber - Bradford Leeds Research Ethics Committee (REC reference: 19/YH/0403). Findings will be disseminated via peer review publications, and national and international conference presentations. TRIAL REGISTRATION NUMBER ISRCTN82280581.
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Affiliation(s)
- Jessica Faye Johansson
- Academic Unit of Ageing and Stroke Research, Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
- Academic Unit of Ageing and Stroke Research, Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Rosie Shannon
- Academic Unit of Ageing and Stroke Research, Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Rahena Mossabir
- Academic Unit of Ageing and Stroke Research, Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Jennifer Airlie
- Academic Unit of Ageing and Stroke Research, Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Seline Ozer
- Academic Unit of Ageing and Stroke Research, Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Lauren A Moreau
- Leeds Institute of Clinical Trials Research, Clinical Trials Research Unit (CTRU), University of Leeds, Leeds, UK
| | - Amanda Farrin
- Leeds Institute of Clinical Trials Research, Clinical Trials Research Unit (CTRU), University of Leeds, Leeds, UK
| | - Gillian Mead
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Coralie English
- School of Health Sciences, The University of Newcastle, Newcastle, New South Wales, Australia
- Heart and Stroke Research Program, The University of Newcastle Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Claire F Fitzsimons
- Physical Activity for Health and Research Centre, Institute for Sport Physical Education and Health Sciences, University of Edinburgh, Edinburgh, UK
| | - David J Clarke
- Academic Unit of Ageing and Stroke Research, Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
- Academic Unit of Ageing and Stroke Research, Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Anne Forster
- Academic Unit of Ageing and Stroke Research, Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
- Academic Unit of Ageing and Stroke Research, Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
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6
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Carr CM, Keller MB, Paul B, Schubert SW, Clausen KSR, Jensen K, Clarke DJ, Westh P, Dobson ADW. Purification and biochemical characterization of SM14est, a PET-hydrolyzing enzyme from the marine sponge-derived Streptomyces sp. SM14. Front Microbiol 2023; 14:1170880. [PMID: 37250061 PMCID: PMC10213408 DOI: 10.3389/fmicb.2023.1170880] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/21/2023] [Indexed: 05/31/2023] Open
Abstract
The successful enzymatic degradation of polyester substrates has fueled worldwide investigation into the treatment of plastic waste using bio-based processes. Within this realm, marine-associated microorganisms have emerged as a promising source of polyester-degrading enzymes. In this work, we describe the hydrolysis of the synthetic polymer PET by SM14est, a polyesterase which was previously identified from Streptomyces sp. SM14, an isolate of the marine sponge Haliclona simulans. The PET hydrolase activity of purified SM14est was assessed using a suspension-based assay and subsequent analysis of reaction products by UV-spectrophotometry and RP-HPLC. SM14est displayed a preference for high salt conditions, with activity significantly increasing at sodium chloride concentrations from 100 mM up to 1,000 mM. The initial rate of PET hydrolysis by SM14est was determined to be 0.004 s-1 at 45°C, which was increased by 5-fold to 0.02 s-1 upon addition of 500 mM sodium chloride. Sequence alignment and structural comparison with known PET hydrolases, including the marine halophile PET6, and the highly efficient, thermophilic PHL7, revealed conserved features of interest. Based on this work, SM14est emerges as a useful enzyme that is more similar to key players in the area of PET hydrolysis, like PHL7 and IsPETase, than it is to its marine counterparts. Salt-tolerant polyesterases such as SM14est are potentially valuable in the biological degradation of plastic particles that readily contaminate marine ecosystems and industrial wastewaters.
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Affiliation(s)
- Clodagh M. Carr
- School of Microbiology, University College Cork, Cork, Ireland
- SSPC-SFI Research Centre for Pharmaceuticals, University College Cork, Cork, Ireland
| | - Malene B. Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Bijoya Paul
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Sune W. Schubert
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Kristine S. R. Clausen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - David J. Clarke
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- SSPC-SFI Research Centre for Pharmaceuticals, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
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7
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Jeacock K, Chappard A, Gallagher KJ, Mackay CL, Kilgour DPA, Horrocks MH, Kunath T, Clarke DJ. Determining the Location of the α-Synuclein Dimer Interface Using Native Top-Down Fragmentation and Isotope Depletion-Mass Spectrometry. J Am Soc Mass Spectrom 2023; 34:847-856. [PMID: 36976861 PMCID: PMC10161212 DOI: 10.1021/jasms.2c00339] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
α-Synuclein (αSyn), a 140-residue intrinsically disordered protein, comprises the primary proteinaceous component of pathology-associated Lewy body inclusions in Parkinson's disease (PD). Due to its association with PD, αSyn is studied extensively; however, the endogenous structure and physiological roles of this protein are yet to be fully understood. Here, ion mobility-mass spectrometry and native top-down electron capture dissociation fragmentation have been used to elucidate the structural properties associated with a stable, naturally occurring dimeric species of αSyn. This stable dimer appears in both wild-type (WT) αSyn and the PD-associated variant A53E. Furthermore, we integrated a novel method for generating isotopically depleted protein into our native top-down workflow. Isotope depletion increases signal-to-noise ratio and reduces the spectral complexity of fragmentation data, enabling the monoisotopic peak of low abundant fragment ions to be observed. This enables the accurate and confident assignment of fragments unique to the αSyn dimer to be assigned and structural information about this species to be inferred. Using this approach, we were able to identify fragments unique to the dimer, which demonstrates a C-terminal to C-terminal interaction between the monomer subunits. The approach in this study holds promise for further investigation into the structural properties of endogenous multimeric species of αSyn.
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Affiliation(s)
- Kiani Jeacock
- The EastCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K
| | - Alexandre Chappard
- The EastCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K
| | - Kelly J Gallagher
- The EastCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K
| | - C Logan Mackay
- The EastCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K
| | - David P A Kilgour
- Chemistry and Forensics, Nottingham Trent University, Nottingham NG11 8NS, U.K
| | - Mathew H Horrocks
- The EastCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K
| | - Tilo Kunath
- Centre for Regenerative Medicine, Institute for Stem Cell Research, University of Edinburgh, Edinburgh EH16 4UU, U.K
| | - David J Clarke
- The EastCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K
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8
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Chappard A, Leighton C, Saleeb RS, Jeacock K, Ball SR, Morris K, Kantelberg O, Lee J, Zacco E, Pastore A, Sunde M, Clarke DJ, Downey P, Kunath T, Horrocks MH. Single-Molecule Two-Color Coincidence Detection of Unlabeled alpha-Synuclein Aggregates. Angew Chem Int Ed Engl 2023; 62:e202216771. [PMID: 36762870 PMCID: PMC10946743 DOI: 10.1002/anie.202216771] [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: 11/14/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/11/2023]
Abstract
Protein misfolding and aggregation into oligomeric and fibrillar structures is a common feature of many neurogenerative disorders. Single-molecule techniques have enabled characterization of these lowly abundant, highly heterogeneous protein aggregates, previously inaccessible using ensemble averaging techniques. However, they usually rely on the use of recombinantly-expressed labeled protein, or on the addition of amyloid stains that are not protein-specific. To circumvent these challenges, we have made use of a high affinity antibody labeled with orthogonal fluorophores combined with fast-flow microfluidics and single-molecule confocal microscopy to specifically detect α-synuclein, the protein associated with Parkinson's disease. We used this approach to determine the number and size of α-synuclein aggregates down to picomolar concentrations in biologically relevant samples.
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Affiliation(s)
- Alexandre Chappard
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
| | - Craig Leighton
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
- Centre for Regenerative MedicineInstitute for Stem Cell ResearchSchool of Biological SciencesThe University of EdinburghEdinburghEH16 4UUUK
| | - Rebecca S. Saleeb
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
| | - Kiani Jeacock
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
| | - Sarah R. Ball
- School of Medical SciencesFaculty of Medicine and Health, and Sydney NanoThe University of SydneySydneyNSW 2006Australia
| | - Katie Morris
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
| | - Owen Kantelberg
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
| | - Ji‐Eun Lee
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
| | - Elsa Zacco
- Centre for Human Technologies (CHT)Istituto Italiano di Tecnologia (IIT)Via Enrico Melen, 8316152GenovaItaly
| | - Annalisa Pastore
- European Synchrotron Radiation Facility71 Ave des Martyrs38000GrenobleFrance
| | - Margaret Sunde
- School of Medical SciencesFaculty of Medicine and Health, and Sydney NanoThe University of SydneySydneyNSW 2006Australia
| | - David J. Clarke
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
| | | | - Tilo Kunath
- Centre for Regenerative MedicineInstitute for Stem Cell ResearchSchool of Biological SciencesThe University of EdinburghEdinburghEH16 4UUUK
| | - Mathew H. Horrocks
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
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9
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Chappard A, Leighton C, Saleeb RS, Jeacock K, Ball SR, Morris K, Kantelberg O, Lee J, Zacco E, Pastore A, Sunde M, Clarke DJ, Downey P, Kunath T, Horrocks MH. Single-Molecule Two-Color Coincidence Detection of Unlabeled alpha-Synuclein Aggregates. Angew Chem Weinheim Bergstr Ger 2023; 135:e202216771. [PMID: 38516037 PMCID: PMC10952349 DOI: 10.1002/ange.202216771] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Indexed: 02/12/2023]
Abstract
Protein misfolding and aggregation into oligomeric and fibrillar structures is a common feature of many neurogenerative disorders. Single-molecule techniques have enabled characterization of these lowly abundant, highly heterogeneous protein aggregates, previously inaccessible using ensemble averaging techniques. However, they usually rely on the use of recombinantly-expressed labeled protein, or on the addition of amyloid stains that are not protein-specific. To circumvent these challenges, we have made use of a high affinity antibody labeled with orthogonal fluorophores combined with fast-flow microfluidics and single-molecule confocal microscopy to specifically detect α-synuclein, the protein associated with Parkinson's disease. We used this approach to determine the number and size of α-synuclein aggregates down to picomolar concentrations in biologically relevant samples.
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Affiliation(s)
- Alexandre Chappard
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
| | - Craig Leighton
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
- Centre for Regenerative MedicineInstitute for Stem Cell ResearchSchool of Biological SciencesThe University of EdinburghEdinburghEH16 4UUUK
| | - Rebecca S. Saleeb
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
| | - Kiani Jeacock
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
| | - Sarah R. Ball
- School of Medical SciencesFaculty of Medicine and Health, and Sydney NanoThe University of SydneySydneyNSW 2006Australia
| | - Katie Morris
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
| | - Owen Kantelberg
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
| | - Ji‐Eun Lee
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
| | - Elsa Zacco
- Centre for Human Technologies (CHT)Istituto Italiano di Tecnologia (IIT)Via Enrico Melen, 8316152GenovaItaly
| | - Annalisa Pastore
- European Synchrotron Radiation Facility71 Ave des Martyrs38000GrenobleFrance
| | - Margaret Sunde
- School of Medical SciencesFaculty of Medicine and Health, and Sydney NanoThe University of SydneySydneyNSW 2006Australia
| | - David J. Clarke
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
| | | | - Tilo Kunath
- Centre for Regenerative MedicineInstitute for Stem Cell ResearchSchool of Biological SciencesThe University of EdinburghEdinburghEH16 4UUUK
| | - Mathew H. Horrocks
- EaStCHEM School of ChemistryThe University of EdinburghEdinburghEH9 3FJUK
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10
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Ryan E, Joyce SA, Clarke DJ. Membrane lipids from gut microbiome-associated bacteria as structural and signalling molecules. Microbiology (Reading) 2023; 169. [PMID: 36952261 DOI: 10.1099/mic.0.001315] [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] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Bacteria produce an array of diverse, dynamic and often complex lipid structures, some of which function beyond their typical role in membrane structure. The model organism, E. coli, has three major membrane lipids, which are glycerophosphoglycerol (phosphatidylglycerol), glycerophosphoethanolamine (phosphatidylethanolamine) and cardiolipin. However, it is now appreciated that some bacteria have the capacity to synthesize a range of lipids, including glycerophosphocholines, glycerophosphoinositols, 'phosphorous-free' N-acyl amines, sphingolipids and plasmalogens. In recent years, some of these bacterial lipids have emerged as influential contributors to the microbe-host molecular dialogue. This review outlines our current knowledge of bacterial lipid diversity, with a focus on the membrane lipids of microbiome-associated bacteria that have documented roles as signalling molecules.
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Affiliation(s)
- Eileen Ryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Susan A Joyce
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - David J Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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11
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Ryan E, Gonzalez Pastor B, Gethings LA, Clarke DJ, Joyce SA. Lipidomic Analysis Reveals Differences in Bacteroides Species Driven Largely by Plasmalogens, Glycerophosphoinositols and Certain Sphingolipids. Metabolites 2023; 13:metabo13030360. [PMID: 36984802 PMCID: PMC10056535 DOI: 10.3390/metabo13030360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/23/2023] [Accepted: 02/26/2023] [Indexed: 03/04/2023] Open
Abstract
There has been increasing interest in bacterial lipids in recent years due, in part, to their emerging role as molecular signalling molecules. Bacteroides thetaiotaomicron is an important member of the mammalian gut microbiota that has been shown to produce sphingolipids (SP) that pass through the gut epithelial barrier to impact host SP metabolism and signal into host inflammation pathways. B. thetaiotaomicron also produces a novel family of N-acyl amines (called glycine lipids) that are potent ligands of host Toll-like receptor 2 (TLR2). Here, we specifically examine the lipid signatures of four species of gut-associated Bacteroides. In total we identify 170 different lipids, and we report that the range and diversity of Bacteroides lipids is species specific. Multivariate analysis reveals that the differences in the lipid signatures are largely driven by the presence and absence of plasmalogens, glycerophosphoinositols and certain SP. Moreover, we show that, in B. thetaiotaomicron, mutations altering either SP or glycine lipid biosynthesis result in significant changes in the levels of other lipids, suggesting the existence of a compensatory mechanisms required to maintain the functionality of the bacterial membrane.
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Affiliation(s)
- Eileen Ryan
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland
- School of Biochemistry & Cell Biology, University College Cork, T12 K8AF Cork, Ireland
| | - Belén Gonzalez Pastor
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
| | - Lee A. Gethings
- Waters, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
| | - David J. Clarke
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
- Correspondence: (D.J.C.); (S.A.J.)
| | - Susan A. Joyce
- APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland
- School of Biochemistry & Cell Biology, University College Cork, T12 K8AF Cork, Ireland
- Correspondence: (D.J.C.); (S.A.J.)
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12
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Tsiamis A, Buchoux A, Mahon ST, Walton AJ, Smith S, Clarke DJ, Stokes AA. Design and Fabrication of a Fully-Integrated, Miniaturised Fluidic System for the Analysis of Enzyme Kinetics. Micromachines (Basel) 2023; 14:537. [PMID: 36984943 PMCID: PMC10051508 DOI: 10.3390/mi14030537] [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] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
The lab-on-a-chip concept, enabled by microfluidic technology, promises the integration of multiple discrete laboratory techniques into a miniaturised system. Research into microfluidics has generally focused on the development of individual elements of the total system (often with relatively limited functionality), without full consideration for integration into a complete fully optimised and miniaturised system. Typically, the operation of many of the reported lab-on-a-chip devices is dependent on the support of a laboratory framework. In this paper, a demonstrator platform for routine laboratory analysis is designed and built, which fully integrates a number of technologies into a single device with multiple domains such as fluidics, electronics, pneumatics, hydraulics, and photonics. This facilitates the delivery of breakthroughs in research, by incorporating all physical requirements into a single device. To highlight this proposed approach, this demonstrator microsystem acts as a fully integrated biochemical assay reaction system. The resulting design determines enzyme kinetics in an automated process and combines reservoirs, three-dimensional fluidic channels, optical sensing, and electronics in a low-cost, low-power and portable package.
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Affiliation(s)
- Andreas Tsiamis
- School of Engineering, Institute for Integrated Micro and Nano Systems, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3FF, UK
| | - Anthony Buchoux
- School of Engineering, Institute for Multiscale Thermofluids, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3LJ, UK
| | - Stephen T. Mahon
- School of Engineering, Institute for Integrated Micro and Nano Systems, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3FF, UK
| | - Anthony J. Walton
- School of Engineering, Institute for Integrated Micro and Nano Systems, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3FF, UK
| | - Stewart Smith
- School of Engineering, Institute for Bio-Engineering, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3FF, UK
| | - David J. Clarke
- EaStCHEM School of Chemistry, The University of Edinburgh, Edinburgh EH9 3FJ, UK
| | - Adam A. Stokes
- School of Engineering, Institute for Integrated Micro and Nano Systems, The University of Edinburgh, The King’s Buildings, Edinburgh EH9 3FF, UK
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13
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Shelley JR, McHugh BJ, Wills J, Dorin JR, Weller R, Clarke DJ, Davidson DJ. A mechanistic evaluation of human beta defensin 2 mediated protection of human skin barrier in vitro. Sci Rep 2023; 13:2271. [PMID: 36755116 PMCID: PMC9908873 DOI: 10.1038/s41598-023-29558-0] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
The human skin barrier, a biological imperative, is impaired in inflammatory skin diseases such as atopic dermatitis (AD). Staphylococcus aureus is associated with AD lesions and contributes to pathological inflammation and further barrier impairment. S. aureus secretes extracellular proteases, such as V8 (or 'SspA'), which cleave extracellular proteins to reduce skin barrier. Previous studies demonstrated that the host defence peptide human beta-defensin 2 (HBD2) prevented V8-mediated damage. Here, the mechanism of HBD2-mediated barrier protection in vitro is examined. Application of exogenous HBD2 provided protection against V8, irrespective of timeline of application or native peptide folding, raising the prospect of simple peptide analogues as therapeutics. HBD2 treatment, in context of V8-mediated damage, modulated the proteomic/secretomic profiles of HaCaT cells, altering levels of specific extracellular matrix proteins, potentially recovering V8 damage. However, HBD2 alone did not substantially modulate cellular proteomic/secretomics profiles in the absence of damage, suggesting possible therapeutic targeting of lesion damage sites only. HBD2 did not show any direct protease inhibition or induce expression of known antiproteases, did not alter keratinocyte migration or proliferation, or form protective nanonet structures. These data validate the barrier-protective properties of HBD2 in vitro and establish key protein datasets for further targeted mechanistic analyses.
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Affiliation(s)
- Jennifer R Shelley
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, BioQuarter, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK.
- The Commonwealth Building, The Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK.
| | - Brian J McHugh
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, BioQuarter, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK
| | - Jimi Wills
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital Campus, Crewe Road, Edinburgh, EH4 2XU, Scotland, UK
| | - Julia R Dorin
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, BioQuarter, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK
| | - Richard Weller
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, BioQuarter, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK
| | - David J Clarke
- The EastChem School of Chemistry, University of Edinburgh, Joseph Black Building, Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Donald J Davidson
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, BioQuarter, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK
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14
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Vaaltyn MC, Mateos‐Jimenez M, Müller R, Mackay CL, Edkins AL, Clarke DJ, Veale CGL. Native Mass Spectrometry-Guided Screening Identifies Hit Fragments for HOP-HSP90 PPI Inhibition. Chembiochem 2022; 23:e202200322. [PMID: 36017658 PMCID: PMC9826382 DOI: 10.1002/cbic.202200322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/25/2022] [Indexed: 01/11/2023]
Abstract
Contemporary medicinal chemistry considers fragment-based drug discovery (FBDD) and inhibition of protein-protein interactions (PPI) as important means of expanding the volume of druggable chemical space. However, the ability to robustly identify valid fragments and PPI inhibitors is an enormous challenge, requiring the application of sensitive biophysical methodology. Accordingly, in this study, we exploited the speed and sensitivity of nanoelectrospray (nano-ESI) native mass spectrometry to identify a small collection of fragments which bind to the TPR2AB domain of HOP. Follow-up biophysical assessment of a small selection of binding fragments confirmed binding to the single TPR2A domain, and that this binding translated into PPI inhibitory activity between TPR2A and the HSP90 C-terminal domain. An in-silico assessment of binding fragments at the PPI interfacial region, provided valuable structural insight for future fragment elaboration strategies, including the identification of losartan as a weak, albeit dose-dependent inhibitor of the target PPI.
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Affiliation(s)
- Michaelone C. Vaaltyn
- The Biomedical Biotechnology Research Unit (BioBRU) Department of Biochemistry and Microbiology DepartmentRhodes UniversityMakhanda6139South Africa
| | - Maria Mateos‐Jimenez
- EaStCHEM School of ChemistryJoseph Black Building, David Brewster RoadEdinburghEH93FJUK
| | - Ronel Müller
- School of Chemistry and PhysicsUniversity of KwaZulu-NatalScottsville3209South Africa
| | - C. Logan Mackay
- EaStCHEM School of ChemistryJoseph Black Building, David Brewster RoadEdinburghEH93FJUK
| | - Adrienne L. Edkins
- The Biomedical Biotechnology Research Unit (BioBRU) Department of Biochemistry and Microbiology DepartmentRhodes UniversityMakhanda6139South Africa
| | - David J. Clarke
- EaStCHEM School of ChemistryJoseph Black Building, David Brewster RoadEdinburghEH93FJUK
| | - Clinton G. L. Veale
- Department of ChemistryUniversity of Cape Town RondeboschCape Town7700South Africa
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15
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Choi ML, Chappard A, Singh BP, Maclachlan C, Rodrigues M, Fedotova EI, Berezhnov AV, De S, Peddie CJ, Athauda D, Virdi GS, Zhang W, Evans JR, Wernick AI, Zanjani ZS, Angelova PR, Esteras N, Vinokurov AY, Morris K, Jeacock K, Tosatto L, Little D, Gissen P, Clarke DJ, Kunath T, Collinson L, Klenerman D, Abramov AY, Horrocks MH, Gandhi S. Author Correction: Pathological structural conversion of α-synuclein at the mitochondria induces neuronal toxicity. Nat Neurosci 2022; 25:1582. [PMID: 36261654 PMCID: PMC9630127 DOI: 10.1038/s41593-022-01206-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Minee L Choi
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.,The Francis Crick Institute, London, UK.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | | | - Bhanu P Singh
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK.,School of Physics, University of Edinburgh, Edinburgh, UK
| | | | - Margarida Rodrigues
- Department of Chemistry, University of Cambridge, Cambridge, UK.,Dementia Research institute at University of Cambridge, Cambridge, UK
| | - Evgeniya I Fedotova
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Russia.,Cell Physiology and Pathology Laboratory, Orel State University, Orel, Russia
| | - Alexey V Berezhnov
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Russia.,Cell Physiology and Pathology Laboratory, Orel State University, Orel, Russia
| | - Suman De
- Department of Chemistry, University of Cambridge, Cambridge, UK.,Dementia Research institute at University of Cambridge, Cambridge, UK
| | | | - Dilan Athauda
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.,The Francis Crick Institute, London, UK
| | - Gurvir S Virdi
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.,The Francis Crick Institute, London, UK.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Weijia Zhang
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.,The Francis Crick Institute, London, UK
| | - James R Evans
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.,The Francis Crick Institute, London, UK.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Anna I Wernick
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.,The Francis Crick Institute, London, UK.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Zeinab Shadman Zanjani
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.,The Francis Crick Institute, London, UK.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Plamena R Angelova
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Noemi Esteras
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Andrey Y Vinokurov
- Cell Physiology and Pathology Laboratory, Orel State University, Orel, Russia
| | - Katie Morris
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - Kiani Jeacock
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - Laura Tosatto
- Department of Chemistry, University of Cambridge, Cambridge, UK.,Istituto di Biofisica, National Council of Research, Trento, Italy
| | - Daniel Little
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK.,NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | - Paul Gissen
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK.,NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | - David J Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - Tilo Kunath
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - David Klenerman
- Department of Chemistry, University of Cambridge, Cambridge, UK.,Dementia Research institute at University of Cambridge, Cambridge, UK
| | - Andrey Y Abramov
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK. .,Cell Physiology and Pathology Laboratory, Orel State University, Orel, Russia.
| | - Mathew H Horrocks
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK.
| | - Sonia Gandhi
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK. .,The Francis Crick Institute, London, UK. .,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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16
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Choi ML, Chappard A, Singh BP, Maclachlan C, Rodrigues M, Fedotova EI, Berezhnov AV, De S, Peddie CJ, Athauda D, Virdi GS, Zhang W, Evans JR, Wernick AI, Zanjani ZS, Angelova PR, Esteras N, Vinokurov AY, Morris K, Jeacock K, Tosatto L, Little D, Gissen P, Clarke DJ, Kunath T, Collinson L, Klenerman D, Abramov AY, Horrocks MH, Gandhi S. Pathological structural conversion of α-synuclein at the mitochondria induces neuronal toxicity. Nat Neurosci 2022; 25:1134-1148. [PMID: 36042314 PMCID: PMC9448679 DOI: 10.1038/s41593-022-01140-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [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: 03/08/2021] [Accepted: 07/12/2022] [Indexed: 11/08/2022]
Abstract
Aggregation of alpha-synuclein (α-Syn) drives Parkinson's disease (PD), although the initial stages of self-assembly and structural conversion have not been directly observed inside neurons. In this study, we tracked the intracellular conformational states of α-Syn using a single-molecule Förster resonance energy transfer (smFRET) biosensor, and we show here that α-Syn converts from a monomeric state into two distinct oligomeric states in neurons in a concentration-dependent and sequence-specific manner. Three-dimensional FRET-correlative light and electron microscopy (FRET-CLEM) revealed that intracellular seeding events occur preferentially on membrane surfaces, especially at mitochondrial membranes. The mitochondrial lipid cardiolipin triggers rapid oligomerization of A53T α-Syn, and cardiolipin is sequestered within aggregating lipid-protein complexes. Mitochondrial aggregates impair complex I activity and increase mitochondrial reactive oxygen species (ROS) generation, which accelerates the oligomerization of A53T α-Syn and causes permeabilization of mitochondrial membranes and cell death. These processes were also observed in induced pluripotent stem cell (iPSC)-derived neurons harboring A53T mutations from patients with PD. Our study highlights a mechanism of de novo α-Syn oligomerization at mitochondrial membranes and subsequent neuronal toxicity.
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Affiliation(s)
- Minee L Choi
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | | | - Bhanu P Singh
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
- School of Physics, University of Edinburgh, Edinburgh, UK
| | | | - Margarida Rodrigues
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Dementia Research institute at University of Cambridge, Cambridge, UK
| | - Evgeniya I Fedotova
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Russia
- Cell Physiology and Pathology Laboratory, Orel State University, Orel, Russia
| | - Alexey V Berezhnov
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Russia
- Cell Physiology and Pathology Laboratory, Orel State University, Orel, Russia
| | - Suman De
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Dementia Research institute at University of Cambridge, Cambridge, UK
| | | | - Dilan Athauda
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
| | - Gurvir S Virdi
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Weijia Zhang
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
| | - James R Evans
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Anna I Wernick
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Zeinab Shadman Zanjani
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Plamena R Angelova
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Noemi Esteras
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Andrey Y Vinokurov
- Cell Physiology and Pathology Laboratory, Orel State University, Orel, Russia
| | - Katie Morris
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - Kiani Jeacock
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - Laura Tosatto
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Istituto di Biofisica, National Council of Research, Trento, Italy
| | - Daniel Little
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | - Paul Gissen
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | - David J Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - Tilo Kunath
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - David Klenerman
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Dementia Research institute at University of Cambridge, Cambridge, UK
| | - Andrey Y Abramov
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.
- Cell Physiology and Pathology Laboratory, Orel State University, Orel, Russia.
| | - Mathew H Horrocks
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK.
| | - Sonia Gandhi
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.
- The Francis Crick Institute, London, UK.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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17
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Wang S, Lin S, Fang Q, Gyampoh R, Lu Z, Gao Y, Clarke DJ, Wu K, Trembleau L, Yu Y, Kyeremeh K, Milne BF, Tabudravu J, Deng H. A ribosomally synthesised and post-translationally modified peptide containing a β-enamino acid and a macrocyclic motif. Nat Commun 2022; 13:5044. [PMID: 36028509 PMCID: PMC9415263 DOI: 10.1038/s41467-022-32774-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 08/16/2022] [Indexed: 11/22/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are structurally complex natural products with diverse bioactivities. Here we report discovery of a RiPP, kintamdin, for which the structure is determined through spectroscopy, spectrometry and genomic analysis to feature a bis-thioether macrocyclic ring and a β-enamino acid residue. Biosynthetic investigation demonstrated that its pathway relies on four dedicated proteins: phosphotransferase KinD, Lyase KinC, kinase homolog KinH and flavoprotein KinI, which share low homologues to enzymes known in other RiPP biosynthesis. During the posttranslational modifications, KinCD is responsible for the formation of the characteristic dehydroamino acid residues including the β-enamino acid residue, followed by oxidative decarboxylation on the C-terminal Cys and subsequent cyclization to provide the bis-thioether ring moiety mediated by coordinated action of KinH and KinI. Finally, conserved genomic investigation allows further identification of two kintamdin-like peptides among the kin-like BGCs, suggesting the occurrence of RiPPs from actinobacteria. The chemical diversity of peptides from ribosomal origin is a growing field of research. Here, the authors report the discovery, genomic and biosynthetic investigations of kintamdin, a ribosomally synthesized and post-translationally modified peptides featuring a beta-enamino acid and a bis-thioether macrocyclic motif.
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Affiliation(s)
- Shan Wang
- Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Sixing Lin
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Hubei Province Engineering and Technology Research Centre for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Qing Fang
- Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Roland Gyampoh
- Department of Chemistry, University of Ghana, P.O. Box LG56, Legon-Accra, Ghana
| | - Zhou Lu
- Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Yingli Gao
- Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK.,College of Marine Life and Fisheries, Jiangsu Ocean University, Lianyungang, Jiangsu Province, China
| | - David J Clarke
- EastChem, School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - Kewen Wu
- Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Laurent Trembleau
- Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Yi Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Hubei Province Engineering and Technology Research Centre for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| | - Kwaku Kyeremeh
- Department of Chemistry, University of Ghana, P.O. Box LG56, Legon-Accra, Ghana.
| | - Bruce F Milne
- Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK. .,CFisUC, Department of Physics, University of Coimbra, Rua Larga, 3004-516, Coimbra, Portugal.
| | - Jioji Tabudravu
- School of Natural Sciences, University of Central Lancashire, PR1 2HE, Preston, England, United Kingdom.
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK.
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18
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Clarke DJ, Murray E, Faktor J, Vojtesek B, MacKay CL, Smith PL, Hupp TR. Corrigendum to "Mass spectrometry analysis of the oxidation states of the pro oncogenic protein anterior gradient-2 reveals covalent dimerization via an intermolecular disulphide bond" [Biochimica et Biophysica Acta 1864 (2016) 551-561]. Biochim Biophys Acta Proteins Proteom 2022; 1870:140806. [PMID: 35786535 DOI: 10.1016/j.bbapap.2022.140806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- David J Clarke
- School of Chemistry, Edinburgh, Scotland EH4 2XR, United Kingdom.
| | - Euan Murray
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Division of Cancer Biology, Edinburgh, Scotland EH4 2XR, United Kingdom
| | - Jakub Faktor
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Borek Vojtesek
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - C Logan MacKay
- School of Chemistry, Edinburgh, Scotland EH4 2XR, United Kingdom
| | | | - Ted R Hupp
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Division of Cancer Biology, Edinburgh, Scotland EH4 2XR, United Kingdom; Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic.
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19
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Zacco E, Kantelberg O, Milanetti E, Armaos A, Panei FP, Gregory J, Jeacock K, Clarke DJ, Chandran S, Ruocco G, Gustincich S, Horrocks MH, Pastore A, Tartaglia GG. Probing TDP-43 condensation using an in silico designed aptamer. Nat Commun 2022; 13:3306. [PMID: 35739092 PMCID: PMC9226187 DOI: 10.1038/s41467-022-30944-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 10/05/2021] [Accepted: 05/23/2022] [Indexed: 12/03/2022] Open
Abstract
Aptamers are artificial oligonucleotides binding to specific molecular targets. They have a promising role in therapeutics and diagnostics but are often difficult to design. Here, we exploited the catRAPID algorithm to generate aptamers targeting TAR DNA-binding protein 43 (TDP-43), whose aggregation is associated with Amyotrophic Lateral Sclerosis. On the pathway to forming insoluble inclusions, TDP-43 adopts a heterogeneous population of assemblies, many smaller than the diffraction-limit of light. We demonstrated that our aptamers bind TDP-43 and used the tightest interactor, Apt-1, as a probe to visualize TDP-43 condensates with super-resolution microscopy. At a resolution of 10 nanometers, we tracked TDP-43 oligomers undetectable by standard approaches. In cells, Apt-1 interacts with both diffuse and condensed forms of TDP-43, indicating that Apt-1 can be exploited to follow TDP-43 phase transition. The de novo generation of aptamers and their use for microscopy opens a new page to study protein condensation.
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Affiliation(s)
- Elsa Zacco
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Owen Kantelberg
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - Edoardo Milanetti
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy.,Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Alexandros Armaos
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Francesco Paolo Panei
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Jenna Gregory
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little F, Edinburgh, UK.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
| | - Kiani Jeacock
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - David J Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - Siddharthan Chandran
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little F, Edinburgh, UK.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
| | - Giancarlo Ruocco
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy.,Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Stefano Gustincich
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Mathew H Horrocks
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK.
| | - Annalisa Pastore
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London, SE5 9RT, UK.
| | - Gian Gaetano Tartaglia
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy. .,Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Catalan Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain. .,Department of Biology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome, 00185, Italy.
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20
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Carr CM, Clarke DJ, Dobson ADW. Polyesterase activities in bacterial isolates from seaweed and sponges, with potential utility in polyethylene terephthalate plastic and nanoparticle hydrolysis. Access Microbiol 2022. [DOI: 10.1099/acmi.ac2021.po0249] [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: 11/18/2022] Open
Abstract
Many marine bacteria have evolved to produce a range of extracellular enzymes which facilitate their growth and survival in the harsh, oligotrophic conditions often present in marine environments. Marine sponge derived Streptomycesstrains have previously been reported to produce polyesterase enzymes, which are of interest for several biotechnological applications, including polyethylene terephthalate (PET) plastic hydrolysis.
Bacteria isolated from sponges and seaweed were screened for polyester hydrolysis activities using plate-clearing assays. Lipolytic and polyesterolytic activities were initially identified by employing tributyrin and polycaprolactone diol agar-based assay systems, respectively. Polyesterase activity was subsequently confirmed on both polycaprolactone and on PET-nanoparticle agar plates, resulting in the prioritisation of six isolates for Illumina next-generation genome sequencing.
These include three Bacillusspp., isolated from the brown seaweed Ascophyllum nodosum,and from marine lake sponges Stelligera stuposaand Eurypon major, together with a Maribacterstrain again isolated from S. stuposa, and Brachybacteriumsp. and Micrococcussp. isolates of deep-sea sponges Pheronemasp. and Inflatella pellicula, that were sampled at depths of 2129m and 2900m, respectively. Genome mining and comparative genomic analysis of these isolates is currently underway to identify genes encoding the observed activities and to assess homology with known PET hydrolases.
Microbes found living in association with filter-feeding sponges may have increased exposure to the plastics and microplastics that widely contaminate our marine ecosystems, thus representing a promising source of degradative activities towards synthetic polymers that could contribute to new plastic waste management strategies.
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Affiliation(s)
| | | | - Alan D. W. Dobson
- SSPC-SFI Research Centre for Pharmaceuticals, University College Cork, Ireland
- School of Microbiology, University College Cork, Ireland
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21
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Carr CM, de Oliveira BFR, Jackson SA, Laport MS, Clarke DJ, Dobson ADW. Identification of BgP, a Cutinase-Like Polyesterase From a Deep-Sea Sponge-Derived Actinobacterium. Front Microbiol 2022; 13:888343. [PMID: 35495686 PMCID: PMC9039725 DOI: 10.3389/fmicb.2022.888343] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Many marine bacteria produce extracellular enzymes that degrade complex molecules to facilitate their growth in environmental conditions that are often harsh and low in nutrients. Marine bacteria, including those inhabiting sea sponges, have previously been reported to be a promising source of polyesterase enzymes, which have received recent attention due to their potential ability to degrade polyethylene terephthalate (PET) plastic. During the screening of 51 marine bacterial isolates for hydrolytic activities targeting ester and polyester substrates, a Brachybacterium ginsengisoli B129SM11 isolate from the deep-sea sponge Pheronema sp. was identified as a polyesterase producer. Sequence analysis of genomic DNA from strain B129SM11, coupled with a genome "mining" strategy, allowed the identification of potential polyesterases, using a custom database of enzymes that had previously been reported to hydrolyze PET or other synthetic polyesters. This resulted in the identification of a putative PET hydrolase gene, encoding a polyesterase-type enzyme which we named BgP that shared high overall similarity with three well-characterized PET hydrolases-LCC, TfCut2, and Cut190, all of which are key enzymes currently under investigation for the biological recycling of PET. In silico protein analyses and homology protein modeling offered structural and functional insights into BgP, and a detailed comparison with Cut190 revealed highly conserved features with implications for both catalysis and substrate binding. Polyesterase activity was confirmed using an agar-based polycaprolactone (PCL) clearing assay, following heterologous expression of BgP in Escherichia coli. This is the first report of a polyesterase being identified from a deep-sea sponge bacterium such as Brachybacterium ginsengisoli and provides further insights into marine-derived polyesterases, an important family of enzymes for PET plastic hydrolysis. Microorganisms living in association with sponges are likely to have increased exposure to plastics and microplastics given the wide-scale contamination of marine ecosystems with these plastics, and thus they may represent a worthwhile source of enzymes for use in new plastic waste management systems. This study adds to the growing knowledge of microbial polyesterases and endorses further exploration of marine host-associated microorganisms as a potentially valuable source of this family of enzymes for PET plastic hydrolysis.
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Affiliation(s)
- Clodagh M. Carr
- School of Microbiology, University College Cork, Cork, Ireland
- SSPC-SFI Research Centre for Pharmaceuticals, University College Cork, Cork, Ireland
| | - Bruno Francesco Rodrigues de Oliveira
- School of Microbiology, University College Cork, Cork, Ireland
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Brazil
| | - Stephen A. Jackson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - David J. Clarke
- School of Microbiology, University College Cork, Cork, Ireland
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- SSPC-SFI Research Centre for Pharmaceuticals, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
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22
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Fodor A, Clarke DJ, Dillman AR, Tarasco E, Hazir S. Editorial: New Antimicrobial Peptides From Bacteria/Invertebrate Obligate Symbiotic Associations. Front Microbiol 2022; 13:862198. [PMID: 35350613 PMCID: PMC8957908 DOI: 10.3389/fmicb.2022.862198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- András Fodor
- Department of Genetics, Eötvös University, Budapest, Hungary.,Department of Genetics, University of Szeged, Szeged, Hungary
| | - David J Clarke
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Adler R Dillman
- Department of Nematology, University of California, Riverside, Riverside, CA, United States
| | - Eustachio Tarasco
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Bari, Italy.,Institute for Sustainable Plant Protection of CNR, Bari, Italy
| | - Selcuk Hazir
- Department of Biology, Faculty of Arts and Sciences, Adnan Menderes University, Aydin, Turkey
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23
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Ross J, McIver Z, Lambert T, Piergentili C, Bird JE, Gallagher KJ, Cruickshank FL, James P, Zarazúa-Arvizu E, Horsfall LE, Waldron KJ, Wilson MD, Mackay CL, Baslé A, Clarke DJ, Marles-Wright J. Pore dynamics and asymmetric cargo loading in an encapsulin nanocompartment. Sci Adv 2022; 8:eabj4461. [PMID: 35080974 PMCID: PMC8791618 DOI: 10.1126/sciadv.abj4461] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
Encapsulins are protein nanocompartments that house various cargo enzymes, including a family of decameric ferritin-like proteins. Here, we study a recombinant Haliangium ochraceum encapsulin:encapsulated ferritin complex using cryo-electron microscopy and hydrogen/deuterium exchange mass spectrometry to gain insight into the structural relationship between the encapsulin shell and its protein cargo. An asymmetric single-particle reconstruction reveals four encapsulated ferritin decamers in a tetrahedral arrangement within the encapsulin nanocompartment. This leads to a symmetry mismatch between the protein cargo and the icosahedral encapsulin shell. The encapsulated ferritin decamers are offset from the interior face of the encapsulin shell. Using hydrogen/deuterium exchange mass spectrometry, we observed the dynamic behavior of the major fivefold pore in the encapsulin shell and show the pore opening via the movement of the encapsulin A-domain. These data will accelerate efforts to engineer the encapsulation of heterologous cargo proteins and to alter the permeability of the encapsulin shell via pore modifications.
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Affiliation(s)
- Jennifer Ross
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Zak McIver
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Thomas Lambert
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Cecilia Piergentili
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jasmine Emma Bird
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Kelly J. Gallagher
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Faye L. Cruickshank
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Patrick James
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | | | - Louise E. Horsfall
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Kevin J. Waldron
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Marcus D. Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - C. Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Arnaud Baslé
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - David J. Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Jon Marles-Wright
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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24
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Amirloo B, Staroseletz Y, Yousaf S, Clarke DJ, Brown T, Aojula H, Zenkova MA, Bichenkova EV. "Bind, cleave and leave": multiple turnover catalysis of RNA cleavage by bulge-loop inducing supramolecular conjugates. Nucleic Acids Res 2021; 50:651-673. [PMID: 34967410 PMCID: PMC8789077 DOI: 10.1093/nar/gkab1273] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022] Open
Abstract
Antisense sequence-specific knockdown of pathogenic RNA offers opportunities to find new solutions for therapeutic treatments. However, to gain a desired therapeutic effect, the multiple turnover catalysis is critical to inactivate many copies of emerging RNA sequences, which is difficult to achieve without sacrificing the sequence-specificity of cleavage. Here, engineering two or three catalytic peptides into the bulge-loop inducing molecular framework of antisense oligonucleotides achieved catalytic turnover of targeted RNA. Different supramolecular configurations revealed that cleavage of the RNA backbone upon sequence-specific hybridization with the catalyst accelerated with increase in the number of catalytic guanidinium groups, with almost complete demolition of target RNA in 24 h. Multiple sequence-specific cuts at different locations within and around the bulge-loop facilitated release of the catalyst for subsequent attacks of at least 10 further RNA substrate copies, such that delivery of only a few catalytic molecules could be sufficient to maintain knockdown of typical RNA copy numbers. We have developed fluorescent assay and kinetic simulation tools to characterise how the limited availability of different targets and catalysts had restrained catalytic reaction progress considerably, and to inform how to accelerate the catalytic destruction of shorter linear and larger RNAs even further.
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Affiliation(s)
- Bahareh Amirloo
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Yaroslav Staroseletz
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russian Federation
| | - Sameen Yousaf
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - David J Clarke
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Harmesh Aojula
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russian Federation
| | - Elena V Bichenkova
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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25
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Donetto S, Jones F, Clarke DJ, Cloud GC, Gombert-Waldron K, Ruth H, Macdonald A, McKevitt C, Robert G. Exploring liminality in the co-design of rehabilitation environments: The case of one acute stroke unit. Health Place 2021; 72:102695. [PMID: 34768039 PMCID: PMC8633757 DOI: 10.1016/j.healthplace.2021.102695] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 08/30/2021] [Accepted: 10/06/2021] [Indexed: 11/24/2022]
Abstract
This paper describes an Experience-based Co-design (EBCD) project that aimed to increase patient activity within an acute stroke unit. We apply the concept of liminality to explore ways in which the EBCD process, a form of Participatory Action Research, may dilute or even dissolve social hierarchies and challenge assumptions about practices and constraints in this care setting, thereby opening up possibilities for transformation that enhances the therapeutic value of the space for patients and care providers alike. By occasioning a liminal phase of possibility for change, the work of one co-design group explored in detail here suggests that, in this process, the sociomaterial interactions involving patients, family members, staff, and the physical space are refashioned and re-inscribed in transformed ‘emplaced’ relationships of care. EBCD improved an acute stroke unit environment to provide greater opportunity for social and therapeutic activity. The structured EBCD approach provided a ‘liminal’ space within which collaborative change could be enabled. Liminality facilitated trust and built a sense of community between participating patients, families and staff. The different roles adopted by participants during the process challenged norms and effected change.
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Affiliation(s)
- Sara Donetto
- Florence Nightingale Faculty of Nursing, Midwifery & Palliative Care, King's College London, UK
| | - Fiona Jones
- Faculty of Health and Social Care Sciences. Kingston University & St George's, University of London, UK.
| | - David J Clarke
- Leeds Institute of Health Sciences, University of Leeds, UK
| | - Geoffrey C Cloud
- Department of Clinical Neuroscience, CCS, Monash University Melbourne and Alfred Health, Melbourne, Australia
| | - Karolina Gombert-Waldron
- Faculty of Health and Social Care Sciences. Kingston University & St George's, University of London, UK
| | - Harris Ruth
- Florence Nightingale Faculty of Nursing, Midwifery & Palliative Care, King's College London, UK
| | | | - Christopher McKevitt
- School of Population Health & Environmental Sciences, Faculty of Life Sciences and Medicine, King's College London, UK
| | - Glenn Robert
- Department of Clinical Neuroscience, CCS, Monash University Melbourne and Alfred Health, Melbourne, Australia
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26
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Veale CGL, Mateos-Jiménez M, Vaaltyn MC, Müller R, Makhubu MP, Alhassan M, de la Torre BG, Albericio F, Mackay CL, Edkins AL, Clarke DJ. A native mass spectrometry platform identifies HOP inhibitors that modulate the HSP90-HOP protein-protein interaction. Chem Commun (Camb) 2021; 57:10919-10922. [PMID: 34591048 DOI: 10.1039/d1cc04257b] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Herein we describe a native mass spectromery protein-peptide model as a competent surrogate for the HOP-HSP90 protein-protein interaction (PPI), application of which led to the qualititive identification of two new peptides capable of in vitro PPI disruption. This proof of concept study offers a viable alternative for PPI inhibitor screening.
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Affiliation(s)
- Clinton G L Veale
- FLAIR Research Fellow, School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa.
| | - Maria Mateos-Jiménez
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH93FJ, UK.
| | - Michaelone C Vaaltyn
- The Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Ronel Müller
- FLAIR Research Fellow, School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa.
| | - Matodzi P Makhubu
- The Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Mahama Alhassan
- FLAIR Research Fellow, School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa.
| | - Beatriz G de la Torre
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, South Africa
| | - Fernando Albericio
- FLAIR Research Fellow, School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa.
| | - C Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH93FJ, UK.
| | - Adrienne L Edkins
- The Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - David J Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH93FJ, UK.
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27
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Kaczorowska J, Casey E, Lugli GA, Ventura M, Clarke DJ, van Sinderen D, Mahony J. In Vitro and In Vivo Assessment of the Potential of Escherichia coli Phages to Treat Infections and Survive Gastric Conditions. Microorganisms 2021; 9:microorganisms9091869. [PMID: 34576765 PMCID: PMC8472732 DOI: 10.3390/microorganisms9091869] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 11/17/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) and Shigella ssp. infections are associated with high rates of mortality, especially in infants in developing countries. Due to increasing levels of global antibiotic resistance exhibited by many pathogenic organisms, alternative strategies to combat such infections are urgently required. In this study, we evaluated the stability of five coliphages (four Myoviridae and one Siphoviridae phage) over a range of pH conditions and in simulated gastric conditions. The Myoviridae phages were stable across the range of pH 2 to 7, while the Siphoviridae phage, JK16, exhibited higher sensitivity to low pH. A composite mixture of these five phages was tested in vivo in a Galleria mellonella model. The obtained data clearly shows potential in treating E. coli infections prophylactically.
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Affiliation(s)
- Joanna Kaczorowska
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland; (J.K.); (E.C.); (D.J.C.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
| | - Eoghan Casey
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland; (J.K.); (E.C.); (D.J.C.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
| | - Gabriele A. Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43121 Parma, Italy; (G.A.L.); (M.V.)
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43121 Parma, Italy; (G.A.L.); (M.V.)
| | - David J. Clarke
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland; (J.K.); (E.C.); (D.J.C.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland; (J.K.); (E.C.); (D.J.C.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
- Correspondence: (D.v.S.); (J.M.); Tel.: +353-21-4901365 (D.v.S.); +353-21-4902730 (J.M.)
| | - Jennifer Mahony
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland; (J.K.); (E.C.); (D.J.C.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
- Correspondence: (D.v.S.); (J.M.); Tel.: +353-21-4901365 (D.v.S.); +353-21-4902730 (J.M.)
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Morton S, Hall J, Fitzsimons C, Hall J, English C, Forster A, Lawton R, Patel A, Mead G, Clarke DJ. A qualitative study of sedentary behaviours in stroke survivors: non-participant observations and interviews with stroke service staff in stroke units and community services. Disabil Rehabil 2021; 44:5964-5973. [PMID: 34304649 DOI: 10.1080/09638288.2021.1955307] [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] [Indexed: 10/20/2022]
Abstract
PURPOSE Sedentary behaviour (SB) is associated with negative health outcomes and is prevalent post-stroke. This study explored SB after stroke from the perspective of stroke service staff. METHODS Qualitative mixed-methods study. Non-participant observations in two stroke services (England/Scotland) and semi-structured interviews with staff underpinned by the COM-B model of behaviour change. Observations were analysed thematically; interviews were analysed using the Framework approach. RESULTS One hundred and thirty-two observation hours (October - December 2017), and 31 staff interviewed (January -June 2018). Four themes were identified: (1) Opportunities for staff to support stroke survivors to reduce SB; (2) Physical and psychological capability of staff to support stroke survivors to reduce SB; (3) Motivating factors influencing staff behaviour to support stroke survivors to reduce SB; (4) Staff suggestions for a future intervention to support stroke survivors to reduce SB. CONCLUSIONS Staff are aware of the consequences of prolonged sitting but did not relate to SB. Explicit knowledge of SB was limited. Staff need training to support stroke survivors to reduce SB. Sedentary behaviour in the community was not reported to change markedly, highlighting the need to engage stroke survivors in movement from when capable in hospital, following through to home.Implications for rehabilitationStroke survivor sedentary behaviour is influenced, directly and indirectly, by the actions and instructions of stroke service staff in the inpatient and community setting.The built and social environment, both in the inpatient and community settings, may limit opportunities for safe movement and can result in stroke survivors spending more time sedentary.Stroke service staff appreciate the benefit of encouraging stroke survivors to stand and move more, if it is safe for them to do so.Staff would be amenable to encourage stroke survivors to reduce sedentary behaviour, provided they have the knowledge and resources to equip them to support this.
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Affiliation(s)
- Sarah Morton
- Centre for Clinical Brain Sciences, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, Scotland
| | - Jennifer Hall
- Academic Unit for Ageing and Stroke Research, Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, England
| | - Claire Fitzsimons
- Physical Activity for Health Research Centre, St Leonards Land, University of Edinburgh, Edinburgh, Scotland
| | - Jessica Hall
- Academic Unit for Ageing and Stroke Research, Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, England
| | - Coralie English
- School of Health Sciences,The University of Newcastle, Callaghan, Australia
| | - Anne Forster
- Academic Unit for Ageing and Stroke Research, Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, England
| | - Rebecca Lawton
- School of Psychology, Faculty of Health and Medicine, University of Leeds, Leeds, England
| | - Anita Patel
- Anita Patel Health Economics Consulting Ltd., London, England
| | - Gillian Mead
- Centre for Clinical Brain Sciences, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, Scotland
| | - David J Clarke
- Academic Unit for Ageing and Stroke Research, Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, England
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Burton LJ, Forster A, Johnson J, Crocker TF, Tyson SF, Wray F, Clarke DJ. Experiences and views of receiving and delivering information about recovery in acquired neurological conditions: a systematic review of qualitative literature. BMJ Open 2021; 11:e045297. [PMID: 33906841 PMCID: PMC8088240 DOI: 10.1136/bmjopen-2020-045297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
OBJECTIVE To review and synthesise qualitative literature relating to the views, perceptions and experiences of patients with acquired neurological conditions and their caregivers about the process of receiving information about recovery; as well as the views and experiences of healthcare professionals involved in delivering this information. DESIGN Systematic review of qualitative studies. DATA SOURCES MEDLINE, Embase, AMED, CINAHL, PsycINFO, Web of Science and the Cochrane library were searched from their inception to July 2019. DATA EXTRACTION AND SYNTHESIS Two reviewers extracted data from the included studies and assessed quality using an established tool. Thematic synthesis was used to synthesise the findings of included studies. RESULTS Searches yielded 9105 titles, with 145 retained for full-text screening. Twenty-eight studies (30 papers) from eight countries were included. Inductive analysis resulted in 11 descriptive themes, from which 5 analytical themes were generated: the right information at the right time; managing expectations; it's not what you say, it's how you say it; learning how to talk about recovery and manage emotions; the context of uncertainty. CONCLUSIONS Our findings highlight the inherent challenges in talking about recovery in an emotional context, where breaking bad news is a key feature. Future interventions should focus on preparing staff to meet patients' and families' information needs, as well as ensuring they have the skills to discuss potential recovery and break bad news compassionately and share the uncertain trajectory characteristic of acquired neurological conditions. An agreed team-based approach to talking about recovery is recommended to ensure consistency and improve the experiences of patients and their families.
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Affiliation(s)
- Louisa-Jane Burton
- Academic Unit for Ageing and Stroke Research, University of Leeds, Leeds, UK
- Academic Unit for Ageing and Stroke Research, Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Anne Forster
- Academic Unit for Ageing and Stroke Research, University of Leeds, Leeds, UK
- Academic Unit for Ageing and Stroke Research, Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Judith Johnson
- School of Psychology, University of Leeds Faculty of Biological Sciences, Leeds, UK
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
- School of Public Health and Community Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Thomas F Crocker
- Academic Unit for Ageing and Stroke Research, Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Sarah F Tyson
- Division of Nursing, Midwifery and Social Work, The University of Manchester, Manchester, UK
| | - Faye Wray
- Academic Unit for Ageing and Stroke Research, University of Leeds, Leeds, UK
| | - David J Clarke
- Academic Unit for Ageing and Stroke Research, University of Leeds, Leeds, UK
- Academic Unit for Ageing and Stroke Research, Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
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Johansson M, Azuma Y, Clarke DJ. Role of Aurora B and Haspin kinases in the metaphase Topoisomerase II checkpoint. Cell Cycle 2021; 20:345-352. [PMID: 33459116 DOI: 10.1080/15384101.2021.1875671] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
DNA Topoisomerase II (TopoII) uses ATP hydrolysis to decatenate chromosomes so that sister chromatids can faithfully segregate in mitosis. When the TopoII enzyme cycle stalls due to failed ATP hydrolysis, the onset of anaphase is delayed, presumably to allow extra time for decatenation to be completed. Recent evidence revealed that, unlike the spindle assembly checkpoint, this TopoII checkpoint response requires Aurora B and Haspin kinases and is triggered by SUMOylation of the C-terminal domain of TopoII.
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Affiliation(s)
- M Johansson
- Department of Genetics, Cell Biology & Development, University of Minnesota , Minneapolis, MN, USA
| | - Y Azuma
- Department of Molecular Biosciences, University of Kansas , Lawrence, KS, USA
| | - D J Clarke
- Department of Genetics, Cell Biology & Development, University of Minnesota , Minneapolis, MN, USA
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31
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Staroseletz Y, Amirloo B, Williams A, Lomzov A, Burusco KK, Clarke DJ, Brown T, Zenkova MA, Bichenkova EV. Strict conformational demands of RNA cleavage in bulge-loops created by peptidyl-oligonucleotide conjugates. Nucleic Acids Res 2020; 48:10662-10679. [PMID: 33010175 PMCID: PMC7641753 DOI: 10.1093/nar/gkaa780] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/04/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
Potent knockdown of pathogenic RNA in vivo is an urgent health need unmet by both small-molecule and biologic drugs. ‘Smart’ supramolecular assembly of catalysts offers precise recognition and potent destruction of targeted RNA, hitherto not found in nature. Peptidyl-oligonucleotide ribonucleases are here chemically engineered to create and attack bulge-loop regions upon hybridization to target RNA. Catalytic peptide was incorporated either via a centrally modified nucleotide (Type 1) or through an abasic sugar residue (Type 2) within the RNA-recognition motif to reveal striking differences in biological performance and strict structural demands of ribonuclease activity. None of the Type 1 conjugates were catalytically active, whereas all Type 2 conjugates cleaved RNA target in a sequence-specific manner, with up to 90% cleavage from 5-nt bulge-loops (BC5-α and BC5L-β anomers) through multiple cuts, including in folds nearby. Molecular dynamics simulations provided structural explanation of accessibility of the RNA cleavage sites to the peptide with adoption of an ‘in-line’ attack conformation for catalysis. Hybridization assays and enzymatic probing with RNases illuminated how RNA binding specificity and dissociation after cleavage can be balanced to permit turnover of the catalytic reaction. This is an essential requirement for inactivation of multiple copies of disease-associated RNA and therapeutic efficacy.
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Affiliation(s)
- Yaroslav Staroseletz
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russia
| | - Bahareh Amirloo
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Aled Williams
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Alexander Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russia
| | - Kepa K Burusco
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - David J Clarke
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russia
| | - Elena V Bichenkova
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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32
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Piergentili C, Ross J, He D, Gallagher KJ, Stanley WA, Adam L, Mackay CL, Baslé A, Waldron KJ, Clarke DJ, Marles-Wright J. Dissecting the structural and functional roles of a putative metal entry site in encapsulated ferritins. J Biol Chem 2020; 295:15511-15526. [PMID: 32878987 DOI: 10.1074/jbc.ra120.014502] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 05/25/2020] [Revised: 08/24/2020] [Indexed: 11/06/2022] Open
Abstract
Encapsulated ferritins belong to the universally distributed ferritin superfamily, whose members function as iron detoxification and storage systems. Encapsulated ferritins have a distinct annular structure and must associate with an encapsulin nanocage to form a competent iron store that is capable of holding significantly more iron than classical ferritins. The catalytic mechanism of iron oxidation in the ferritin family is still an open question because of the differences in organization of the ferroxidase catalytic site and neighboring secondary metal-binding sites. We have previously identified a putative metal-binding site on the inner surface of the Rhodospirillum rubrum encapsulated ferritin at the interface between the two-helix subunits and proximal to the ferroxidase center. Here we present a comprehensive structural and functional study to investigate the functional relevance of this putative iron-entry site by means of enzymatic assays, MS, and X-ray crystallography. We show that catalysis occurs in the ferroxidase center and suggest a dual role for the secondary site, which both serves to attract metal ions to the ferroxidase center and acts as a flow-restricting valve to limit the activity of the ferroxidase center. Moreover, confinement of encapsulated ferritins within the encapsulin nanocage, although enhancing the ability of the encapsulated ferritin to undergo catalysis, does not influence the function of the secondary site. Our study demonstrates a novel molecular mechanism by which substrate flux to the ferroxidase center is controlled, potentially to ensure that iron oxidation is productively coupled to mineralization.
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Affiliation(s)
- Cecilia Piergentili
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jennifer Ross
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, Scotland
| | - Didi He
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland
| | - Kelly J Gallagher
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, Scotland
| | - Will A Stanley
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Laurène Adam
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - C Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, Scotland
| | - Arnaud Baslé
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kevin J Waldron
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David J Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, Scotland.
| | - Jon Marles-Wright
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.
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Carr CM, Clarke DJ, Dobson ADW. Microbial Polyethylene Terephthalate Hydrolases: Current and Future Perspectives. Front Microbiol 2020; 11:571265. [PMID: 33262744 PMCID: PMC7686037 DOI: 10.3389/fmicb.2020.571265] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [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: 06/10/2020] [Accepted: 10/19/2020] [Indexed: 12/18/2022] Open
Abstract
Plastic has rapidly transformed our world, with many aspects of human life now relying on a variety of plastic materials. Biological plastic degradation, which employs microorganisms and their degradative enzymes, has emerged as one way to address the unforeseen consequences of the waste streams that have resulted from mass plastic production. The focus of this review is microbial hydrolase enzymes which have been found to act on polyethylene terephthalate (PET) plastic. The best characterized examples are discussed together with the use of genomic and protein engineering technologies to obtain PET hydrolase enzymes for different applications. In addition, the obstacles which are currently limiting the development of efficient PET bioprocessing are presented. By continuing to study the possible mechanisms and the structural elements of key enzymes involved in microbial PET hydrolysis, and by assessing the ability of PET hydrolase enzymes to work under practical conditions, this research will help inform large-scale waste management operations. Finally, the contribution of microbial PET hydrolases in creating a potential circular PET economy will be explored. This review combines the current knowledge on enzymatic PET processing with proposed strategies for optimization and use, to help clarify the next steps in addressing pollution by PET and other plastics.
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Affiliation(s)
- Clodagh M. Carr
- School of Microbiology, University College Cork, Cork, Ireland
| | - David J. Clarke
- School of Microbiology, University College Cork, Cork, Ireland
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- SSPC-SFI Research Centre for Pharmaceuticals, University College Cork, Cork, Ireland
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34
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Li J, Oh J, Kienesberger S, Kim NY, Clarke DJ, Zechner EL, Crawford JM. Making and Breaking Leupeptin Protease Inhibitors in Pathogenic Gammaproteobacteria. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jhe‐Hao Li
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical Biology Institute Yale University West Haven CT 06516 USA
| | - Joonseok Oh
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical Biology Institute Yale University West Haven CT 06516 USA
| | | | - Nam Yoon Kim
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical Biology Institute Yale University West Haven CT 06516 USA
| | - David J. Clarke
- School of Microbiology and APC Microbiome Ireland University College Cork Cork Ireland
| | - Ellen L. Zechner
- Institute of Molecular Biosciences University of Graz 8010 Graz Austria
- BioTechMed-Graz 8010 Graz Austria
| | - Jason M. Crawford
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical Biology Institute Yale University West Haven CT 06516 USA
- Department of Microbial Pathogenesis Yale University School of Medicine New Haven CT 06536 USA
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35
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Srzentić K, Fornelli L, Tsybin YO, Loo JA, Seckler H, Agar JN, Anderson LC, Bai DL, Beck A, Brodbelt JS, van der Burgt YEM, Chamot-Rooke J, Chatterjee S, Chen Y, Clarke DJ, Danis PO, Diedrich JK, D'Ippolito RA, Dupré M, Gasilova N, Ge Y, Goo YA, Goodlett DR, Greer S, Haselmann KF, He L, Hendrickson CL, Hinkle JD, Holt MV, Hughes S, Hunt DF, Kelleher NL, Kozhinov AN, Lin Z, Malosse C, Marshall AG, Menin L, Millikin RJ, Nagornov KO, Nicolardi S, Paša-Tolić L, Pengelley S, Quebbemann NR, Resemann A, Sandoval W, Sarin R, Schmitt ND, Shabanowitz J, Shaw JB, Shortreed MR, Smith LM, Sobott F, Suckau D, Toby T, Weisbrod CR, Wildburger NC, Yates JR, Yoon SH, Young NL, Zhou M. Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry. J Am Soc Mass Spectrom 2020; 31:1783-1802. [PMID: 32812765 PMCID: PMC7539639 DOI: 10.1021/jasms.0c00036] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 05/02/2023]
Abstract
The Consortium for Top-Down Proteomics (www.topdownproteomics.org) launched the present study to assess the current state of top-down mass spectrometry (TD MS) and middle-down mass spectrometry (MD MS) for characterizing monoclonal antibody (mAb) primary structures, including their modifications. To meet the needs of the rapidly growing therapeutic antibody market, it is important to develop analytical strategies to characterize the heterogeneity of a therapeutic product's primary structure accurately and reproducibly. The major objective of the present study is to determine whether current TD/MD MS technologies and protocols can add value to the more commonly employed bottom-up (BU) approaches with regard to confirming protein integrity, sequencing variable domains, avoiding artifacts, and revealing modifications and their locations. We also aim to gather information on the common TD/MD MS methods and practices in the field. A panel of three mAbs was selected and centrally provided to 20 laboratories worldwide for the analysis: Sigma mAb standard (SiLuLite), NIST mAb standard, and the therapeutic mAb Herceptin (trastuzumab). Various MS instrument platforms and ion dissociation techniques were employed. The present study confirms that TD/MD MS tools are available in laboratories worldwide and provide complementary information to the BU approach that can be crucial for comprehensive mAb characterization. The current limitations, as well as possible solutions to overcome them, are also outlined. A primary limitation revealed by the results of the present study is that the expert knowledge in both experiment and data analysis is indispensable to practice TD/MD MS.
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Affiliation(s)
- Kristina Srzentić
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Luca Fornelli
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Yury O Tsybin
- Spectroswiss, EPFL Innovation Park, Building I, 1015 Lausanne, Switzerland
| | - Joseph A Loo
- University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Henrique Seckler
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Jeffrey N Agar
- Northeastern University, Boston, Massachusetts 02115, United States
| | - Lissa C Anderson
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Dina L Bai
- University of Virginia, Charlottesville, Virginia 22901, United States
| | - Alain Beck
- Centre d'immunologie Pierre Fabre, 74160 Saint-Julien-en-Genevois, France
| | | | | | | | | | - Yunqiu Chen
- Biogen, Inc., Cambridge, Massachusetts 02142-1031, United States
| | - David J Clarke
- The University of Edinburgh, EH9 3FJ Edinburgh, United Kingdom
| | - Paul O Danis
- Consortium for Top-Down Proteomics, Cambridge, Massachusetts 02142, United States
| | - Jolene K Diedrich
- The Scripps Research Institute, La Jolla, California 92037, United States
| | | | | | - Natalia Gasilova
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ying Ge
- University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Young Ah Goo
- University of Maryland, Baltimore, Maryland 21201, United States
| | - David R Goodlett
- University of Maryland, Baltimore, Maryland 21201, United States
| | - Sylvester Greer
- University of Texas at Austin, Austin, Texas 78712-1224, United States
| | | | - Lidong He
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | | | - Joshua D Hinkle
- University of Virginia, Charlottesville, Virginia 22901, United States
| | - Matthew V Holt
- Baylor College of Medicine, Houston, Texas 77030-3411, United States
| | - Sam Hughes
- The University of Edinburgh, EH9 3FJ Edinburgh, United Kingdom
| | - Donald F Hunt
- University of Virginia, Charlottesville, Virginia 22901, United States
| | - Neil L Kelleher
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Anton N Kozhinov
- Spectroswiss, EPFL Innovation Park, Building I, 1015 Lausanne, Switzerland
| | - Ziqing Lin
- University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | | | - Alan G Marshall
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
- Florida State University, Tallahassee, Florida 32310-4005, United States
| | - Laure Menin
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Robert J Millikin
- University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | | | - Simone Nicolardi
- Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Ljiljana Paša-Tolić
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | | | - Neil R Quebbemann
- University of California-Los Angeles, Los Angeles, California 90095, United States
| | | | - Wendy Sandoval
- Genentech, Inc., South San Francisco, California 94080-4990, United States
| | - Richa Sarin
- Biogen, Inc., Cambridge, Massachusetts 02142-1031, United States
| | | | | | - Jared B Shaw
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | | | - Lloyd M Smith
- University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Frank Sobott
- University of Antwerp, 2000 Antwerp, Belgium
- University of Leeds, LS2 9JT Leeds, United Kingdom
| | | | - Timothy Toby
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Chad R Weisbrod
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Norelle C Wildburger
- Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - John R Yates
- The Scripps Research Institute, La Jolla, California 92037, United States
| | - Sung Hwan Yoon
- University of Maryland, Baltimore, Maryland 21201, United States
| | - Nicolas L Young
- Baylor College of Medicine, Houston, Texas 77030-3411, United States
| | - Mowei Zhou
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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36
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Hall J, Morton S, Hall J, Clarke DJ, Fitzsimons CF, English C, Forster A, Mead GE, Lawton R. A co-production approach guided by the behaviour change wheel to develop an intervention for reducing sedentary behaviour after stroke. Pilot Feasibility Stud 2020; 6:115. [PMID: 32821421 PMCID: PMC7429798 DOI: 10.1186/s40814-020-00667-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 03/14/2020] [Accepted: 08/07/2020] [Indexed: 11/10/2022] Open
Abstract
Background Stroke survivors are highly sedentary; thus, breaking up long uninterrupted bouts of sedentary behaviour could have substantial health benefit. However, there are no intervention strategies specifically aimed at reducing sedentary behaviour tailored for stroke survivors. The purpose of this study was to use co-production approaches to develop an intervention to reduce sedentary behaviour after stroke. Methods A series of five co-production workshops with stroke survivors, their caregivers, stroke service staff, exercise professionals, and researchers were conducted in parallel in two-stroke services (England and Scotland). Workshop format was informed by the behaviour change wheel (BCW) framework for developing interventions and incorporated systematic review and empirical evidence. Taking an iterative approach, data from activities and audio recordings were analysed following each workshop and findings used to inform subsequent workshops, to inform both the activities of the next workshop and ongoing intervention development. Findings Co-production workshop participants (n = 43) included 17 staff, 14 stroke survivors, six caregivers and six researchers. The target behaviour for stroke survivors is to increase standing and moving, and the target behaviour for caregivers and staff is to support and encourage stroke survivors to increase standing and moving. The developed intervention is primarily based on co-produced solutions to barriers to achieving the target behaviour. The developed intervention includes 34 behaviour change techniques. The intervention is to be delivered through stroke services, commencing in the inpatient setting and following through discharge into the community. Participants reported that taking part in intervention development was a positive experience. Conclusions To our knowledge, this is the first study that has combined the use of co-production and the BCW to develop an intervention for use in stroke care. In-depth reporting of how a co-production approach was combined with the BCW framework, including the design of bespoke materials for workshop activities, should prove useful to other researchers and practitioners involved in intervention development in stroke.
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Affiliation(s)
- Jennifer Hall
- Academic Unit for Ageing and Stroke Research, Leeds Institute of Health Sciences, University of Leeds, Bradford, BD9 6RJ UK.,Academic Unit for Ageing and Stroke Research, Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, BD9 6RJ UK
| | - Sarah Morton
- Centre for Clinical Brain Sciences, University of Edinburgh, EH16 4A, Edinburgh, UK
| | - Jessica Hall
- Academic Unit for Ageing and Stroke Research, Leeds Institute of Health Sciences, University of Leeds, Bradford, BD9 6RJ UK.,Academic Unit for Ageing and Stroke Research, Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, BD9 6RJ UK
| | - David J Clarke
- Academic Unit for Ageing and Stroke Research, Leeds Institute of Health Sciences, University of Leeds, Bradford, BD9 6RJ UK
| | - Claire F Fitzsimons
- Physical Activity for Health Research Centre, St Leonards Land, Holyrood Road, Edinburgh, EH8 8AQ UK
| | - Coralie English
- School of Health Sciences and Priority Research Centre for Stroke and Brain Injury, University of Newcastle, Newcastle, Australia
| | - Anne Forster
- Academic Unit for Ageing and Stroke Research, Leeds Institute of Health Sciences, University of Leeds, Bradford, BD9 6RJ UK
| | - Gillian E Mead
- Centre for Clinical Brain Sciences, University of Edinburgh, EH16 4A, Edinburgh, UK
| | - Rebecca Lawton
- School of Psychology, University of Leeds, Leeds, LS2 9JT UK
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Li JH, Oh J, Kienesberger S, Kim NY, Clarke DJ, Zechner EL, Crawford JM. Making and Breaking Leupeptin Protease Inhibitors in Pathogenic Gammaproteobacteria. Angew Chem Int Ed Engl 2020; 59:17872-17880. [PMID: 32609431 DOI: 10.1002/anie.202005506] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/29/2020] [Indexed: 12/12/2022]
Abstract
Leupeptin is a bacterial small molecule that is used worldwide as a protease inhibitor. However, its biosynthesis and genetic distribution remain unknown. We identified a family of leupeptins in gammaproteobacterial pathogens, including Photorhabdus, Xenorhabdus, and Klebsiella species, amongst others. Through genetic, metabolomic, and heterologous expression analyses, we established their construction by discretely expressed ligases and accessory enzymes. In Photorhabdus species, a hypothetical protein required for colonizing nematode hosts was established as a new class of proteases. This enzyme cleaved the tripeptide aldehyde protease inhibitors, leading to the formation of "pro-pyrazinones" featuring a hetero-tricyclic architecture. In Klebsiella oxytoca, the pathway was enriched in clinical isolates associated with respiratory tract infections. Thus, the bacterial production and proteolytic degradation of leupeptins can be associated with animal colonization phenotypes.
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Affiliation(s)
- Jhe-Hao Li
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA.,Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Joonseok Oh
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA.,Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
| | | | - Nam Yoon Kim
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA.,Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - David J Clarke
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Ellen L Zechner
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria.,BioTechMed-Graz, 8010, Graz, Austria
| | - Jason M Crawford
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA.,Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA.,Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06536, USA
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38
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Hall J, Morton S, Fitzsimons CF, Hall JF, Corepal R, English C, Forster A, Lawton R, Patel A, Mead G, Clarke DJ. Factors influencing sedentary behaviours after stroke: findings from qualitative observations and interviews with stroke survivors and their caregivers. BMC Public Health 2020; 20:967. [PMID: 32560713 PMCID: PMC7305625 DOI: 10.1186/s12889-020-09113-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 06/15/2020] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Stroke survivors are more sedentary than healthy, age-matched controls, independent of functional capacity. Interventions are needed to encourage a reduction in overall sedentary time, and regular breaks in prolonged periods of sedentary behaviour. This study captured the views and experiences of stroke survivors and their caregivers related to sedentary behaviour after stroke, to inform the development of an intervention to reduce sedentary behaviour. METHODS Mixed-methods qualitative study. Non-participant observations were completed in two stroke services, inclusive of inpatient and community settings in the United Kingdom. Semi-structured interviews were conducted with stroke survivors and their caregivers (if available) at six- or nine-months post-stroke. Underpinned by the capability, opportunity and motivation (COM-B) model of behaviour change, observational data (132 h) were analysed thematically and interview data (n = 31 stroke survivors, n = 12 caregivers) were analysed using the Framework approach. RESULTS Observation participants differed in functional ability whereas stroke survivor interviewees were all ambulant. Six themes related to sedentary behaviour after stroke were generated: (1) sedentary behaviour levels and patterns after stroke; (2) the physical and social environment in the stroke service and in the home; (3) standing and movement capability after stroke; (4) emotion and motivation after stroke; (5) caregivers' influence on, and role in influencing stroke survivors' sedentary behaviour; and (6) intervening to reduce sedentary behaviour after stroke. Capability, opportunity and motivation were influenced by the impact of the stroke and caregivers' inclination to support sedentary behaviour reduction. Stroke survivors reported being more sedentary than they were pre-stroke due to impaired balance and co-ordination, increased fatigue, and reduced confidence in mobilising. Caregivers inclination to support stroke survivors to reduce sedentary behaviour depended on factors including their willingness to withdraw from the caregiver role, and their perception of whether the stroke survivor would act on their encouragement. CONCLUSIONS Many stroke survivors indicate being open to reducing sedentary behaviour, with appropriate support from stroke service staff and caregivers. The findings from this study have contributed to an intervention development process using the Behaviour Change Wheel (BCW) approach to develop strategies to reduce sedentary behaviour after stroke.
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Affiliation(s)
- Jennifer Hall
- Academic Unit for Ageing and Stroke Research, University of Leeds, Bradford Royal Infirmary, Bradford, BD9 6RJ, UK. .,Bradford Institute for Health Research, Bradford Teaching Hospitals Foundation Trust, Bradford, UK.
| | - Sarah Morton
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Claire F Fitzsimons
- Physical Activity for Health Research Centre, University of Edinburgh, Edinburgh, UK
| | - Jessica Faye Hall
- Academic Unit for Ageing and Stroke Research, University of Leeds, Bradford Royal Infirmary, Bradford, BD9 6RJ, UK.,Bradford Institute for Health Research, Bradford Teaching Hospitals Foundation Trust, Bradford, UK
| | - Rekesh Corepal
- Academic Unit for Ageing and Stroke Research, University of Leeds, Bradford Royal Infirmary, Bradford, BD9 6RJ, UK.,Bradford Institute for Health Research, Bradford Teaching Hospitals Foundation Trust, Bradford, UK
| | - Coralie English
- School of Health Sciences and Priority Research Centre for Stroke and Brain Injury, University of Newcastle, Newcastle, Australia
| | - Anne Forster
- Academic Unit for Ageing and Stroke Research, University of Leeds, Bradford Royal Infirmary, Bradford, BD9 6RJ, UK
| | | | - Anita Patel
- Anita Patel Health Economics Consulting Ltd, London, UK
| | - Gillian Mead
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - David J Clarke
- Academic Unit for Ageing and Stroke Research, University of Leeds, Bradford Royal Infirmary, Bradford, BD9 6RJ, UK
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39
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Gebrezgiabher M, Zalloum WA, Clarke DJ, Miles SM, Fedorova AA, Zenkova MA, Bichenkova EV. RNA knockdown by synthetic peptidyl-oligonucleotide ribonucleases: behavior of recognition and cleavage elements under physiological conditions. J Biomol Struct Dyn 2020; 39:2555-2574. [PMID: 32248755 DOI: 10.1080/07391102.2020.1751711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Sequence-specific protein-based ribonucleases are not found in nature. Absolute sequence selectivity in RNA cleavage in vivo normally requires multi-component complexes that recruit a guide RNA or DNA for target recognition and a protein-RNA assembly for catalytic functioning (e.g. RNAi molecular machinery, RNase H). Recently discovered peptidyl-oligonucleotide synthetic ribonucleases selectively knock down pathogenic RNAs by irreversible cleavage to offer unprecedented opportunities for control of disease-relevant RNA. Understanding how to increase their potency, selectivity and catalytic turnover will open the translational pathway to successful therapeutics. Yet, very little is known about how these chemical ribonucleases bind, cleave and leave their target. Rational design awaits this understanding in order to control therapy, particularly how to overcome the trade-off between sequence specificity and potency through catalytic turnover. We illuminate this here by characterizing the interactions of these chemical RNases with both complementary and non-complementary RNAs using Tm profiles, fluorescence, UV-visible and NMR spectroscopies. Crucially, the level of counter cations, which are tightly-controlled within cellular compartments, also controlled these interactions. The oligonucleotide component dominated interaction between conjugates and complementary targets in the presence of physiological levels of counter cations (K+), sufficient to prevent repulsion between the complementary nucleic acid strands to allow Watson-Crick hydrogen bonding. In contrast, the positively-charged catalytic peptide interacted poorly with target RNA, when counter cations similarly screened the negatively-charged sugar-phosphate RNA backbones. The peptide only became the key player, when counter cations were insufficient for charge screening; moreover, only under such non-physiological conditions did conjugates form strong complexes with non-complementary RNAs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mengisteab Gebrezgiabher
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Waleed A Zalloum
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - David J Clarke
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Steven M Miles
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Antonina A Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena V Bichenkova
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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40
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Abstract
Different model systems have, over the years, contributed to our current understanding of the molecular mechanisms underpinning the various types of interaction between bacteria and their animal hosts. The genus
Photorhabdus
comprises Gram-negative insect pathogenic bacteria that are normally found as symbionts that colonize the gut of the infective juvenile stage of soil-dwelling nematodes from the family Heterorhabditis. The nematodes infect susceptible insects and release the bacteria into the insect haemolymph where the bacteria grow, resulting in the death of the insect. At this stage the nematodes feed on the bacterial biomass and, following several rounds of reproduction, the nematodes develop into infective juveniles that leave the insect cadaver in search of new hosts. Therefore
Photorhabdus
has three distinct and obligate roles to play during this life-cycle: (1)
Photorhabdus
must kill the insect host; (2)
Photorhabdus
must be capable of supporting nematode growth and development; and (3)
Photorhabdus
must be able to colonize the gut of the next generation of infective juveniles before they leave the insect cadaver. In this review I will discuss how genetic analysis has identified key genes involved in mediating, and regulating, the interaction between
Photorhabdus
and each of its invertebrate hosts. These studies have resulted in the characterization of several new families of toxins and a novel inter-kingdom signalling molecule and have also uncovered an important role for phase variation in the regulation of these different roles.
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Affiliation(s)
- David J Clarke
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
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41
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Ross J, Lambert T, Piergentili C, He D, Waldron KJ, Mackay CL, Marles-Wright J, Clarke DJ. Mass spectrometry reveals the assembly pathway of encapsulated ferritins and highlights a dynamic ferroxidase interface. Chem Commun (Camb) 2020; 56:3417-3420. [PMID: 32090213 DOI: 10.1039/c9cc08130e] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Encapsulated ferritins (EncFtn) are a recently characterised member of the ferritin superfamily. EncFtn proteins are sequestered within encapsulin nanocompartments and form a unique biological iron storage system. Here, we use native mass spectrometry and hydrogen-deuterium exchange mass spectrometry to elucidate the metal-mediated assembly pathway of EncFtn.
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Affiliation(s)
- Jennifer Ross
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, Scotland, UK.
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42
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Gallagher KJ, Palasser M, Hughes S, Mackay CL, Kilgour DPA, Clarke DJ. Isotope Depletion Mass Spectrometry (ID-MS) for Accurate Mass Determination and Improved Top-Down Sequence Coverage of Intact Proteins. J Am Soc Mass Spectrom 2020; 31:700-710. [PMID: 32003978 DOI: 10.1021/jasms.9b00119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Top-down mass spectrometry (MS) is an increasingly important technique for protein characterization. However, in many biological MS experiments, the practicality of applying top-down methodologies is still limited at higher molecular mass. In large part, this is due to the detrimental effect resulting from the partitioning of the mass spectral signal into an increasing number of isotopic peaks as molecular mass increases. Reducing the isotopologue distribution of proteins via depletion of heavy stable isotopes was first reported over 20 years ago (Marshall, A. G.; Senko, M. W.; Li, W.; Li, M.; Dillon, S., Guan, S.; Logan, T. M.. Protein Molecular Mass to 1 Da by 13C, 15N Double-Depletion and FT-ICR Mass Spectrometry. J. Am. Chem. Soc. 1997, 119, 433-434.) and has been demonstrated for several small proteins. Here we extend this approach, introducing a new highly efficient method for the production of recombinant proteins depleted in 13C and 15N and demonstrating its advantages for top-down analysis of larger proteins (up to ∼50 kDa). FT-ICR MS of isotopically depleted proteins reveals dramatically reduced isotope distributions with monoisotopic signal observed up to 50 kDa. In top-down fragmentation experiments, the reduced spectral complexity alleviates fragment-ion signal overlap, the presence of monoisotopic signals allows assignment with higher mass accuracy, and the dramatic increase in signal-to-noise ratio (up to 7-fold) permits vastly reduced acquisition times. These compounding benefits allow the assignment of ∼3-fold more fragment ions than comparable analyses of proteins with natural isotopic abundances. Finally, we demonstrate greatly increased sequence coverage in time-limited top-down experiments-highlighting advantages for top-down LC-MS/MS workflows and top-down proteomics.
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Affiliation(s)
- Kelly J Gallagher
- The EastChem School of Chemistry, University of Edinburgh, Joseph Black Building, Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Michael Palasser
- The EastChem School of Chemistry, University of Edinburgh, Joseph Black Building, Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Sam Hughes
- The EastChem School of Chemistry, University of Edinburgh, Joseph Black Building, Brewster Road, Edinburgh EH9 3FJ, U.K
| | - C Logan Mackay
- The EastChem School of Chemistry, University of Edinburgh, Joseph Black Building, Brewster Road, Edinburgh EH9 3FJ, U.K
| | - David P A Kilgour
- Chemistry and Forensics, Nottingham Trent University, Rosalind Franklin Building, Clifton Lane, Nottingham NG11 8NS, U.K
| | - David J Clarke
- The EastChem School of Chemistry, University of Edinburgh, Joseph Black Building, Brewster Road, Edinburgh EH9 3FJ, U.K
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43
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Veale CGL, Mateos Jimenez M, Mackay CL, Clarke DJ. Native ion mobility mass spectrometry reveals that small organic acid fragments impart gas-phase stability to carbonic anhydrase II. Rapid Commun Mass Spectrom 2020; 34:e8570. [PMID: 31479545 DOI: 10.1002/rcm.8570] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/25/2019] [Accepted: 08/28/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE A key element of studies that utilise ion mobility mass spectrometry (IM-MS) under native electrospray conditions for the analysis of protein-ligand binding is the maintenance of the native conformation of a protein during the removal of bulk solvent. Ruotolo and co-workers have demonstrated that the binding and subsequent dissociation of the anionic component of inorganic salts stabilise native protein conformations in the gas phase. In this study, we investigated the effect that organic acid fragments identified from a fragment-based drug discovery (FBDD) campaign might have on the gas-phase stability of carbonic anhydrase II (CA II). METHODS We utilised native IM-MS to monitor changes in the conformation of CA II in the absence and presence of four acidic fragments. By performing a series of collision-induced unfolding (CIU) experiments we determined the effect of fragment binding on the gas-phase stability of CA II. RESULTS Binding and dissociation of acidic fragments result in increased gas-phase stability of CA II. CFU experiments revealed that the native-like compact gas-phase conformation of the protein is stable with higher degree of pre-activation when bound to a series of acidic fragments. Importantly, although acetate was present in high concentrations, the stabilising effect was not observed without the addition of the acidic fragments. CONCLUSIONS Binding and subsequent dissociation of acidic fragments from CA II significantly delayed CIU in a manner which is probably analogous to the effect of inorganic anions. Furthermore, we saw a slightly altered stabilising effect between the different fragments investigated in this study. This suggests that the prevention of CIU by organic acids may be tuneable to specific properties of a bound ligand. These observations may open avenues to exploit IM-MS as a screening platform in FBDD.
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Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
| | - Maria Mateos Jimenez
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - C Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - David J Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
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44
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O'Donovan SM, Crowley EK, Brown JRM, O'Sullivan O, O'Leary OF, Timmons S, Nolan YM, Clarke DJ, Hyland NP, Joyce SA, Sullivan AM, O'Neill C. Nigral overexpression of α-synuclein in a rat Parkinson's disease model indicates alterations in the enteric nervous system and the gut microbiome. Neurogastroenterol Motil 2020; 32:e13726. [PMID: 31576631 DOI: 10.1111/nmo.13726] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 09/02/2019] [Accepted: 09/02/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND A hallmark feature of Parkinson's disease (PD) is the build-up of α-synuclein protein aggregates throughout the brain; however α-synuclein is also expressed in enteric neurons. Gastrointestinal (GI) symptoms and pathology are frequently reported in PD, including constipation, increased intestinal permeability, glial pathology, and alterations to gut microbiota composition. α-synuclein can propagate through neuronal systems but the site of origin of α-synuclein pathology, whether it be the gut or the brain, is still unknown. Physical exercise is associated with alleviating symptoms of PD and with altering the composition of the gut microbiota. METHODS This study investigated the effects of bilateral nigral injection of adeno-associated virus (AAV)-α-synuclein on enteric neurons, glia and neurochemistry, the gut microbiome, and bile acid metabolism in rats, some of whom were exposed to voluntary exercise. KEY RESULTS Nigral overexpression of α-synuclein resulted in significant neuronal loss in the ileal submucosal plexus with no change in enteric glia. In contrast, the myenteric plexus showed a significant increase in glial expression, while neuronal numbers were maintained. Concomitant alterations were observed in the gut microbiome and related bile acid metabolism. Voluntary running protected against neuronal loss, increased enteric glial expression, and modified gut microbiome composition in the brain-injected AAV-α-synuclein PD model. CONCLUSIONS AND INFERENCES These results show that developing nigral α-synuclein pathology in this PD model exerts significant alterations on the enteric nervous system (ENS) and gut microbiome that are receptive to modification by exercise. This highlights brain to gut communication as an important mechanism in PD pathology.
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Affiliation(s)
- Sarah M O'Donovan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.,Cork Neuroscience Centre, University College Cork, Cork, Ireland
| | - Erin K Crowley
- Cork Neuroscience Centre, University College Cork, Cork, Ireland.,Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | | | - Orla O'Sullivan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Centre Moorepark, Cork, Ireland
| | - Olivia F O'Leary
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Cork Neuroscience Centre, University College Cork, Cork, Ireland.,Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Suzanne Timmons
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Cork Neuroscience Centre, University College Cork, Cork, Ireland.,Centre of Gerontology and Rehabilitation, University College Cork, Cork, Ireland
| | - Yvonne M Nolan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Cork Neuroscience Centre, University College Cork, Cork, Ireland.,Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - David J Clarke
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Niall P Hyland
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Physiology, University College Cork, Cork, Ireland
| | - Susan A Joyce
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Aideen M Sullivan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Cork Neuroscience Centre, University College Cork, Cork, Ireland.,Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Cora O'Neill
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.,Cork Neuroscience Centre, University College Cork, Cork, Ireland
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45
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Hall JF, Crocker TF, Clarke DJ, Forster A. Supporting carers of stroke survivors to reduce carer burden: development of the Preparing is Caring intervention using Intervention Mapping. BMC Public Health 2019; 19:1408. [PMID: 31664985 PMCID: PMC6819539 DOI: 10.1186/s12889-019-7615-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 02/19/2019] [Accepted: 09/12/2019] [Indexed: 01/19/2023] Open
Abstract
Background Burden is well documented among carers of stroke survivors, yet current evidence is insufficient to determine if any strategies reduce this negative outcome. Existing interventions for carers of stroke survivors typically involve supporting carers according to their individual needs through face-to-face interactions and provision of information including workbooks or educational guides. To date, no interventions have been developed using a method which systematically incorporates evidence, behaviour change theories, and stakeholder involvement to change the behaviours of carers and relevant individuals who support carers. This study aimed to develop a programme plan for a theory and evidence-based intervention to reduce burden in carers of stroke survivors. Methods Informed by evidence from two systematic reviews and 33 qualitative interviews, the first four stages of Intervention Mapping were used to guide the intervention development process: 1) needs assessment; 2) identifying outcomes and objectives; 3) selecting theoretical methods and practical applications; and 4) creating a programme plan. Structured and facilitated involvement from stakeholders, including carers, researchers, and professionals from health and community services was integral to the intervention development process. Stakeholders helped to prioritise the focus of the intervention, develop the goals, outcomes and objectives for the programme, and generate and refine intervention ideas. Results Stakeholders prioritised the need for carers to feel prepared before and during the transition from hospital to home as key to reducing burden. The proposed intervention ‘Preparing is Caring’ targets this need and involves providing and signposting carers to relevant information and support for practical and emotional needs. This is to be delivered before, during, and immediately after the stroke survivor’s transition from hospital to home by a person taking on a single point of contact role. It is comprised of multiple theory-based components including: training packages for information and support providers working with carers and wider staff teams, plus elements to support carers to feel prepared. Conclusions We have developed a comprehensive programme plan for a multiple-component, theory and evidence informed behaviour change intervention aimed at preparing carers before and during the transition from hospital to home. Future work is required to refine, implement and evaluate the Preparing is Caring intervention.
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Affiliation(s)
- Jessica F Hall
- Academic Unit of Elderly Care and Rehabilitation, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK. .,Academic Unit of Elderly Care and Rehabilitation, Leeds Institute of Health Sciences, University of Leeds, Leeds, UK.
| | - Thomas F Crocker
- Academic Unit of Elderly Care and Rehabilitation, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK.,Academic Unit of Elderly Care and Rehabilitation, Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | - David J Clarke
- Academic Unit of Elderly Care and Rehabilitation, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK.,Academic Unit of Elderly Care and Rehabilitation, Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | - Anne Forster
- Academic Unit of Elderly Care and Rehabilitation, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK.,Academic Unit of Elderly Care and Rehabilitation, Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
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46
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Atkinson N, Velanis CN, Wunder T, Clarke DJ, Mueller-Cajar O, McCormick AJ. The pyrenoidal linker protein EPYC1 phase separates with hybrid Arabidopsis-Chlamydomonas Rubisco through interactions with the algal Rubisco small subunit. J Exp Bot 2019; 70:5271-5285. [PMID: 31504763 PMCID: PMC6793452 DOI: 10.1093/jxb/erz275] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 03/07/2019] [Accepted: 06/13/2019] [Indexed: 05/21/2023]
Abstract
Photosynthetic efficiencies in plants are restricted by the CO2-fixing enzyme Rubisco but could be enhanced by introducing a CO2-concentrating mechanism (CCM) from green algae, such as Chlamydomonas reinhardtii (hereafter Chlamydomonas). A key feature of the algal CCM is aggregation of Rubisco in the pyrenoid, a liquid-like organelle in the chloroplast. Here we have used a yeast two-hybrid system and higher plants to investigate the protein-protein interaction between Rubisco and essential pyrenoid component 1 (EPYC1), a linker protein required for Rubisco aggregation. We showed that EPYC1 interacts with the small subunit of Rubisco (SSU) from Chlamydomonas and that EPYC1 has at least five SSU interaction sites. Interaction is crucially dependent on the two surface-exposed α-helices of the Chlamydomonas SSU. EPYC1 could be localized to the chloroplast in higher plants and was not detrimental to growth when expressed stably in Arabidopsis with or without a Chlamydomonas SSU. Although EPYC1 interacted with Rubisco in planta, EPYC1 was a target for proteolytic degradation. Plants expressing EPYC1 did not show obvious evidence of Rubisco aggregation. Nevertheless, hybrid Arabidopsis Rubisco containing the Chlamydomonas SSU could phase separate into liquid droplets with purified EPYC1 in vitro, providing the first evidence of pyrenoid-like aggregation for Rubisco derived from a higher plant.
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Affiliation(s)
- Nicky Atkinson
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Christos N Velanis
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Tobias Wunder
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - David J Clarke
- School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Alistair J McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Correspondence:
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Payelleville A, Blackburn D, Lanois A, Pagès S, Cambon MC, Ginibre N, Clarke DJ, Givaudan A, Brillard J. Role of the Photorhabdus Dam methyltransferase during interactions with its invertebrate hosts. PLoS One 2019; 14:e0212655. [PMID: 31596856 PMCID: PMC6785176 DOI: 10.1371/journal.pone.0212655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 02/05/2019] [Accepted: 09/20/2019] [Indexed: 11/19/2022] Open
Abstract
Photorhabdus luminescens is an entomopathogenic bacterium found in symbiosis with the nematode Heterorhabditis. Dam DNA methylation is involved in the pathogenicity of many bacteria, including P. luminescens, whereas studies about the role of bacterial DNA methylation during symbiosis are scarce. The aim of this study was to determine the role of Dam DNA methylation in P. luminescens during the whole bacterial life cycle including during symbiosis with H. bacteriophora. We constructed a strain overexpressing dam by inserting an additional copy of the dam gene under the control of a constitutive promoter in the chromosome of P. luminescens and then achieved association between this recombinant strain and nematodes. The dam overexpressing strain was able to feed the nematode in vitro and in vivo similarly as a control strain, and to re-associate with Infective Juvenile (IJ) stages in the insect. No difference in the amount of emerging IJs from the cadaver was observed between the two strains. Compared to the nematode in symbiosis with the control strain, a significant increase in LT50 was observed during insect infestation with the nematode associated with the dam overexpressing strain. These results suggest that during the life cycle of P. luminescens, Dam is not involved the bacterial symbiosis with the nematode H. bacteriophora, but it contributes to the pathogenicity of the nemato-bacterial complex.
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Affiliation(s)
| | - Dana Blackburn
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Anne Lanois
- DGIMI, INRA, Univ. Montpellier, Montpellier, France
| | - Sylvie Pagès
- DGIMI, INRA, Univ. Montpellier, Montpellier, France
| | - Marine C. Cambon
- DGIMI, INRA, Univ. Montpellier, Montpellier, France
- Évolution et Diversité Biologique, CNRS, UPS Université Paul Sabatier, Toulouse, France
| | | | - David J. Clarke
- Department of Microbiology, University College Cork, Cork, Ireland
| | | | - Julien Brillard
- DGIMI, INRA, Univ. Montpellier, Montpellier, France
- * E-mail: (JB); (AP)
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48
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Rawlings GH, Williams RK, Clarke DJ, English C, Fitzsimons C, Holloway I, Lawton R, Mead G, Patel A, Forster A. Exploring adults' experiences of sedentary behaviour and participation in non-workplace interventions designed to reduce sedentary behaviour: a thematic synthesis of qualitative studies. BMC Public Health 2019; 19:1099. [PMID: 31409324 PMCID: PMC6692932 DOI: 10.1186/s12889-019-7365-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 11/19/2018] [Accepted: 07/24/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Sedentary behaviour is any waking behaviour characterised by an energy expenditure of ≤1.5 metabolic equivalent of task while in a sitting or reclining posture. Prolonged bouts of sedentary behaviour have been associated with negative health outcomes in all age groups. We examined qualitative research investigating perceptions and experiences of sedentary behaviour and of participation in non-workplace interventions designed to reduce sedentary behaviour in adult populations. METHOD A systematic search of seven databases (MEDLINE, AMED, Cochrane, PsychINFO, SPORTDiscus, CINAHL and Web of Science) was conducted in September 2017. Studies were assessed for methodological quality and a thematic synthesis was conducted. Prospero database ID: CRD42017083436. RESULTS Thirty individual studies capturing the experiences of 918 individuals were included. Eleven studies examined experiences and/or perceptions of sedentary behaviour in older adults (typically ≥60 years); ten studies focused on sedentary behaviour in people experiencing a clinical condition, four explored influences on sedentary behaviour in adults living in socio-economically disadvantaged communities, two examined university students' experiences of sedentary behaviour, two on those of working-age adults, and one focused on cultural influences on sedentary behaviour. Three analytical themes were identified: 1) the impact of different life stages on sedentary behaviour 2) lifestyle factors influencing sedentary behaviour and 3) barriers and facilitators to changing sedentary behaviour. CONCLUSIONS Sedentary behaviour is multifaceted and influenced by a complex interaction between individual, environmental and socio-cultural factors. Micro and macro pressures are experienced at different life stages and in the context of illness; these shape individuals' beliefs and behaviour related to sedentariness. Knowledge of sedentary behaviour and the associated health consequences appears limited in adult populations, therefore there is a need for provision of accessible information about ways in which sedentary behaviour reduction can be integrated in people's daily lives. Interventions targeting a reduction in sedentary behaviour need to consider the multiple influences on sedentariness when designing and implementing interventions.
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Affiliation(s)
- G H Rawlings
- Department of Clinical Psychology, University of Sheffield, Sheffield, UK
| | - R K Williams
- Academic Unit of Elderly Care and Rehabilitation, Leeds Institute of Health Sciences, Temple Bank House, University of Leeds, Bradford Royal Infirmary, Bradford, BD9 6RJ, UK
| | - D J Clarke
- Academic Unit of Elderly Care and Rehabilitation, Leeds Institute of Health Sciences, Temple Bank House, University of Leeds, Bradford Royal Infirmary, Bradford, BD9 6RJ, UK.
| | - C English
- School of Health Sciences and Priority Research Centre for Stroke and Brain Injury, University of Newcastle, Newcastle, Australia
| | - C Fitzsimons
- Physical Activity for Health Research Centre, University of Edinburgh, Edinburgh, UK
| | - I Holloway
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - R Lawton
- School of Psychology, University of Leeds, Leeds, UK
| | - G Mead
- Geriatric Medicine, Division of Health Sciences, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - A Patel
- Anita Patel Health Economics Consulting Ltd, London, UK
| | - A Forster
- Academic Unit of Elderly Care and Rehabilitation, Leeds Institute of Health Sciences, Temple Bank House, University of Leeds, Bradford Royal Infirmary, Bradford, BD9 6RJ, UK
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49
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Patutina OA, Miroshnichenko SK, Mironova NL, Sen'kova AV, Bichenkova EV, Clarke DJ, Vlassov VV, Zenkova MA. Catalytic Knockdown of miR-21 by Artificial Ribonuclease: Biological Performance in Tumor Model. Front Pharmacol 2019; 10:879. [PMID: 31456683 PMCID: PMC6698794 DOI: 10.3389/fphar.2019.00879] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/10/2019] [Indexed: 12/25/2022] Open
Abstract
Control of the expression of oncogenic small non-coding RNAs, notably microRNAs (miRNAs), is an attractive therapeutic approach. We report a design platform for catalytic knockdown of miRNA targets with artificial, sequence-specific ribonucleases. miRNases comprise a peptide [(LeuArg)2Gly]2 capable of RNA cleavage conjugated to the miRNA-targeted oligodeoxyribonucleotide, which becomes nuclease-resistant within the conjugate design, without resort to chemically modified nucleotides. Our data presented here showed for the first time a truly catalytic character of our miR-21-miRNase and its ability to cleave miR-21 in a multiple catalytic turnover mode. We demonstrate that miRNase targeted to miR-21 (miR-21-miRNase) knocked down malignant behavior of tumor cells, including induction of apoptosis, inhibition of cell invasiveness, and retardation of tumor growth, which persisted on transplantation into mice of tumor cells treated once with miR-21-miRNase. Crucially, we discover that the high biological activity of miR-21-miRNase can be directly related not only to its truly catalytic sequence-specific cleavage of miRNA but also to its ability to recruit the non-sequence specific RNase H found in most cells to elevate catalytic turnover further. miR-21-miRNase worked synergistically even with low levels of RNase H. Estimated degradation in the presence of RNase H exceeded 103 miRNA target molecules per hour for each miR-21-miRNase molecule, which provides the potency to minimize delivery requirements to a few molecules per cell. In contrast to the comparatively high doses required for the simple steric block of antisense oligonucleotides, truly catalytic inactivation of miRNA offers more effective, irreversible, and persistent suppression of many copy target sequences. miRNase design can be readily adapted to target other pathogenic microRNAs overexpressed in many disease states.
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Affiliation(s)
- Olga A Patutina
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Svetlana K Miroshnichenko
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Nadezhda L Mironova
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Aleksandra V Sen'kova
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Elena V Bichenkova
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - David J Clarke
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Valentin V Vlassov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Marina A Zenkova
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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50
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Yousaf S, King PJS, Miller AF, Saiani A, Clarke DJ, Trivoluzzi LT, Aojula HS, Bichenkova EV. Sequence-Specific Detection of Unlabeled Nucleic Acid Biomarkers Using a "One-Pot" 3D Molecular Sensor. Anal Chem 2019; 91:10016-10025. [PMID: 31246004 PMCID: PMC6745626 DOI: 10.1021/acs.analchem.9b01841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 04/15/2019] [Accepted: 06/27/2019] [Indexed: 01/18/2023]
Abstract
DNA and RNA biomarkers have not progressed beyond the automated specialized clinic due to failure in the reproducibility necessary to standardize robust and rapid nucleic acid detection at the point of care, where health outcomes can be most improved by early-stage diagnosis and precise monitoring of therapy and disease prognosis. We demonstrate here a new analytical platform to meet this challenge using functional 3D hydrogels engineered from peptide and oligonucleotide building blocks to provide sequence-specific, PCR-free fluorescent detection of unlabeled nucleic acid sequences. We discriminated at picomolar detection limits (<7 pM) "perfect-match" from mismatched sequences, down to a single nucleotide mutation, buried within longer lengths of the target. Detailed characterization by NMR, TEM, mass spectrometry, and rheology provided the structural understanding to design these hybrid peptide-oligonucleotide biomaterials with the desired sequence sensitivity and detection limit. We discuss the generic design, which is based on a highly predictable secondary structure of the oligonucleotide components, as a platform to detect genetic abnormalities and to screen for pathogenic conditions at the level of both DNA (e.g., SNPs) and RNA (messenger, micro, and viral genomic RNA).
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Affiliation(s)
- Sameen Yousaf
- School
of Health Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, U.K.
| | - Patrick J. S. King
- School
of Health Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, U.K.
| | - Aline F. Miller
- Manchester
Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Alberto Saiani
- Manchester
Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - David J. Clarke
- School
of Health Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, U.K.
| | - Linda T. Trivoluzzi
- School
of Health Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, U.K.
| | - Harmesh S. Aojula
- School
of Health Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, U.K.
| | - Elena V. Bichenkova
- School
of Health Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, U.K.
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