1
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Hulme CH, Fuller HR, Riddell J, Shirran SL, Botting CH, Osman A, Wright KT. Investigation of the blood proteome in response to spinal cord injury in rodent models. Spinal Cord 2021; 60:320-325. [PMID: 34601498 PMCID: PMC8989679 DOI: 10.1038/s41393-021-00692-8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022]
Abstract
Study design Explanatory and mechanistic study. Objectives A better understanding of the ‘whole-body’ response following spinal cord injury (SCI) is needed to guide future research aimed at developing novel therapeutic interventions and identifying prognostic indicators for SCI. This study aimed to characterise the blood proteome following contusion or complete SCI compared to a sham injury in rat models. Setting United Kingdom. Methods Pooled blood samples from one and seven days after a contusion (serum; n = 5) or from 14 days and 112 days post-complete transection SCI (plasma; n = 8) and their sham-injured counterparts were subjected to independent iTRAQ nanoflow liquid chromatography tandem mass-spectrometry proteomic analyses. Pathway analyses of the proteins that were differentially abundant between SCI and their matched sham injured counterparts were completed to indicate biological pathways that may be changed in response to SCI. Results Eleven and 42 proteins were differentially abundant (≥±2.0 FC; p ≤ 0.05) between the contusion SCI and sham injured animals at 24 h and seven days post-injury, respectively. Seven and tweleve proteins were differentially abundant between complete and sham injured rats at 14 and 112 days post-injury, respectively. Acute-phase response signalling and Liver X Receptor/Retinoic X Receptor activation were identified as differentially regulated pathways in both models of SCI. Conclusions We have utilised longitudinal preclinical SCI models to provide an insight into the blood proteome changes that result following SCI and to highlight a number of biological pathways of interest for future studies.
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Affiliation(s)
- Charlotte H Hulme
- School of Pharmacy and Bioengineering, Keele University, Keele, Staffordshire, UK.,Midlands Centre for Spinal Injuries, RJAH Orthopaedic Hospital, Oswestry, Shropshire, UK
| | - Heidi R Fuller
- School of Pharmacy and Bioengineering, Keele University, Keele, Staffordshire, UK
| | - John Riddell
- Institute of Neuroscience and Psychology, University of Glasgow, Glasgow, UK
| | - Sally L Shirran
- BSRC Mass Spectrometry and Proteomics Facility, University of St Andrews, North Haugh, St Andrews, UK
| | - Catherine H Botting
- BSRC Mass Spectrometry and Proteomics Facility, University of St Andrews, North Haugh, St Andrews, UK
| | - Aheed Osman
- Midlands Centre for Spinal Injuries, RJAH Orthopaedic Hospital, Oswestry, Shropshire, UK
| | - Karina T Wright
- School of Pharmacy and Bioengineering, Keele University, Keele, Staffordshire, UK. .,Midlands Centre for Spinal Injuries, RJAH Orthopaedic Hospital, Oswestry, Shropshire, UK.
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2
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Beiersdorf J, Hevesi Z, Calvigioni D, Pyszkowski J, Romanov R, Szodorai E, Lubec G, Shirran S, Botting CH, Kasper S, Guy GW, Gray R, Di Marzo V, Harkany T, Keimpema E. Adverse effects of Δ9-tetrahydrocannabinol on neuronal bioenergetics during postnatal development. JCI Insight 2020; 5:135418. [PMID: 33141759 PMCID: PMC7714410 DOI: 10.1172/jci.insight.135418] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 10/28/2020] [Indexed: 11/22/2022] Open
Abstract
Ongoing societal changes in views on the medical and recreational roles of cannabis increased the use of concentrated plant extracts with a Δ9-tetrahydrocannabinol (THC) content of more than 90%. Even though prenatal THC exposure is widely considered adverse for neuronal development, equivalent experimental data for young age cohorts are largely lacking. Here, we administered plant-derived THC (1 or 5 mg/kg) to mice daily during P5–P16 and P5–P35 and monitored its effects on hippocampal neuronal survival and specification by high-resolution imaging and iTRAQ proteomics, respectively. We found that THC indiscriminately affects pyramidal cells and both cannabinoid receptor 1+ (CB1R)+ and CB1R– interneurons by P16. THC particularly disrupted the expression of mitochondrial proteins (complexes I–IV), a change that had persisted even 4 months after the end of drug exposure. This was reflected by a THC-induced loss of membrane integrity occluding mitochondrial respiration and could be partially or completely rescued by pH stabilization, antioxidants, bypassed glycolysis, and targeting either mitochondrial soluble adenylyl cyclase or the mitochondrial voltage-dependent anion channel. Overall, THC exposure during infancy induces significant and long-lasting reorganization of neuronal circuits through mechanisms that, in large part, render cellular bioenergetics insufficient to sustain key developmental processes in otherwise healthy neurons. Repeated THC exposure in juvenile mice compromises the limbic circuitry, with life-long impairment to the respiration of neurons.
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Affiliation(s)
- Johannes Beiersdorf
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Zsofia Hevesi
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Daniela Calvigioni
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | | | - Roman Romanov
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Edit Szodorai
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Gert Lubec
- Paracelsus Private Medical University, Salzburg, Austria
| | - Sally Shirran
- School of Chemistry, University of St. Andrews, St. Andrews, United Kingdom
| | | | - Siegfried Kasper
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | | | - Roy Gray
- GW Phamaceuticals, Salisbury, Wiltshire, United Kingdom
| | - Vincenzo Di Marzo
- Endocannabinoid Research Group, Institute of Biomolecular Chemistry, Consiglio Nazionale delle Ricerche, Pozzuoli, Italy.,Canada Excellence Research Chair, Institut Universitaire de Cardiologie et de Pneumologie de Québec and Institut sur la Nutrition et les Aliments Fonctionnels, Université Laval, Québec, Québec, Canada
| | - Tibor Harkany
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria.,Department of Neuroscience, Biomedikum D7, Karolinska Institutet, Solna, Sweden
| | - Erik Keimpema
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
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3
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Cinquina V, Calvigioni D, Farlik M, Halbritter F, Fife-Gernedl V, Shirran SL, Fuszard MA, Botting CH, Poullet P, Piscitelli F, Máté Z, Szabó G, Yanagawa Y, Kasper S, Di Marzo V, Mackie K, McBain CJ, Bock C, Keimpema E, Harkany T. Life-long epigenetic programming of cortical architecture by maternal 'Western' diet during pregnancy. Mol Psychiatry 2020; 25:22-36. [PMID: 31735910 DOI: 10.1038/s41380-019-0580-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 10/11/2019] [Accepted: 10/24/2019] [Indexed: 01/08/2023]
Abstract
The evolution of human diets led to preferences toward polyunsaturated fatty acid (PUFA) content with 'Western' diets enriched in ω-6 PUFAs. Mounting evidence points to ω-6 PUFA excess limiting metabolic and cognitive processes that define longevity in humans. When chosen during pregnancy, ω-6 PUFA-enriched 'Western' diets can reprogram maternal bodily metabolism with maternal nutrient supply precipitating the body-wide imprinting of molecular and cellular adaptations at the level of long-range intercellular signaling networks in the unborn fetus. Even though unfavorable neurological outcomes are amongst the most common complications of intrauterine ω-6 PUFA excess, cellular underpinnings of life-long modifications to brain architecture remain unknown. Here, we show that nutritional ω-6 PUFA-derived endocannabinoids desensitize CB1 cannabinoid receptors, thus inducing epigenetic repression of transcriptional regulatory networks controlling neuronal differentiation. We found that cortical neurons lose their positional identity and axonal selectivity when mouse fetuses are exposed to excess ω-6 PUFAs in utero. Conversion of ω-6 PUFAs into endocannabinoids disrupted the temporal precision of signaling at neuronal CB1 cannabinoid receptors, chiefly deregulating Stat3-dependent transcriptional cascades otherwise required to execute neuronal differentiation programs. Global proteomics identified the immunoglobulin family of cell adhesion molecules (IgCAMs) as direct substrates, with DNA methylation and chromatin accessibility profiling uncovering epigenetic reprogramming at >1400 sites in neurons after prolonged cannabinoid exposure. We found anxiety and depression-like behavioral traits to manifest in adult offspring, which is consistent with genetic models of reduced IgCAM expression, to suggest causality for cortical wiring defects. Overall, our data uncover a regulatory mechanism whose disruption by maternal food choices could limit an offspring's brain function for life.
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Affiliation(s)
- Valentina Cinquina
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Daniela Calvigioni
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Florian Halbritter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Victoria Fife-Gernedl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sally L Shirran
- School of Chemistry, University of St. Andrews, St. Andrews, United Kingdom
| | - Matthew A Fuszard
- School of Chemistry, University of St. Andrews, St. Andrews, United Kingdom.,Faculty of Medicine, Martin-Luther University, Halle-Wittenberg, Halle, Germany
| | | | | | - Fabiana Piscitelli
- Endocannabinoid Research Group, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Pozzuoli, Italy
| | - Zoltán Máté
- Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary
| | - Gábor Szabó
- Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary
| | - Yuchio Yanagawa
- Department of Genetic and Behavioral Neuroscience, Gunma University School of Medicine, Maebashi, Japan
| | - Siegfried Kasper
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Vincenzo Di Marzo
- Endocannabinoid Research Group, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Pozzuoli, Italy.,Canada Excellence Research Chair, Institut Universitaire de Cardiologie et de Pneumologie de Québec and Institut sur la Nutrition et les Aliments Fonctionnels, Université Laval, Québec, QC, Canada
| | - Ken Mackie
- Department of Psychological & Brain Sciences, Indiana University, Bloomington, Indiana, USA
| | - Chris J McBain
- Program in Developmental Neuroscience, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, NIH, Bethesda, USA
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Erik Keimpema
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Tibor Harkany
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria. .,Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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4
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Abstract
![]()
Cyanobactin
heterocyclases share the same catalytic domain (YcaO)
as heterocyclases/cyclodehydratases from other ribosomal peptide (RiPPs)
biosynthetic pathways. These enzymes process multiple residues (Cys/Thr/Ser)
within the same substrate. The processing of cysteine residues proceeds
with a known order. We show the order of reaction for threonines is
different and depends in part on a leader peptide within the substrate.
In contrast to other YcaO domains, which have been reported to exclusively
break down ATP into ADP and inorganic phosphate, cyanobactin heterocyclases
have been observed to produce AMP and inorganic pyrophosphate during
catalysis. We dissect the nucleotide profiles associated with heterocyclization
and propose a unifying mechanism, where the γ-phosphate of ATP
is transferred in a kinase mechanism to the substrate to yield a phosphorylated
intermediate common to all YcaO domains. In cyanobactin heterocyclases,
this phosphorylated intermediate, in a proportion of turnovers, reacts
with ADP to yield AMP and pyrophosphate.
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Affiliation(s)
- Ying Ge
- Biomedical Sciences Research Complex , University of St Andrews , St Andrews, Fife KY16 9ST , United Kingdom
| | - Clarissa Melo Czekster
- Biomedical Sciences Research Complex , University of St Andrews , St Andrews, Fife KY16 9ST , United Kingdom
| | - Ona K Miller
- Biomedical Sciences Research Complex , University of St Andrews , St Andrews, Fife KY16 9ST , United Kingdom
| | - Catherine H Botting
- Biomedical Sciences Research Complex , University of St Andrews , St Andrews, Fife KY16 9ST , United Kingdom
| | - Ulrich Schwarz-Linek
- Biomedical Sciences Research Complex , University of St Andrews , St Andrews, Fife KY16 9ST , United Kingdom
| | - James H Naismith
- Research Complex at Harwell , Didcot, Oxon OX11 0FA , United Kingdom.,Division of Structural Biology , University of Oxford , Oxford OX3 7BN , United Kingdom.,Rosalind Franklin Institute , Harwell, Didcot, Oxon OX11 0FA , United Kingdom
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5
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Arya S, Wiatrek-Moumoulidis D, Synowsky SA, Shirran SL, Botting CH, Powis SJ, Stewart AJ. Quantitative proteomic changes in LPS-activated monocyte-derived dendritic cells: A SWATH-MS study. Sci Rep 2019; 9:4343. [PMID: 30867486 PMCID: PMC6416353 DOI: 10.1038/s41598-019-40773-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 02/22/2019] [Indexed: 01/20/2023] Open
Abstract
Dendritic cells are key immune cells that respond to pathogens and co-ordinate many innate and adaptive immune responses. Quantitative mass spectrometry using Sequential Window Acquisition of all THeoretical fragment-ion spectra-Mass Spectrometry (SWATH-MS) was performed here to determine the global alterations in monocyte-derived dendritic cells (moDCs) in response to stimulation with lipopolysaccharide (LPS). A moDC library of 4,666 proteins was generated and proteins were quantified at 0, 6 and 24 h post-LPS stimulation using SWATH-MS. At 6 h and 24 h post-LPS exposure, the relative abundance of 227 and 282 proteins was statistically significantly altered (p-value ≤ 0.05), respectively. Functional annotation of proteins exhibiting significant changes in expression between the various time points led to the identification of clusters of proteins implicated in distinct cellular processes including interferon and interleukin signalling, endocytosis, the ER-phagosome pathway and antigen-presentation. In SWATH-MS major histocompatibility complex (MHC) class I proteins were highly upregulated at 24 h, whilst MHC class II proteins exhibited comparatively fewer changes over this period. This study provides new detailed insight into the global proteomic changes that occur in moDCs during antigen processing and presentation and further demonstrates the potential of SWATH-MS for the quantitative study of proteins involved in cellular processes.
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Affiliation(s)
- Swati Arya
- School of Medicine, University of St Andrews, St Andrews, KY16 9TF, UK.,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Dagmara Wiatrek-Moumoulidis
- School of Medicine, University of St Andrews, St Andrews, KY16 9TF, UK.,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Silvia A Synowsky
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Sally L Shirran
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Catherine H Botting
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Simon J Powis
- School of Medicine, University of St Andrews, St Andrews, KY16 9TF, UK. .,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK.
| | - Alan J Stewart
- School of Medicine, University of St Andrews, St Andrews, KY16 9TF, UK. .,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK.
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6
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Arya S, Emri E, Synowsky SA, Shirran SL, Barzegar-Befroei N, Peto T, Botting CH, Lengyel I, Stewart AJ. Quantitative analysis of hydroxyapatite-binding plasma proteins in genotyped individuals with late-stage age-related macular degeneration. Exp Eye Res 2018; 172:21-29. [DOI: 10.1016/j.exer.2018.03.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/16/2018] [Accepted: 03/22/2018] [Indexed: 12/17/2022]
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7
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Hulme CH, Wilson EL, Fuller HR, Roberts S, Richardson JB, Gallacher P, Peffers MJ, Shirran SL, Botting CH, Wright KT. Two independent proteomic approaches provide a comprehensive analysis of the synovial fluid proteome response to Autologous Chondrocyte Implantation. Arthritis Res Ther 2018; 20:87. [PMID: 29720234 PMCID: PMC5932832 DOI: 10.1186/s13075-018-1573-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/21/2018] [Indexed: 02/06/2023] Open
Abstract
Background Autologous chondrocyte implantation (ACI) has a failure rate of approximately 20%, but it is yet to be fully understood why. Biomarkers are needed that can pre-operatively predict in which patients it is likely to fail, so that alternative or individualised therapies can be offered. We previously used label-free quantitation (LF) with a dynamic range compression proteomic approach to assess the synovial fluid (SF) of ACI responders and non-responders. However, we were able to identify only a few differentially abundant proteins at baseline. In the present study, we built upon these previous findings by assessing higher-abundance proteins within this SF, providing a more global proteomic analysis on the basis of which more of the biology underlying ACI success or failure can be understood. Methods Isobaric tagging for relative and absolute quantitation (iTRAQ) proteomic analysis was used to assess SF from ACI responders (mean Lysholm improvement of 33; n = 14) and non-responders (mean Lysholm decrease of 14; n = 13) at the two stages of surgery (cartilage harvest and chondrocyte implantation). Differentially abundant proteins in iTRAQ and combined iTRAQ and LF datasets were investigated using pathway and network analyses. Results iTRAQ proteomic analysis confirmed our previous finding that there is a marked proteomic shift in response to cartilage harvest (70 and 54 proteins demonstrating ≥ 2.0-fold change and p < 0.05 between stages I and II in responders and non-responders, respectively). Further, it highlighted 28 proteins that were differentially abundant between responders and non-responders to ACI, which were not found in the LF study, 16 of which were altered at baseline. The differential expression of two proteins (complement C1s subcomponent and matrix metalloproteinase 3) was confirmed biochemically. Combination of the iTRAQ and LF proteomic datasets generated in-depth SF proteome information that was used to generate interactome networks representing ACI success or failure. Functional pathways that are dysregulated in ACI non-responders were identified, including acute-phase response signalling. Conclusions Several candidate biomarkers for baseline prediction of ACI outcome were identified. A holistic overview of the SF proteome in responders and non-responders to ACI has been profiled, providing a better understanding of the biological pathways underlying clinical outcome, particularly the differential response to cartilage harvest in non-responders. Electronic supplementary material The online version of this article (10.1186/s13075-018-1573-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Charlotte H Hulme
- Institute of Science and Technology in Medicine, Keele University, Keele, Staffordshire, ST5 5BG, UK.,Robert Jones and Agnes Hunt Orthopaedic Hospital, Oswestry, Shropshire, SY10 7AG, UK
| | - Emma L Wilson
- Robert Jones and Agnes Hunt Orthopaedic Hospital, Oswestry, Shropshire, SY10 7AG, UK.,Chester Medical School, Chester University, Chester, CH1 4BJ, UK
| | - Heidi R Fuller
- Institute of Science and Technology in Medicine, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Sally Roberts
- Institute of Science and Technology in Medicine, Keele University, Keele, Staffordshire, ST5 5BG, UK.,Robert Jones and Agnes Hunt Orthopaedic Hospital, Oswestry, Shropshire, SY10 7AG, UK
| | - James B Richardson
- Institute of Science and Technology in Medicine, Keele University, Keele, Staffordshire, ST5 5BG, UK.,Robert Jones and Agnes Hunt Orthopaedic Hospital, Oswestry, Shropshire, SY10 7AG, UK
| | - Pete Gallacher
- Institute of Science and Technology in Medicine, Keele University, Keele, Staffordshire, ST5 5BG, UK.,Robert Jones and Agnes Hunt Orthopaedic Hospital, Oswestry, Shropshire, SY10 7AG, UK
| | - Mandy J Peffers
- Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Sally L Shirran
- BSRC Mass Spectrometry and Proteomics Facility, University of St Andrews, North Haugh, Fife, KY16 9ST, UK
| | - Catherine H Botting
- BSRC Mass Spectrometry and Proteomics Facility, University of St Andrews, North Haugh, Fife, KY16 9ST, UK
| | - Karina T Wright
- Institute of Science and Technology in Medicine, Keele University, Keele, Staffordshire, ST5 5BG, UK. .,Robert Jones and Agnes Hunt Orthopaedic Hospital, Oswestry, Shropshire, SY10 7AG, UK.
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8
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Thompson LW, Morrison KD, Shirran SL, Groen EJN, Gillingwater TH, Botting CH, Sleeman JE. Neurochondrin interacts with the SMN protein suggesting a novel mechanism for spinal muscular atrophy pathology. J Cell Sci 2018; 131:jcs.211482. [PMID: 29507115 PMCID: PMC5963842 DOI: 10.1242/jcs.211482] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 09/27/2017] [Accepted: 02/16/2018] [Indexed: 12/15/2022] Open
Abstract
Spinal muscular atrophy (SMA) is an inherited neurodegenerative condition caused by a reduction in the amount of functional survival motor neuron (SMN) protein. SMN has been implicated in transport of mRNA in neural cells for local translation. We previously identified microtubule-dependent mobile vesicles rich in SMN and SNRPB, a member of the Sm family of small nuclear ribonucleoprotein (snRNP)-associated proteins, in neural cells. By comparing the interactomes of SNRPB and SNRPN, a neural-specific Sm protein, we now show that the essential neural protein neurochondrin (NCDN) interacts with Sm proteins and SMN in the context of mobile vesicles in neurites. NCDN has roles in protein localisation in neural cells and in maintenance of cell polarity. NCDN is required for the correct localisation of SMN, suggesting they may both be required for formation and transport of trafficking vesicles. NCDN may have potential as a therapeutic target for SMA together with, or in place of the targeting of SMN expression. This article has an associated First Person interview with the first author of the paper. Highlighted Article: The essential neural protein neurochondrin interacts with the spinal muscular atrophy (SMA) protein SMN in cell lines and in mice. This might be relevant to the molecular pathology of SMA.
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Affiliation(s)
- Luke W Thompson
- School of Biology, University of St Andrews, BSRC Complex, North Haugh St Andrews, KY16 9ST, UK
| | - Kim D Morrison
- School of Biology, University of St Andrews, BSRC Complex, North Haugh St Andrews, KY16 9ST, UK
| | - Sally L Shirran
- School of Biology, University of St Andrews, BSRC Complex, North Haugh St Andrews, KY16 9ST, UK
| | - Ewout J N Groen
- Edinburgh Medical School, Biomedical Sciences and Euan MacDonald Centre for Motor Neuron Disease Research, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK
| | - Thomas H Gillingwater
- Edinburgh Medical School, Biomedical Sciences and Euan MacDonald Centre for Motor Neuron Disease Research, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK
| | - Catherine H Botting
- School of Biology, University of St Andrews, BSRC Complex, North Haugh St Andrews, KY16 9ST, UK
| | - Judith E Sleeman
- School of Biology, University of St Andrews, BSRC Complex, North Haugh St Andrews, KY16 9ST, UK
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9
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Joyce A, Ijaz UZ, Nzeteu C, Vaughan A, Shirran SL, Botting CH, Quince C, O'Flaherty V, Abram F. Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass. Front Microbiol 2018; 9:540. [PMID: 29619022 PMCID: PMC5871674 DOI: 10.3389/fmicb.2018.00540] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 10/17/2017] [Accepted: 03/09/2018] [Indexed: 11/13/2022] Open
Abstract
Harvesting valuable bioproducts from various renewable feedstocks is necessary for the critical development of a sustainable bioeconomy. Anaerobic digestion is a well-established technology for the conversion of wastewater and solid feedstocks to energy with the additional potential for production of process intermediates of high market values (e.g., carboxylates). In recent years, first-generation biofuels typically derived from food crops have been widely utilized as a renewable source of energy. The environmental and socioeconomic limitations of such strategy, however, have led to the development of second-generation biofuels utilizing, amongst other feedstocks, lignocellulosic biomass. In this context, the anaerobic digestion of perennial grass holds great promise for the conversion of sustainable renewable feedstock to energy and other process intermediates. The advancement of this technology however, and its implementation for industrial applications, relies on a greater understanding of the microbiome underpinning the process. To this end, microbial communities recovered from replicated anaerobic bioreactors digesting grass were analyzed. The bioreactors leachates were not buffered and acidic pH (between 5.5 and 6.3) prevailed at the time of sampling as a result of microbial activities. Community composition and transcriptionally active taxa were examined using 16S rRNA sequencing and microbial functions were investigated using metaproteomics. Bioreactor fraction, i.e., grass or leachate, was found to be the main discriminator of community analysis across the three molecular level of investigation (DNA, RNA, and proteins). Six taxa, namely Bacteroidia, Betaproteobacteria, Clostridia, Gammaproteobacteria, Methanomicrobia, and Negativicutes accounted for the large majority of the three datasets. The initial stages of grass hydrolysis were carried out by Bacteroidia, Gammaproteobacteria, and Negativicutes in the grass biofilms, in addition to Clostridia in the bioreactor leachates. Numerous glycolytic enzymes and carbohydrate transporters were detected throughout the bioreactors in addition to proteins involved in butanol and lactate production. Finally, evidence of the prevalence of stressful conditions within the bioreactors and particularly impacting Clostridia was observed in the metaproteomes. Taken together, this study highlights the functional importance of Clostridia during the anaerobic digestion of grass and thus research avenues allowing members of this taxon to thrive should be explored.
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Affiliation(s)
- Aoife Joyce
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Umer Z Ijaz
- Environmental Omics Laboratory, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Corine Nzeteu
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.,Microbial Ecology Laboratory, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Aoife Vaughan
- Microbial Ecology Laboratory, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Sally L Shirran
- Biomedical Sciences Research Complex, University of St Andrews, Fife, United Kingdom
| | - Catherine H Botting
- Biomedical Sciences Research Complex, University of St Andrews, Fife, United Kingdom
| | - Christopher Quince
- Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Florence Abram
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
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10
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Kershaw JL, Botting CH, Brownlow A, Hall AJ. Not just fat: investigating the proteome of cetacean blubber tissue. Conserv Physiol 2018; 6:coy003. [PMID: 29479430 PMCID: PMC5814904 DOI: 10.1093/conphys/coy003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/14/2017] [Accepted: 01/24/2018] [Indexed: 06/01/2023]
Abstract
Mammalian adipose tissue is increasingly being recognized as an endocrine organ involved in the regulation of a number of metabolic processes and pathways. It responds to signals from different hormone systems and the central nervous system, and expresses a variety of protein factors with important paracrine and endocrine functions. This study presents a first step towards the systematic analysis of the protein content of cetacean adipose tissue, the blubber, in order to investigate the kinds of proteins present and their relative abundance. Full depth blubber subsamples were collected from dead-stranded harbour porpoises (Phocoena phocoena) (n = 21). Three total protein extraction methods were trialled, and the highest total protein yields with the lowest extraction variability were achieved using a RIPA cell lysis and extraction buffer based protocol. Extracted proteins were separated using 1D Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE), and identified using nanoflow Liquid Chromatography Electrospray Ionization in tandem with Mass Spectrometry (nLC-ESI-MS/MS). A range of proteins were identified (n = 295) and classed into eight functional groups, the most abundant of which were involved in cell function and metabolism (45%), immune response and inflammation (15%) and lipid metabolism (11%). These proteins likely originate both from the various cell types within the blubber tissue itself, and from the circulation. They therefore have the potential to capture information on the cellular and physiological stresses experienced by individuals at the time of sampling. The importance of this proteomic approach is two-fold: Firstly, it could help to assign novel functions to marine mammal blubber in keeping with current understanding of the multi-functional role of adipose tissue in other mammals. Secondly, it could lead to the development of a suite of biomarkers to better monitor the physiological state and health of live individuals though remote blubber biopsy sampling.
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Affiliation(s)
- Joanna L Kershaw
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, St Andrews KY16 8LB, UK
| | - Catherine H Botting
- Biomedical Sciences Research Complex, School of Chemistry, Biomolecular Sciences Building Annexe, North Haugh, University of St Andrews, St Andrews KY16 9ST, UK
| | - Andrew Brownlow
- Scottish Marine Animals Strandings Scheme, SAC Consulting Veterinary Services, Inverness IV2 5NA, UK
| | - Ailsa J Hall
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, St Andrews KY16 8LB, UK
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11
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Abstract
NS1 proteins of influenza A and B viruses share limited sequence homology, yet both are potent manipulators of host cell processes, particularly interferon (IFN) induction. Although many cellular partners are reported for A/NS1, only a few (e.g. PKR and ISG15) have been identified for B/NS1. Here, affinity-purification and mass spectrometry were used to expand the known host interactome of B/NS1. We identified 22 human proteins as new putative targets for B/NS1, validating several, including DHX9, ILF3, YBX1 and HNRNPC. Consistent with two RNA-binding domains in B/NS1, many of the identified factors bind RNA and some interact with B/NS1 in an RNA-dependent manner. Functional characterization of several B/NS1 interactors identified SNRNP200 as a potential positive regulator of host IFN responses, while ILF3 exhibited dual roles in both IFN induction and influenza B virus replication. These data provide a resource for future investigations into the mechanisms underpinning host cell modulation by influenza B virus NS1.
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Affiliation(s)
- Corinna Patzina
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Catherine H. Botting
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife, KY16 9ST, UK
| | - Adolfo García-Sastre
- Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Richard E. Randall
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife, KY16 9ST, UK
| | - Benjamin G. Hale
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
- *Correspondence: Benjamin G. Hale,
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12
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Synowsky SA, Shirran SL, Cooke FGM, Antoniou AN, Botting CH, Powis SJ. The major histocompatibility complex class I immunopeptidome of extracellular vesicles. J Biol Chem 2017; 292:17084-17092. [PMID: 28860189 DOI: 10.1074/jbc.m117.805895] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/24/2017] [Indexed: 11/06/2022] Open
Abstract
Extracellular vesicles (EVs) are released by most cell types and have been associated with multiple immunomodulatory functions. MHC class I molecules have crucial roles in antigen presentation and in eliciting immune responses and are known to be incorporated into EVs. However, the MHC class I immunopeptidome of EVs has not been established. Here, using a small-scale immunoisolation of the antigen serotypes HLA-A*02:01 and HLA-B*27:05 expressed on the Epstein-Barr virus-transformed B cell line Jesthom and MS of the eluted peptides from both cells and EVs, we identified 516 peptides that bind either HLA-A*02:01 or HLA-B*27:05. Of importance, the predicted serotype-binding affinities and peptide-anchor motifs did not significantly differ between the peptide pools isolated from cells or EVs, indicating that during EV biogenesis, no obvious editing of the MHC class I immunopeptidome occurs. These results, for the first time, establish EVs as a source of MHC class I peptides that can be used for the study of the immunopeptidome and in the discovery of potential neoantigens for immunotherapies.
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Affiliation(s)
- Silvia A Synowsky
- From the Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews KY16 9ST, Scotland
| | - Sally L Shirran
- From the Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews KY16 9ST, Scotland
| | - Fiona G M Cooke
- the School of Medicine, University of St. Andrews, St. Andrews KY16 9TF, Scotland, and
| | - Antony N Antoniou
- The Advanced Centre for Biochemical Engineering, University College London, London WC1E 7JE, United Kingdom
| | - Catherine H Botting
- From the Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews KY16 9ST, Scotland
| | - Simon J Powis
- the School of Medicine, University of St. Andrews, St. Andrews KY16 9TF, Scotland, and
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13
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Labarbuta P, Duckett K, Botting CH, Chahrour O, Malone J, Dalton JP, Law CJ. Recombinant vacuolar iron transporter family homologue PfVIT from human malaria-causing Plasmodium falciparum is a Fe 2+/H +exchanger. Sci Rep 2017; 7:42850. [PMID: 28198449 PMCID: PMC5309874 DOI: 10.1038/srep42850] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 01/18/2017] [Indexed: 02/08/2023] Open
Abstract
Vacuolar iron transporters (VITs) are a poorly understood family of integral membrane proteins that can function in iron homeostasis via sequestration of labile Fe2+ into vacuolar compartments. Here we report on the heterologous overexpression and purification of PfVIT, a vacuolar iron transporter homologue from the human malaria-causing parasite Plasmodium falciparum. Use of synthetic, codon-optimised DNA enabled overexpression of functional PfVIT in the inner membrane of Escherichia coli which, in turn, conferred iron tolerance to the bacterial cells. Cells that expressed PfVIT had decreased levels of total cellular iron compared with cells that did not express the protein. Qualitative transport assays performed on inverted vesicles enriched with PfVIT revealed that the transporter catalysed Fe2+/H+ exchange driven by the proton electrochemical gradient. Furthermore, the PfVIT transport function in this system did not require the presence of any Plasmodium-specific factor such as post-translational phosphorylation. PfVIT purified as a monomer and, as measured by intrinsic protein fluorescence quenching, bound Fe2+ in detergent solution with low micromolar affinity. This study of PfVIT provides material for future detailed biochemical, biophysical and structural studies to advance understanding of the vacuolar iron transporter family of membrane proteins from important human pathogens.
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Affiliation(s)
- Paola Labarbuta
- School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast BT9 7BL, United Kingdom
| | - Katie Duckett
- School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast BT9 7BL, United Kingdom
| | - Catherine H Botting
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
| | - Osama Chahrour
- Spectroscopy Group, Analytical Services, Almac, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, United Kingdom
| | - John Malone
- Spectroscopy Group, Analytical Services, Almac, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, United Kingdom
| | - John P Dalton
- School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast BT9 7BL, United Kingdom
| | - Christopher J Law
- School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast BT9 7BL, United Kingdom
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14
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Kavanagh P, Botting CH, Jana PS, Leech D, Abram F. Comparative Proteomics Implicates a Role for Multiple Secretion Systems in Electrode-Respiring Geobacter sulfurreducens Biofilms. J Proteome Res 2016; 15:4135-4145. [DOI: 10.1021/acs.jproteome.5b01019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Paul Kavanagh
- School
of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Catherine H. Botting
- Biomedical
Sciences Research Complex, University of St. Andrews, North Haugh, Fife KY16 9ST, United Kingdom
| | - Partha S. Jana
- School
of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Dónal Leech
- School
of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Florence Abram
- Functional
Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland
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15
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Tong X, Barberi TT, Botting CH, Sharma SV, Simmons MJH, Overton TW, Goss RJM. Rapid enzyme regeneration results in the striking catalytic longevity of an engineered, single species, biocatalytic biofilm. Microb Cell Fact 2016; 15:180. [PMID: 27769259 PMCID: PMC5073922 DOI: 10.1186/s12934-016-0579-3] [Citation(s) in RCA: 6] [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: 05/11/2016] [Accepted: 10/14/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Engineering of single-species biofilms for enzymatic generation of fine chemicals is attractive. We have recently demonstrated the utility of an engineered Escherichia coli biofilm as a platform for synthesis of 5-halotryptophan. E. coli PHL644, expressing a recombinant tryptophan synthase, was employed to generate a biofilm. Its rapid deposition, and instigation of biofilm formation, was enforced by employing a spin-down method. The biofilm presents a large three-dimensional surface area, excellent for biocatalysis. The catalytic longevity of the engineered biofilm is striking, and we had postulated that this was likely to largely result from protection conferred to recombinant enzymes by biofilm's extracellular matrix. SILAC (stable isotopic labelled amino acids in cell cultures), and in particular dynamic SILAC, in which pulses of different isotopically labelled amino acids are administered to cells over a time course, has been used to follow the fate of proteins. To explore within our spin coated biofilm, whether the recombinant enzyme's longevity might be in part due to its regeneration, we introduced pulses of isotopically labelled lysine and phenylalanine into medium overlaying the biofilm and followed their incorporation over the course of biofilm development. RESULTS Through SILAC analysis, we reveal that constant and complete regeneration of recombinant enzymes occurs within spin coated biofilms. The striking catalytic longevity within the biofilm results from more than just simple protection of active enzyme by the biofilm and its associated extracellular matrix. The replenishment of recombinant enzyme is likely to contribute significantly to the catalytic longevity observed for the engineered biofilm system. CONCLUSIONS Here we provide the first evidence of a recombinant enzyme's regeneration in an engineered biofilm. The recombinant enzyme was constantly replenished over time as evidenced by dynamic SILAC, which suggests that the engineered E. coli biofilms are highly metabolically active, having a not inconsiderable energetic demand. The constant renewal of recombinant enzyme highlights the attractive possibility of utilising this biofilm system as a dynamic platform into which enzymes of interest can be introduced in a "plug-and-play" fashion and potentially be controlled through promoter switching for production of a series of desired fine chemicals.
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Affiliation(s)
- Xiaoxue Tong
- School of Chemistry, University of St. Andrews, St. Andrews, KY16 9ST, UK.,Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, KY16 9ST, UK
| | - Tania Triscari Barberi
- School of Chemistry, University of St. Andrews, St. Andrews, KY16 9ST, UK.,Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, KY16 9ST, UK
| | - Catherine H Botting
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, KY16 9ST, UK
| | - Sunil V Sharma
- School of Chemistry, University of St. Andrews, St. Andrews, KY16 9ST, UK.,Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, KY16 9ST, UK
| | - Mark J H Simmons
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B152TT, UK
| | - Tim W Overton
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B152TT, UK
| | - Rebecca J M Goss
- School of Chemistry, University of St. Andrews, St. Andrews, KY16 9ST, UK. .,Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, KY16 9ST, UK.
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16
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Magill DJ, Hamilton E, Shirran SL, Botting CH, Timson DJ. On the Interaction Between Human IQGAP1 and Actin. Protein Pept Lett 2016; 23:386-95. [PMID: 26845769 DOI: 10.2174/0929866523666160204123331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 01/25/2016] [Accepted: 02/02/2016] [Indexed: 11/22/2022]
Abstract
IQGAPs are eukaryotic proteins which integrate signals from various sources and pass these on the cytoskeleton. Understanding how they do this requires information on the interfaces between the proteins. Here, it is shown that the calponin homology domain of human IQGAP1 (CHD1) can be crosslinked with α-actin. The stoichiometry of the interaction was 1:1. A molecular model was built of the complex and associated bioinformatics analyses predicted that the interaction is likely to involve an electrostatic interaction between Lys-240 of α-actin and Glu-30 of CHD1. These residues are predicted to be accessible and are not involved in many intra-protein interactions; they are thus available for interaction with binding partners. They are both located in regions of the proteins which are predicted to be flexible and disordered; interactions between signalling molecules often involve flexible, disordered regions. The predicted binding region in CHD1 is well conserved in many eukaryotic IQGAP-like proteins. In some cases (e.g Dictyostelium discoideum and Saccharomyces cerevisiae) protein sequence conservation is weak, but molecular modelling reveals that a region of charged, polar residues in a flexible N-terminus is structurally well conserved. Therefore we conclude that the calponin homology domains of IQGAP1-like proteins interact initially through the electrostatic interaction identified here and that there may be subsequent conformational changes to form the final complex.
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Affiliation(s)
| | | | | | | | - David J Timson
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton BN2 4GJ. UK.
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17
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Fuller HR, Mandefro B, Shirran SL, Gross AR, Kaus AS, Botting CH, Morris GE, Sareen D. Spinal Muscular Atrophy Patient iPSC-Derived Motor Neurons Have Reduced Expression of Proteins Important in Neuronal Development. Front Cell Neurosci 2016; 9:506. [PMID: 26793058 PMCID: PMC4707261 DOI: 10.3389/fncel.2015.00506] [Citation(s) in RCA: 40] [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: 09/30/2015] [Accepted: 12/15/2015] [Indexed: 11/15/2022] Open
Abstract
Spinal muscular atrophy (SMA) is an inherited neuromuscular disease primarily characterized by degeneration of spinal motor neurons, and caused by reduced levels of the SMN protein. Previous studies to understand the proteomic consequences of reduced SMN have mostly utilized patient fibroblasts and animal models. We have derived human motor neurons from type I SMA and healthy controls by creating their induced pluripotent stem cells (iPSCs). Quantitative mass spectrometry of these cells revealed increased expression of 63 proteins in control motor neurons compared to respective fibroblasts, whereas 30 proteins were increased in SMA motor neurons vs. their fibroblasts. Notably, UBA1 was significantly decreased in SMA motor neurons, supporting evidence for ubiquitin pathway defects. Subcellular distribution of UBA1 was predominantly cytoplasmic in SMA motor neurons in contrast to nuclear in control motor neurons; suggestive of neurodevelopmental abnormalities. Many of the proteins that were decreased in SMA motor neurons, including beta III-tubulin and UCHL1, were associated with neurodevelopment and differentiation. These neuron-specific consequences of SMN depletion were not evident in fibroblasts, highlighting the importance of iPSC technology. The proteomic profiles identified here provide a useful resource to explore the molecular consequences of reduced SMN in motor neurons, and for the identification of novel biomarker and therapeutic targets for SMA.
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Affiliation(s)
- Heidi R Fuller
- Wolfson Centre for Inherited Neuromuscular Disease, The Robert Jones and Agnes Hunt Orthopaedic HospitalOswestry, UK; Institute for Science and Technology in Medicine, Keele UniversityStaffordshire, UK
| | - Berhan Mandefro
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical CenterLos Angeles, CA, USA; iPSC Core, The David and Janet Polak Foundation Stem Cell Core LaboratoryLos Angeles, CA, USA
| | - Sally L Shirran
- BSRC Mass Spectrometry and Proteomics Facility, University of St Andrews Fife, UK
| | - Andrew R Gross
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center Los Angeles, CA, USA
| | - Anjoscha S Kaus
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center Los Angeles, CA, USA
| | - Catherine H Botting
- BSRC Mass Spectrometry and Proteomics Facility, University of St Andrews Fife, UK
| | - Glenn E Morris
- Wolfson Centre for Inherited Neuromuscular Disease, The Robert Jones and Agnes Hunt Orthopaedic HospitalOswestry, UK; Institute for Science and Technology in Medicine, Keele UniversityStaffordshire, UK
| | - Dhruv Sareen
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical CenterLos Angeles, CA, USA; iPSC Core, The David and Janet Polak Foundation Stem Cell Core LaboratoryLos Angeles, CA, USA; Department of Biomedical Sciences, Cedars-Sinai Medical CenterLos Angeles, CA, USA
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18
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Gunnigle E, Nielsen JL, Fuszard M, Botting CH, Sheahan J, O'Flaherty V, Abram F. Functional responses and adaptation of mesophilic microbial communities to psychrophilic anaerobic digestion. FEMS Microbiol Ecol 2015; 91:fiv132. [PMID: 26507125 DOI: 10.1093/femsec/fiv132] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2015] [Indexed: 11/14/2022] Open
Abstract
Psychrophilic (<20°C) anaerobic digestion (AD) represents an attractive alternative to mesophilic wastewater treatment. In order to investigate the AD microbiome response to temperature change, with particular emphasis on methanogenic archaea, duplicate laboratory-scale AD bioreactors were operated at 37°C followed by a temperature drop to 15°C. A volatile fatty acid-based wastewater (composed of propionic acid, butyric acid, acetic acid and ethanol) was used to provide substrates representing the later stages of AD. Community structure was monitored using 16S rRNA gene clone libraries, as well as DNA and cDNA-based DGGE analysis, while the abundance of relevant methanogens was followed using qPCR. In addition, metaproteomics, microautoradiography-fluorescence in situ hybridization, and methanogenic activity measurements were employed to investigate microbial activities and functions. Methanomicrobiales abundance increased at low temperature, which correlated with an increased contribution of CH4 production from hydrogenotrophic methanogenesis at 15°C. Methanosarcinales utilized acetate and H2/CO2 as CH4 precursors at both temperatures and a partial shift from acetoclastic to hydrogenotrophic methanogenesis was observed for this archaeal population at 15°C. An upregulation of protein expression was reported at low temperature as well as the detection of chaperones indicating that mesophilic communities experienced stress during long-term exposure to 15°C. Overall, changes in microbial community structure and function were found to underpin the adaptation of mesophilic sludge to psychrophilic AD.
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Affiliation(s)
- Eoin Gunnigle
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Jeppe L Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Matthew Fuszard
- Biomedical Sciences Research Complex, Biomolecular Sciences Building, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, UK
| | - Catherine H Botting
- Biomedical Sciences Research Complex, Biomolecular Sciences Building, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, UK
| | - Jerome Sheahan
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Florence Abram
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
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19
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Fuller HR, Slade R, Jovanov-Milošević N, Babić M, Sedmak G, Šimić G, Fuszard MA, Shirran SL, Botting CH, Gates MA. Stathmin is enriched in the developing corticospinal tract. Mol Cell Neurosci 2015; 69:12-21. [PMID: 26370173 DOI: 10.1016/j.mcn.2015.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 09/02/2015] [Accepted: 09/07/2015] [Indexed: 01/28/2023] Open
Abstract
Understanding the intra- and extracellular proteins involved in the development of the corticospinal tract (CST) may offer insights into how the pathway could be regenerated following traumatic spinal cord injury. Currently, however, little is known about the proteome of the developing corticospinal system. The present study, therefore, has used quantitative proteomics and bioinformatics to detail the protein profile of the rat CST during its formation in the spinal cord. This analysis identified increased expression of 65 proteins during the early ingrowth of corticospinal axons into the spinal cord, and 36 proteins at the period of heightened CST growth. A majority of these proteins were involved in cellular assembly and organization, with annotations being most highly associated with cytoskeletal organization, microtubule dynamics, neurite outgrowth, and the formation, polymerization and quantity of microtubules. In addition, 22 proteins were more highly expressed within the developing CST in comparison to other developing white matter tracts of the spinal cord of age-matched animals. Of these differentially expressed proteins, only one, stathmin 1 (a protein known to be involved in microtubule dynamics), was both highly enriched in the developing CST and relatively sparse in other developing descending and ascending spinal tracts. Immunohistochemical analyses of the developing rat spinal cord and fetal human brain stem confirmed the enriched pattern of stathmin expression along the developing CST, and in vitro growth assays of rat corticospinal neurons showed a reduced length of neurite processes in response to pharmacological perturbation of stathmin activity. Combined, these findings suggest that stathmin activity may modulate axonal growth during development of the corticospinal projection, and reinforces the notion that microtubule dynamics could play an important role in the generation and regeneration of the CST.
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Affiliation(s)
- Heidi R Fuller
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK; Institute for Science and Technology in Medicine, Keele University, Keele, Staffordshire ST5 5BG, UK; Postgraduate Medicine, Keele University, Staffordshire ST5 5BG, UK
| | - Robert Slade
- Institute for Science and Technology in Medicine, Keele University, Keele, Staffordshire ST5 5BG, UK; Postgraduate Medicine, Keele University, Staffordshire ST5 5BG, UK
| | | | - Mirjana Babić
- Croatian Institute for Brain Research, Zagreb 10000, Croatia
| | - Goran Sedmak
- Croatian Institute for Brain Research, Zagreb 10000, Croatia
| | - Goran Šimić
- Croatian Institute for Brain Research, Zagreb 10000, Croatia
| | - Matthew A Fuszard
- BSRC Mass Spectrometry and Proteomics Facility, Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Sally L Shirran
- BSRC Mass Spectrometry and Proteomics Facility, Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Catherine H Botting
- BSRC Mass Spectrometry and Proteomics Facility, Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Monte A Gates
- Institute for Science and Technology in Medicine, Keele University, Keele, Staffordshire ST5 5BG, UK.
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20
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Walden M, Edwards JM, Dziewulska AM, Bergmann R, Saalbach G, Kan SY, Miller OK, Weckener M, Jackson RJ, Shirran SL, Botting CH, Florence GJ, Rohde M, Banfield MJ, Schwarz-Linek U. An internal thioester in a pathogen surface protein mediates covalent host binding. eLife 2015; 4. [PMID: 26032562 PMCID: PMC4450167 DOI: 10.7554/elife.06638] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/01/2015] [Indexed: 01/19/2023] Open
Abstract
To cause disease and persist in a host, pathogenic and commensal microbes must adhere to tissues. Colonization and infection depend on specific molecular interactions at the host-microbe interface that involve microbial surface proteins, or adhesins. To date, adhesins are only known to bind to host receptors non-covalently. Here we show that the streptococcal surface protein SfbI mediates covalent interaction with the host protein fibrinogen using an unusual internal thioester bond as a ‘chemical harpoon’. This cross-linking reaction allows bacterial attachment to fibrin and SfbI binding to human cells in a model of inflammation. Thioester-containing domains are unexpectedly prevalent in Gram-positive bacteria, including many clinically relevant pathogens. Our findings support bacterial-encoded covalent binding as a new molecular principle in host-microbe interactions. This represents an as yet unexploited target to treat bacterial infection and may also offer novel opportunities for engineering beneficial interactions. DOI:http://dx.doi.org/10.7554/eLife.06638.001 The human body is home to many trillions of microbes; most are harmless, but some may cause disease. To live inside a host, microbes must first attach to host tissues. This process involves multiple proteins on each microbe's surface, called adhesins, which interact with the molecules that make up these tissues. Like all proteins, adhesins are long chains of simpler building blocks called amino acids, and each amino acid is connected to the next via a strong ‘covalent’ bond. Adhesins, however, typically attach bacteria to host molecules through the combined strength of many weak ‘non-covalent’ interactions. It was recently discovered that one adhesin from a bacterium called Streptococcus pyogenes contains a rare, extra covalent bond—called a thioester—in an unusual location between two of its amino acids. S. pyogenes is a common cause of throat infections in humans, and can also cause the life-threatening ‘flesh-eating disease’. Walden, Edwards et al. have now used a range of computational, biochemical, structural biology and cell-based techniques to study other adhesins that have thioester bonds in more detail. Computational searches identified hundreds of bacterial proteins containing similar bonds. These included many from bacteria that infect humans: such as Streptococcus pneumoniae, which is the most common cause of pneumonia in adults; and Clostridium difficile, which is notorious for causing severe gut infections in hospital patients. Closer examination of the three-dimensional structures of three of these proteins—including one called SfbI from S. pyogenes—revealed that each had a clear thioester bond. Biochemical tests of an additional nine of the identified proteins strongly suggested they too contained thioester bonds. Walden, Edwards et al. then showed that SfbI was able to not only attach to tissues like conventional adhesins, but also chemically react with fibrinogen: a human protein that is essential for blood clotting and commonly found in inflamed tissues and healing wounds. This chemical reaction results in the formation of a covalent bond between SfbI and fibrinogen, which is as stable as the bonds that link the amino acids in a protein chain. Further experiments revealed that SfbI strongly binds to human cells grown in the lab under conditions that mimic tissue inflammation. Finally, Walden, Edwards et al. made a mutant version of SfbI that did not contain a thioester, and found that it could not interact with fibrinogen nor bind to human cells. Together, these findings suggest that thioesters in bacterial adhesins act like ‘chemical harpoons’, which microbes can use to irreversibly attach themselves to molecules within their host's tissues. This attachment mechanism has not been seen before in host-microbe interactions, and further research is now needed to explore whether interfering with this process could represent a new way to treat bacterial infections. DOI:http://dx.doi.org/10.7554/eLife.06638.002
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Affiliation(s)
- Miriam Walden
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - John M Edwards
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | | | - Rene Bergmann
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Gerhard Saalbach
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Su-Yin Kan
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | - Ona K Miller
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | - Miriam Weckener
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | - Rosemary J Jackson
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | - Sally L Shirran
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | - Catherine H Botting
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | - Gordon J Florence
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Ulrich Schwarz-Linek
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
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21
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Gunnigle E, Siggins A, Botting CH, Fuszard M, O'Flaherty V, Abram F. Low-temperature anaerobic digestion is associated with differential methanogenic protein expression. FEMS Microbiol Lett 2015; 362:fnv059. [PMID: 25862577 DOI: 10.1093/femsle/fnv059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2015] [Indexed: 11/14/2022] Open
Abstract
Anaerobic digestion (AD) is an attractive wastewater treatment technology, leading to the generation of recoverable biofuel (methane). Most industrial AD applications, carry excessive heating costs, however, as AD reactors are commonly operated at mesophilic temperatures while handling waste streams discharged at ambient or cold temperatures. Consequently, low-temperature AD represents a cost-effective strategy for wastewater treatment. The comparative investigation of key microbial groups underpinning laboratory-scale AD bioreactors operated at 37, 15 and 7°C was carried out. Community structure was monitored using 16S rRNA clone libraries, while abundance of the most prominent methanogens was investigated using qPCR. In addition, metaproteomics was employed to access the microbial functions carried out in situ. While δ-Proteobacteria were prevalent at 37°C, their abundance decreased dramatically at lower temperatures with inverse trends observed for Bacteroidetes and Firmicutes. Methanobacteriales and Methanosaeta were predominant at all temperatures investigated while Methanomicrobiales abundance increased at 15°C compared to 37 and 7°C. Changes in operating temperature resulted in the differential expression of proteins involved in methanogenesis, which was found to occur in all bioreactors, as corroborated by bioreactors' performance. This study demonstrated the value of employing a polyphasic approach to address microbial community dynamics and highlighted the functional redundancy of AD microbiomes.
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Affiliation(s)
- Eoin Gunnigle
- Microbial Ecology Laboratory, School of Natural Sciences, National University of Ireland, Galway, University Road, Galway, Ireland Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Alma Siggins
- Microbial Ecology Laboratory, School of Natural Sciences, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Catherine H Botting
- BSRC Mass Spectrometry and Proteomics Facility, Biomedical Sciences Research Complex, North Haugh, University of St Andrews, Fife KY16 9ST, Scotland
| | - Matthew Fuszard
- BSRC Mass Spectrometry and Proteomics Facility, Biomedical Sciences Research Complex, North Haugh, University of St Andrews, Fife KY16 9ST, Scotland
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory, School of Natural Sciences, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Florence Abram
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland, Galway, University Road, Galway, Ireland
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22
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Romanov RA, Alpár A, Zhang MD, Zeisel A, Calas A, Landry M, Fuszard M, Shirran SL, Schnell R, Dobolyi Á, Oláh M, Spence L, Mulder J, Martens H, Palkovits M, Uhlen M, Sitte HH, Botting CH, Wagner L, Linnarsson S, Hökfelt T, Harkany T. A secretagogin locus of the mammalian hypothalamus controls stress hormone release. EMBO J 2014; 34:36-54. [PMID: 25430741 DOI: 10.15252/embj.201488977] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A hierarchical hormonal cascade along the hypothalamic-pituitary-adrenal axis orchestrates bodily responses to stress. Although corticotropin-releasing hormone (CRH), produced by parvocellular neurons of the hypothalamic paraventricular nucleus (PVN) and released into the portal circulation at the median eminence, is known to prime downstream hormone release, the molecular mechanism regulating phasic CRH release remains poorly understood. Here, we find a cohort of parvocellular cells interspersed with magnocellular PVN neurons expressing secretagogin. Single-cell transcriptome analysis combined with protein interactome profiling identifies secretagogin neurons as a distinct CRH-releasing neuron population reliant on secretagogin's Ca(2+) sensor properties and protein interactions with the vesicular traffic and exocytosis release machineries to liberate this key hypothalamic releasing hormone. Pharmacological tools combined with RNA interference demonstrate that secretagogin's loss of function occludes adrenocorticotropic hormone release from the pituitary and lowers peripheral corticosterone levels in response to acute stress. Cumulatively, these data define a novel secretagogin neuronal locus and molecular axis underpinning stress responsiveness.
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Affiliation(s)
- Roman A Romanov
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Alán Alpár
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ming-Dong Zhang
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Amit Zeisel
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - André Calas
- Laboratory for Central Mechanisms of Pain Sensitization, Interdisciplinary Institute for Neuroscience, CNRS UMR 5297 Université Bordeaux 2, Bordeaux, France
| | - Marc Landry
- Laboratory for Central Mechanisms of Pain Sensitization, Interdisciplinary Institute for Neuroscience, CNRS UMR 5297 Université Bordeaux 2, Bordeaux, France
| | - Matthew Fuszard
- School of Chemistry, University of St. Andrews, St. Andrews, UK
| | - Sally L Shirran
- School of Chemistry, University of St. Andrews, St. Andrews, UK
| | - Robert Schnell
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Árpád Dobolyi
- Department of Anatomy, Semmelweis University, Budapest, Hungary
| | - Márk Oláh
- Department of Human Morphology and Developmental Biology, Semmelweis University, Budapest, Hungary
| | - Lauren Spence
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Jan Mulder
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | | | - Miklós Palkovits
- Human Brain Tissue Bank and Laboratory, Semmelweis University, Budapest, Hungary
| | - Mathias Uhlen
- Science for Life Laboratory, Albanova University Center, Royal Institute of Technology, Stockholm, Sweden
| | - Harald H Sitte
- Center for Physiology and Pharmacology, Institute of Pharmacology Medical University of Vienna, Vienna, Austria
| | | | - Ludwig Wagner
- University Clinic for Internal Medicine III General Hospital Vienna, Vienna, Austria
| | - Sten Linnarsson
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Hökfelt
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Tibor Harkany
- Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
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23
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Kasioulis I, Syred HM, Tate P, Finch A, Shaw J, Seawright A, Fuszard M, Botting CH, Shirran S, Adams IR, Jackson IJ, van Heyningen V, Yeyati PL. Kdm3a lysine demethylase is an Hsp90 client required for cytoskeletal rearrangements during spermatogenesis. Mol Biol Cell 2014; 25:1216-33. [PMID: 24554764 PMCID: PMC3982988 DOI: 10.1091/mbc.e13-08-0471] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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: 08/16/2013] [Revised: 02/06/2014] [Accepted: 02/10/2014] [Indexed: 11/30/2022] Open
Abstract
The lysine demethylase Kdm3a (Jhdm2a, Jmjd1a) is required for male fertility, sex determination, and metabolic homeostasis through its nuclear role in chromatin remodeling. Many histone-modifying enzymes have additional nonhistone substrates, as well as nonenzymatic functions, contributing to the full spectrum of events underlying their biological roles. We present two Kdm3a mouse models that exhibit cytoplasmic defects that may account in part for the globozoospermia phenotype reported previously. Electron microscopy revealed abnormal acrosome and manchette and the absence of implantation fossa at the caudal end of the nucleus in mice without Kdm3a demethylase activity, which affected cytoplasmic structures required to elongate the sperm head. We describe an enzymatically active new Kdm3a isoform and show that subcellular distribution, protein levels, and lysine demethylation activity of Kdm3a depended on Hsp90. We show that Kdm3a localizes to cytoplasmic structures of maturing spermatids affected in Kdm3a mutant mice, which in turn display altered fractionation of β-actin and γ-tubulin. Kdm3a is therefore a multifunctional Hsp90 client protein that participates directly in the regulation of cytoskeletal components.
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Affiliation(s)
- Ioannis Kasioulis
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Heather M. Syred
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Peri Tate
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1HH, United Kingdom
| | - Andrew Finch
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Joseph Shaw
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Anne Seawright
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Matt Fuszard
- Biomedical Sciences Research Complex Mass Spectrometry and Proteomics Facility, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom
| | - Catherine H. Botting
- Biomedical Sciences Research Complex Mass Spectrometry and Proteomics Facility, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom
| | - Sally Shirran
- Biomedical Sciences Research Complex Mass Spectrometry and Proteomics Facility, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom
| | - Ian R. Adams
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Ian J. Jackson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Veronica van Heyningen
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Patricia L. Yeyati
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
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24
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Shabbiri K, Botting CH, Adnan A, Fuszard M, Naseem S, Ahmed S, Shujaat S, Syed Q, Ahmad W. An investigation into membrane bound redox carriers involved in energy transduction mechanism in Brevibacterium linens DSM 20158 with unsequenced genome. J Membr Biol 2014; 247:345-55. [PMID: 24573306 DOI: 10.1007/s00232-014-9641-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 02/11/2014] [Indexed: 11/29/2022]
Abstract
Brevibacterium linens (B. linens) DSM 20158 with an unsequenced genome can be used as a non-pathogenic model to study features it has in common with other unsequenced pathogens of the same genus on the basis of comparative proteome analysis. The most efficient way to kill a pathogen is to target its energy transduction mechanism. In the present study, we have identified the redox protein complexes involved in the electron transport chain of B. linens DSM 20158 from their clear homology with the shot-gun genome sequenced strain BL2 of B. linens by using the SDS-Polyacrylamide gel electrophoresis coupled with nano LC-MS/MS mass spectrometry. B. linens is found to have a branched electron transport chain (Respiratory chain), in which electrons can enter the respiratory chain either at NADH (Complex I) or at Complex II level or at the cytochrome level. Moreover, we are able to isolate, purify, and characterize the membrane bound Complex II (succinate dehydrogenase), Complex III (menaquinone cytochrome c reductase cytochrome c subunit, Complex IV (cytochrome c oxidase), and Complex V (ATP synthase) of B. linens strain DSM 20158.
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Affiliation(s)
- Khadija Shabbiri
- Department of Chemistry, GC University Lahore, Lahore, 54000, Pakistan
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25
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Babot M, Labarbuta P, Birch A, Kee S, Fuszard M, Botting CH, Wittig I, Heide H, Galkin A. ND3, ND1 and 39kDa subunits are more exposed in the de-active form of bovine mitochondrial complex I. Biochim Biophys Acta 2014; 1837:929-39. [PMID: 24560811 PMCID: PMC4331043 DOI: 10.1016/j.bbabio.2014.02.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 01/20/2014] [Accepted: 02/12/2014] [Indexed: 12/12/2022]
Abstract
An intriguing feature of mitochondrial complex I from several species is the so-called A/D transition, whereby the idle enzyme spontaneously converts from the active (A) form to the de-active (D) form. The A/D transition plays an important role in tissue response to the lack of oxygen and hypoxic deactivation of the enzyme is one of the key regulatory events that occur in mitochondria during ischaemia. We demonstrate for the first time that the A/D conformational change of complex I does not affect the macromolecular organisation of supercomplexes in vitro as revealed by two types of native electrophoresis. Cysteine 39 of the mitochondrially-encoded ND3 subunit is known to become exposed upon de-activation. Here we show that even if complex I is a constituent of the I + III2 + IV (S1) supercomplex, cysteine 39 is accessible for chemical modification in only the D-form. Using lysine-specific fluorescent labelling and a DIGE-like approach we further identified two new subunits involved in structural rearrangements during the A/D transition: ND1 (MT-ND1) and 39 kDa (NDUFA9). These results clearly show that structural rearrangements during de-activation of complex I include several subunits located at the junction between hydrophilic and hydrophobic domains, in the region of the quinone binding site. De-activation of mitochondrial complex I results in concerted structural rearrangement of membrane subunits which leads to the disruption of the sealed quinone chamber required for catalytic turnover. Supercomplex composition is not affected by mitochondrial complex I conformation. The D-form of complex I is selectively inhibited by tyrosine-reactive reagents. ND3, ND1 & 39 kDa subunits become exposed upon deactivation of complex I.
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Affiliation(s)
- Marion Babot
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Paola Labarbuta
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Amanda Birch
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Sara Kee
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Matthew Fuszard
- School of Chemistry, Biomedical Sciences Research Complex, BMS Annexe, University of St. Andrews, KY16 9ST, UK
| | - Catherine H Botting
- School of Chemistry, Biomedical Sciences Research Complex, BMS Annexe, University of St. Andrews, KY16 9ST, UK
| | - Ilka Wittig
- Functional Proteomics, SFB Core Unit, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Heinrich Heide
- Functional Proteomics, SFB Core Unit, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Alexander Galkin
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK.
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26
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Tortoriello G, Morris CV, Alpar A, Fuzik J, Shirran SL, Calvigioni D, Keimpema E, Botting CH, Reinecke K, Herdegen T, Courtney M, Hurd YL, Harkany T. Miswiring the brain: Δ9-tetrahydrocannabinol disrupts cortical development by inducing an SCG10/stathmin-2 degradation pathway. EMBO J 2014; 33:668-85. [PMID: 24469251 DOI: 10.1002/embj.201386035] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Children exposed in utero to cannabis present permanent neurobehavioral and cognitive impairments. Psychoactive constituents from Cannabis spp., particularly Δ(9)-tetrahydrocannabinol (THC), bind to cannabinoid receptors in the fetal brain. However, it is unknown whether THC can trigger a cannabinoid receptor-driven molecular cascade to disrupt neuronal specification. Here, we show that repeated THC exposure disrupts endocannabinoid signaling, particularly the temporal dynamics of CB1 cannabinoid receptor, to rewire the fetal cortical circuitry. By interrogating the THC-sensitive neuronal proteome we identify Superior Cervical Ganglion 10 (SCG10)/stathmin-2, a microtubule-binding protein in axons, as a substrate of altered neuronal connectivity. We find SCG10 mRNA and protein reduced in the hippocampus of midgestational human cannabis-exposed fetuses, defining SCG10 as the first cannabis-driven molecular effector in the developing cerebrum. CB1 cannabinoid receptor activation recruits c-Jun N-terminal kinases to phosphorylate SCG10, promoting its rapid degradation in situ in motile axons and microtubule stabilization. Thus, THC enables ectopic formation of filopodia and alters axon morphology. These data highlight the maintenance of cytoskeletal dynamics as a molecular target for cannabis, whose imbalance can limit the computational power of neuronal circuitries in affected offspring.
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Affiliation(s)
- Giuseppe Tortoriello
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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27
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Koehnke J, Bent AF, Zollman D, Smith K, Houssen WE, Zhu X, Mann G, Lebl T, Scharff R, Shirran S, Botting CH, Jaspars M, Schwarz-Linek U, Naismith JH. The Cyanobactin Heterocyclase Enzyme: A Processive Adenylase That Operates with a Defined Order of Reaction. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306302] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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28
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Koehnke J, Bent AF, Zollman D, Smith K, Houssen WE, Zhu X, Mann G, Lebl T, Scharff R, Shirran S, Botting CH, Jaspars M, Schwarz-Linek U, Naismith JH. The cyanobactin heterocyclase enzyme: a processive adenylase that operates with a defined order of reaction. Angew Chem Int Ed Engl 2013; 52:13991-6. [PMID: 24214017 PMCID: PMC3995012 DOI: 10.1002/anie.201306302] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/03/2013] [Indexed: 11/12/2022]
Affiliation(s)
- Jesko Koehnke
- Biomedical Science Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST (UK)
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29
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Koehnke J, Morawitz F, Bent AF, Houssen WE, Shirran SL, Fuszard MA, Smellie IA, Botting CH, Smith MCM, Jaspars M, Naismith JH. An enzymatic route to selenazolines. Chembiochem 2013; 14:564-7. [PMID: 23483642 PMCID: PMC3625746 DOI: 10.1002/cbic.201300037] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [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: 01/22/2013] [Indexed: 11/11/2022]
Abstract
Ringing the changes: Selenazolines have applications in medicinal chemistry, but their synthesis is challenging. We report a new convenient and less toxic route to these heterocycles that starts from commercially available selenocysteine. The new route depends on a heterocyclase enzyme that creates oxazolines and thiazolines from serines/threonines and cysteines.
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Affiliation(s)
- Jesko Koehnke
- Biomedical Science Research Complex, University of St Andrews, North Haugh, St. Andrews, KY16 9ST, UK
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30
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Shabbiri K, Botting CH, Adnan A, Fuszard M. Charting the cellular and extracellular proteome analysis of Brevibacterium linens DSM 20158 with unsequenced genome by mass spectrometry-driven sequence similarity searches. J Proteomics 2013; 83:99-118. [PMID: 23507220 DOI: 10.1016/j.jprot.2013.02.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 02/27/2013] [Indexed: 11/26/2022]
Abstract
UNLABELLED Brevibacterium linens DSM 20158 is an industrially important actinobacterium which is well-known for the production of amino acids and enzymes. However, as this strain has an unsequenced genome, there is no detailed information regarding its proteome although another strain of this microbe, BL2, has a shotgun genome sequence. However, this still does not cover the entire scope of its proteome. The present study is carried out by first identifying proteins by homology matches using the Mascot search algorithm followed by an advanced approach using de novo sequencing and MS BLAST to expand the B. linens proteome. The proteins identified in the secretome and cellular portion appear to be involved in various metabolic and physiological processes of this unsequenced organism. This study will help to enhance the usability of this strain of B. linens in different areas of research in the future rather than mainly in the food industries. BIOLOGICAL SIGNIFICANCE The present study describes the construction of the first detailed proteomic reference map of B. linens DSM 20158 with unsequenced genome by comparative proteome research analysis. This opens new horizons in proteomics to understand the role of proteins involved in the metabolism and physiology of other organisms with unsequenced genomes.
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Affiliation(s)
- Khadija Shabbiri
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife KY16 9ST, Scotland, United Kingdom
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Ciano M, Fuszard M, Heide H, Botting CH, Galkin A. Conformation-specific crosslinking of mitochondrial complex I. FEBS Lett 2013; 587:867-72. [PMID: 23454639 DOI: 10.1016/j.febslet.2013.02.039] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 02/11/2013] [Accepted: 02/14/2013] [Indexed: 11/17/2022]
Abstract
Complex I is the only component of the eukaryotic respiratory chain of which no high-resolution structure is yet available. A notable feature of mitochondrial complex I is the so-called active/de-active conformational transition of the idle enzyme from the active (A) to the de-active, (D) form. Using an amine- and sulfhydryl-reactive crosslinker of 6.8Å length (SPDP) we found that in the D-form of complex I the ND3 subunit crosslinked to the 39 kDa (NDUFA9) subunit. These proteins could not be crosslinked in the A-form. Most likely, both subunits are closely located in the critical junction region connecting the peripheral hydrophilic domain to the membrane arm of the enzyme where the entrance path for substrate ubiquinone is and where energy transduction takes place.
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Affiliation(s)
- Margherita Ciano
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, UK
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Zilberter M, Ivanov A, Ziyatdinova S, Mukhtarov M, Malkov A, Alpár A, Tortoriello G, Botting CH, Fülöp L, Osypov AA, Pitkänen A, Tanila H, Harkany T, Zilberter Y. Dietary energy substrates reverse early neuronal hyperactivity in a mouse model of Alzheimer's disease. J Neurochem 2013; 125:157-71. [PMID: 23241062 DOI: 10.1111/jnc.12127] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 12/10/2012] [Accepted: 12/11/2012] [Indexed: 01/25/2023]
Abstract
Deficient energy metabolism and network hyperactivity are the early symptoms of Alzheimer's disease (AD). In this study, we show that administration of exogenous oxidative energy substrates (OES) corrects neuronal energy supply deficiency that reduces the amyloid-beta-induced abnormal neuronal activity in vitro and the epileptic phenotype in AD model in vivo. In vitro, acute application of protofibrillar amyloid-β1-42 (Aβ1-42) induced aberrant network activity in wild-type hippocampal slices that was underlain by depolarization of both the neuronal resting membrane potential and GABA-mediated current reversal potential. Aβ1-42 also impaired synaptic function and long-term potentiation. These changes were paralleled by clear indications of impaired energy metabolism, as indicated by abnormal NAD(P)H signaling induced by network activity. However, when glucose was supplemented with OES pyruvate and 3-beta-hydroxybutyrate, Aβ1-42 failed to induce detrimental changes in any of the above parameters. We administered the same OES as chronic supplementation to a standard diet to APPswe/PS1dE9 transgenic mice displaying AD-related epilepsy phenotype. In the ex-vivo slices, we found neuronal subpopulations with significantly depolarized resting and GABA-mediated current reversal potentials, mirroring abnormalities we observed under acute Aβ1-42 application. Ex-vivo cortex of transgenic mice fed with standard diet displayed signs of impaired energy metabolism, such as abnormal NAD(P)H signaling and strongly reduced tolerance to hypoglycemia. Transgenic mice also possessed brain glycogen levels twofold lower than those of wild-type mice. However, none of the above neuronal and metabolic dysfunctions were observed in transgenic mice fed with the OES-enriched diet. In vivo, dietary OES supplementation abated neuronal hyperexcitability, as the frequency of both epileptiform discharges and spikes was strongly decreased in the APPswe/PS1dE9 mice placed on the diet. Altogether, our results suggest that early AD-related neuronal malfunctions underlying hyperexcitability and energy metabolism deficiency can be prevented by dietary supplementation with native energy substrates.
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Affiliation(s)
- Misha Zilberter
- Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
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Brennan FP, Grant J, Botting CH, O'Flaherty V, Richards KG, Abram F. Insights into the low-temperature adaptation and nutritional flexibility of a soil-persistentEscherichia coli. FEMS Microbiol Ecol 2012; 84:75-85. [DOI: 10.1111/1574-6941.12038] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 10/23/2012] [Accepted: 10/24/2012] [Indexed: 01/14/2023] Open
Affiliation(s)
- Fiona P. Brennan
- Ecological Sciences Group; The James Hutton Institute; Craigiebucker, Aberdeen; Scotland
| | - Jim Grant
- Ashtown Research Centre; Teagasc; Dublin; Ireland
| | - Catherine H. Botting
- Biomedical Sciences Research Complex; University of St. Andrews; St. Andrews; Fife; UK
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory; Department of Microbiology; School of Natural Sciences and Ryan Institute; National University of Ireland, Galway; Galway; Ireland
| | | | - Florence Abram
- Functional Environmental Microbiology; Department of Microbiology; School of Natural Sciences; National University of Ireland, Galway; Galway; Ireland
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Mohamed BM, Verma NK, Davies AM, McGowan A, Crosbie-Staunton K, Prina-Mello A, Kelleher D, Botting CH, Causey CP, Thompson PR, Pruijn GJ, Kisin ER, Tkach AV, Shvedova AA, Volkov Y. Citrullination of proteins: a common post-translational modification pathway induced by different nanoparticles in vitro and in vivo. Nanomedicine (Lond) 2012; 7:1181-95. [PMID: 22625207 DOI: 10.2217/nnm.11.177] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
AIM Rapidly expanding manufacture and use of nanomaterials emphasize the requirements for thorough assessment of health outcomes associated with novel applications. Post-translational protein modifications catalyzed by Ca(2+)-dependent peptidylargininedeiminases have been shown to trigger immune responses including autoantibody generation, a hallmark of immune complexes deposition in rheumatoid arthritis. Therefore, the aim of the study was to assess if nanoparticles are able to promote protein citrullination. MATERIALS & METHODS Human A549 and THP-1 cells were exposed to silicon dioxide, carbon black or single-walled carbon nanotubes. C57BL/6 mice were exposed to respirable single-walled carbon nanotubes. Protein citrullination, peptidylargininedeiminases activity and target proteins were evaluated. RESULTS The studied nanoparticles induced protein citrullination both in cultured human cells and mouse lung tissues. Citrullination occurred via the peptidylargininedeiminase-dependent mechanism. Cytokeratines 7, 8, 18 and plectins were identified as intracellular citrullination targets. CONCLUSION Nanoparticle exposure facilitated post-translational citrullination of proteins.
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Affiliation(s)
- Bashir M Mohamed
- Department of Clinical Medicine, Trinity College Dublin, Ireland
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Illingworth RS, Botting CH, Grimes GR, Bickmore WA, Eskeland R. PRC1 and PRC2 are not required for targeting of H2A.Z to developmental genes in embryonic stem cells. PLoS One 2012; 7:e34848. [PMID: 22496869 PMCID: PMC3322156 DOI: 10.1371/journal.pone.0034848] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [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: 10/08/2011] [Accepted: 03/09/2012] [Indexed: 11/19/2022] Open
Abstract
The essential histone variant H2A.Z localises to both active and silent chromatin sites. In embryonic stem cells (ESCs), H2A.Z is also reported to co-localise with polycomb repressive complex 2 (PRC2) at developmentally silenced genes. The mechanism of H2A.Z targeting is not clear, but a role for the PRC2 component Suz12 has been suggested. Given this association, we wished to determine if polycomb functionally directs H2A.Z incorporation in ESCs. We demonstrate that the PRC1 component Ring1B interacts with multiple complexes in ESCs. Moreover, we show that although the genomic distribution of H2A.Z co-localises with PRC2, Ring1B and with the presence of CpG islands, H2A.Z still blankets polycomb target loci in the absence of Suz12, Eed (PRC2) or Ring1B (PRC1). Therefore we conclude that H2A.Z accumulates at developmentally silenced genes in ESCs in a polycomb independent manner.
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Affiliation(s)
- Robert S. Illingworth
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh, United Kingdom
| | - Catherine H. Botting
- BMS Mass Spectrometry and Proteomics Facility, Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife, United Kingdom
| | - Graeme R. Grimes
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh, United Kingdom
| | - Wendy A. Bickmore
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (WB); (RE)
| | - Ragnhild Eskeland
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (WB); (RE)
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Schmelz S, Botting CH, Song L, Kadi NF, Challis GL, Naismith JH. Structural basis for acyl acceptor specificity in the achromobactin biosynthetic enzyme AcsD. J Mol Biol 2011; 412:495-504. [PMID: 21835184 PMCID: PMC3323832 DOI: 10.1016/j.jmb.2011.07.059] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/25/2011] [Accepted: 07/26/2011] [Indexed: 11/17/2022]
Abstract
Siderophores are known virulence factors, and their biosynthesis is a target for new antibacterial agents. A non-ribosomal peptide synthetase-independent siderophore biosynthetic pathway in Dickeya dadantii is responsible for production of the siderophore achromobactin. The D. dadantii achromobactin biosynthesis protein D (AcsD) enzyme has been shown to enantioselectively esterify citric acid with l-serine in the first committed step of achromobactin biosynthesis. The reaction occurs in two steps: stereospecific activation of citric acid by adenylation, followed by attack of the enzyme-bound citryl adenylate by l-serine to produce the homochiral ester. We now report a detailed characterization of the substrate profile and mechanism of the second (acyl transfer) step of AcsD enzyme. We demonstrate that the enzyme catalyzes formation of not only esters but also amides from the citryl-adenylate intermediate. We have rationalized the substrate utilization profile for the acylation reaction by determining the first X-ray crystal structure of a product complex for this enzyme class. We have identified the residues that are important for both recognition of l-serine and catalysis of ester formation. Our hypotheses were tested by biochemical analysis of various mutants, one of which shows a reversal of specificity from the wild type with respect to non-natural substrates. This change can be rationalized on the basis of our structural data. That this change in specificity is accompanied by no loss in activity suggests that AcsD and other members of the non-ribosomal peptide synthetase-independent siderophore superfamily may have biotransformation potential.
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Affiliation(s)
- Stefan Schmelz
- Scottish Structural Proteomics Facility and Centre for Biomolecular Sciences, The University of St Andrews, Scotland KY16 9ST, UK
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Verma NK, Dempsey E, Freeley M, Botting CH, Long A, Kelleher D, Volkov Y. Analysis of dynamic tyrosine phosphoproteome in LFA-1 triggered migrating T-cells. J Cell Physiol 2011; 226:1489-98. [PMID: 20945386 DOI: 10.1002/jcp.22478] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The ordered, directional migration of T-lymphocytes is a key process during immune surveillance and response. This requires cell adhesion to the high endothelial venules or to the extracellular matrix by a series of surface receptor/ligand interactions involving adhesion molecules of the integrin family including lymphocyte function associated molecule-1 (LFA-1) and intercellular adhesion molecules (ICAMs). Reversible protein phosphorylation is emerging as a key player in the regulation of biological functions with tyrosine phosphorylation playing a crucial role in signal transduction. Thus, the study of this type of post-translational modification at the proteomic level has great biological significance. In this work, phospho-enriched cell lysates from LFA-1-triggered migrating human T-cells were subjected to immunoaffinity purification of tyrosine phosphorylated proteins, mass spectrometric, and bioinformatic analysis. In addition to the identification of several well-documented proteins, the analysis suggested involvement of a number of new and novel proteins in LFA-1 induced T-cell migration. This dataset expands the list of the signaling components of the LFA-1 induced phosphotyrosine protein complexes in migrating T-cells that will be extremely useful in the study of their specific roles within LFA-1 associated signaling pathways. Identification of proteins previously not reported in the context of LFA-1 stimulated signal transduction might provide new insights into understanding the LFA-1 signaling networks and aid in the search for new potential therapeutic targets.
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Affiliation(s)
- Navin K Verma
- Department of Clinical Medicine, Institute of Molecular Medicine, Trinity College Dublin, Ireland.
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Overton IM, Graham S, Gould KA, Hinds J, Botting CH, Shirran S, Barton GJ, Coote PJ. Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus. BMC Syst Biol 2011; 5:68. [PMID: 21569391 PMCID: PMC3123200 DOI: 10.1186/1752-0509-5-68] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 05/12/2011] [Indexed: 02/08/2023]
Abstract
BACKGROUND Staphylococcus aureus is a major human pathogen and strains resistant to existing treatments continue to emerge. Development of novel treatments is therefore important. Antimicrobial peptides represent a source of potential novel antibiotics to combat resistant bacteria such as Methicillin-Resistant Staphylococcus aureus (MRSA). A promising antimicrobial peptide is ranalexin, which has potent activity against Gram-positive bacteria, and particularly S. aureus. Understanding mode of action is a key component of drug discovery and network biology approaches enable a global, integrated view of microbial physiology, including mechanisms of antibiotic killing. We developed a systems-wide functional association network approach to integrate proteome and transcriptome profiles, enabling study of drug resistance and mode of action. RESULTS The functional association network was constructed by Bayesian logistic regression, providing a framework for identification of antimicrobial peptide (ranalexin) response modules from S. aureus MRSA-252 transcriptome and proteome profiling. These signatures of ranalexin treatment revealed multiple killing mechanisms, including cell wall activity. Cell wall effects were supported by gene disruption and osmotic fragility experiments. Furthermore, twenty-two novel virulence factors were inferred, while the VraRS two-component system and PhoU-mediated persister formation were implicated in MRSA tolerance to cationic antimicrobial peptides. CONCLUSIONS This work demonstrates a powerful integrative approach to study drug resistance and mode of action. Our findings are informative to the development of novel therapeutic strategies against Staphylococcus aureus and particularly MRSA.
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Affiliation(s)
- Ian M Overton
- Biomedical Systems Analysis, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
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39
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Abram F, Enright AM, O'Reilly J, Botting CH, Collins G, O'Flaherty V. A metaproteomic approach gives functional insights into anaerobic digestion. J Appl Microbiol 2011; 110:1550-60. [PMID: 21447011 DOI: 10.1111/j.1365-2672.2011.05011.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AIMS The objective of this work was to provide functional evidence of key metabolic pathways important for anaerobic digestion processes through the identification of highly expressed proteins in a mixed anaerobic microbial consortium. METHODS AND RESULTS The microbial communities from an anaerobic industrial-like wastewater treatment bioreactor were characterized using phylogenetic analyses and metaproteomics. Clone libraries indicated that the bacterial community in the bioreactor was diverse while the archaeal population was mainly composed of Methanocorpusculum-like (76%) micro-organisms. Three hundred and eighty-eight reproducible protein spots were obtained on 2-D gels, of which 70 were excised and 33 were identified. The putative functions of the proteins detected in the anaerobic bioreactor were related to cellular processes, including methanogenesis from CO(2) and acetate, glycolysis and the pentose phosphate pathway. Metaproteomics also indicated, by protein assignment, the presence of specific micro-organisms in the bioreactor. However, only a limited overlap was observed between the phylogenetic and metaproteomic analyses. CONCLUSIONS This study provides some direct evidence of the microbial activities taking place during anaerobic digestion. SIGNIFICANCE AND IMPACT OF STUDY This study demonstrates metaproteomics as a useful tool to uncover key biochemical pathways underpinning specific anaerobic bioprocesses.
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Affiliation(s)
- F Abram
- Microbial Ecology Laboratory, Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
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40
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Oke M, Carter LG, Johnson KA, Liu H, McMahon SA, Yan X, Kerou M, Weikart ND, Kadi N, Sheikh MA, Schmelz S, Dorward M, Zawadzki M, Cozens C, Falconer H, Powers H, Overton IM, van Niekerk CAJ, Peng X, Patel P, Garrett RA, Prangishvili D, Botting CH, Coote PJ, Dryden DTF, Barton GJ, Schwarz-Linek U, Challis GL, Taylor GL, White MF, Naismith JH. The Scottish Structural Proteomics Facility: targets, methods and outputs. ACTA ACUST UNITED AC 2010; 11:167-80. [PMID: 20419351 PMCID: PMC2883930 DOI: 10.1007/s10969-010-9090-y] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 04/06/2010] [Indexed: 12/19/2022]
Abstract
The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers reporting structural data arising from the pipeline. Nevertheless, the number of structures solved exceeded our ability to analyse and publish each new finding. By reporting the experimental details and depositing the structures we hope to maximize the impact of the project by allowing others to follow up the relevant biology.
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Affiliation(s)
- Muse Oke
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Lester G. Carter
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Stanford Synchrotron Radiation Light Source, 2575 Sand Hill Road, MS 69, Menlo Park, CA 94025 USA
| | - Kenneth A. Johnson
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: The Norwegian Structural Biology Centre, University of Tromsø, 9037 Tromsø, Norway
| | - Huanting Liu
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Stephen A. McMahon
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Xuan Yan
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Melina Kerou
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Nadine D. Weikart
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Faculty of Chemistry, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Nadia Kadi
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL UK
- Present Address: Institute of Cancer Research, 15 Cotswold Road, Belmont, Sutton, Surrey, SM2 5NG UK
| | - Md. Arif Sheikh
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Stefan Schmelz
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Mark Dorward
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Division of Signal Transduction Therapy, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
| | - Michal Zawadzki
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Syngenta Ltd, Jealott’s Hill International Research Centre, Bracknell, Berkshire, RG42 6EY UK
| | - Christopher Cozens
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH UK
| | - Helen Falconer
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Institute of Structural and Molecular Biology, Edinburgh University, Kings Buildings, Edinburgh, EH9 3JR UK
| | - Helen Powers
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Ian M. Overton
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
- Present Address: MRC Human Genetics Unit, Crewe Road South, Edinburgh, EH4 2XU UK
| | - C. A. Johannes van Niekerk
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
| | - Xu Peng
- Department of Biology, Archaea Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Prakash Patel
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL UK
| | - Roger A. Garrett
- Department of Biology, Archaea Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | | | - Catherine H. Botting
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Peter J. Coote
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - David T. F. Dryden
- EaStChem School of Chemistry, University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JJ UK
| | - Geoffrey J. Barton
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
| | - Ulrich Schwarz-Linek
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | | | - Garry L. Taylor
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Malcolm F. White
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - James H. Naismith
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
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Affiliation(s)
- Gu Liu
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
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Shirran SL, Botting CH. A comparison of the accuracy of iTRAQ quantification by nLC-ESI MSMS and nLC-MALDI MSMS methods. J Proteomics 2010; 73:1391-403. [PMID: 20230925 PMCID: PMC2880794 DOI: 10.1016/j.jprot.2010.03.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 03/02/2010] [Accepted: 03/06/2010] [Indexed: 01/18/2023]
Abstract
The accuracy of quantification obtained using the iTRAQ labelling methodology for measuring protein ratios more extreme than 1:1 was investigated. A comparison of nLC-ESI MSMS and nLC-MALDI MSMS analysis routes was performed. A fixed concentration of a standard six protein mix was spiked with two proteins at a range of concentrations. The two data analysis programmes, Mascot and ProteinPilot Paragon, were also compared. Whilst the lower ratios could be measured accurately, greater discrepancies were seen for the higher ratios, particularly by nLC-ESI MSMS. Filtering out the weaker reporter ion signals improved the accuracy of the ratios: this is likely due to several factors which are explored in more detail. Overall, analysis by nLC-MALDI MSMS followed by Mascot interpretation gave the most accurate results.
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Affiliation(s)
- Sally L Shirran
- Centre for Biomolecular Sciences, Biomolecular Sciences Building, North Haugh, University of St Andrews, Fife, KY16 9ST, United Kingdom
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Jahan N, Potter JA, Sheikh MA, Botting CH, Shirran SL, Westwood NJ, Taylor GL. Erratum to “Insights into the Biosynthesis of the Vibrio cholera Major Autoinducer CAI-1 from the Crystal Structure of the PLP-Dependent Enzyme CqsA” [J. Mol. Biol. (2009) 92, 763–773]. J Mol Biol 2009. [DOI: 10.1016/j.jmb.2009.10.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Hill GTH, Irvine DJ, Thurecht KJ, Botting CH, Williamson S, Cole-Hamilton DJ. Preparation of Sodium-Capped Poly(lactic acid) Oligomers by Catalytic Initiation with a Sodium α-, β-, or γ-Hydroxyacids. Macromolecules 2009. [DOI: 10.1021/ma901861u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gavin T. H. Hill
- EaStCHEM, School of Chemistry, University of St. Andrews, St. Andrews, Fife KY16 9ST, Scotland
| | - Derek J. Irvine
- Faculty of Engineering, Department of Chemical & Environmental Engineering, University of Nottingham, University Park NG7 2RD, United Kingdom
| | - Kristofer J. Thurecht
- Faculty of Engineering, Department of Chemical & Environmental Engineering, University of Nottingham, University Park NG7 2RD, United Kingdom
| | - Catherine H. Botting
- EaStCHEM, School of Chemistry, University of St. Andrews, St. Andrews, Fife KY16 9ST, Scotland
| | - Sylvia Williamson
- EaStCHEM, School of Chemistry, University of St. Andrews, St. Andrews, Fife KY16 9ST, Scotland
| | - David J. Cole-Hamilton
- EaStCHEM, School of Chemistry, University of St. Andrews, St. Andrews, Fife KY16 9ST, Scotland
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Jahan N, Potter JA, Sheikh MA, Botting CH, Shirran SL, Westwood NJ, Taylor GL. Insights into the Biosynthesis of the Vibrio cholerae Major Autoinducer CAI-1 from the Crystal Structure of the PLP-Dependent Enzyme CqsA. J Mol Biol 2009; 392:763-73. [DOI: 10.1016/j.jmb.2009.07.042] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 07/12/2009] [Accepted: 07/14/2009] [Indexed: 10/20/2022]
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Mullaney E, Brown PA, Smith SM, Botting CH, Yamaoka YY, Terres AM, Kelleher DP, Windle HJ. Proteomic and functional characterization of the outer membrane vesicles from the gastric pathogen Helicobacter pylori. Proteomics Clin Appl 2009; 3:785-96. [DOI: 10.1002/prca.200800192] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 01/14/2009] [Accepted: 01/19/2009] [Indexed: 12/28/2022]
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47
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Nzoughet JK, Hamilton JTG, Botting CH, Douglas A, Devine L, Nelson J, Elliott CT. Proteomics identification of azaspiracid toxin biomarkers in blue mussels, Mytilus edulis. Mol Cell Proteomics 2009; 8:1811-22. [PMID: 19390117 DOI: 10.1074/mcp.m800561-mcp200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Azaspiracids are a class of recently discovered algae-derived shellfish toxins. Their distribution globally is on the increase with mussels being most widely implicated in azaspiracid-related food poisoning events. Evidence that these toxins were bound to proteins in contaminated mussels has been shown recently. In the present study characterization of these proteins in blue mussels, Mytilus edulis, was achieved using a range of advanced proteomics tools. Four proteins present only in the hepatopancreas of toxin-contaminated mussels sharing identity or homology with cathepsin D, superoxide dismutase, glutathione S-transferase Pi, and a bacterial flagellar protein have been characterized. Several of the proteins are known to be involved in self-defense mechanisms against xenobiotics or up-regulated in the presence of carcinogenic agents. These findings would suggest that azaspiracids should now be considered and evaluated as potential tumorigenic compounds. The presence of a bacterial protein only in contaminated mussels was an unexpected finding and requires further investigation. The proteins identified in this study should assist with development of urgently required processes for the rapid depuration of azaspiracid-contaminated shellfish. Moreover they may serve as early warning indicators of shellfish exposed to this family of toxins.
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Affiliation(s)
- Judith K Nzoughet
- Institute of Agri-food and Land Use, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5AG, Northern Ireland, United Kingdom.
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48
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Schmelz S, Kadi N, McMahon SA, Song L, Oves-Costales D, Oke M, Liu H, Johnson KA, Carter LG, Botting CH, White MF, Challis GL, Naismith JH. AcsD catalyzes enantioselective citrate desymmetrization in siderophore biosynthesis. Nat Chem Biol 2009; 5:174-82. [PMID: 19182782 PMCID: PMC2644304 DOI: 10.1038/nchembio.145] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Accepted: 01/12/2009] [Indexed: 01/12/2023]
Abstract
Bacterial pathogens need to scavenge iron from their host for growth and proliferation during infection. They have evolved several strategies to do this, one being the biosynthesis and excretion of small, high-affinity iron chelators known as siderophores. The biosynthesis of siderophores is an important area of study, not only for potential therapeutic intervention, but also to illuminate new enzyme chemistries. Two general pathways for siderophore biosynthesis exist: the well-characterized nonribosomal peptide synthetase (NRPS)-dependent pathway and the NRPS-independent (NIS) pathway, which relies on a different family of sparsely-investigated synthetases. Here, we report structural and biochemical studies of AcsD from Pectobacterium (formerly Erwinia) chrysanthemi, a NIS synthetase involved in achromobactin biosynthesis. The structures of ATP and citrate complexes provide a mechanistic rationale for stereospecific formation of an enzyme-bound (3R)-citryl-adenylate, which reacts with L-serine to form a likely achromobactin precursor. AcsD is a novel acyl adenylate-forming enzyme with a new fold and chemical catalysis strategy.
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Affiliation(s)
- Stefan Schmelz
- Scottish Structural Proteomics Facility and Centre for Biomolecular Sciences, The University of St Andrews, Scotland KY16 9ST, UK
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49
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Haraldsen JD, Liu G, Botting CH, Walton JGA, Storm J, Phalen TJ, Kwok LY, Soldati-Favre D, Heintz NH, Müller S, Westwood NJ, Ward GE. IDENTIFICATION OF CONOIDIN A AS A COVALENT INHIBITOR OF PEROXIREDOXIN II. Org Biomol Chem 2009; 7:3040-3048. [PMID: 21359112 DOI: 10.1039/b901735f] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Conoidin A (1) is an inhibitor of host cell invasion by the protozoan parasite Toxoplasma gondii. In the course of studies aimed at identifying potential targets of this compound, we determined that it binds to the T. gondii enzyme peroxiredoxin II (TgPrxII). Peroxiredoxins are a widely conserved family of enzymes that function in antioxidant defense and signal transduction, and changes in PrxII expression are associated with a variety of human diseases, including cancer. Disruption of the TgPrxII gene by homologous recombination had no effect on the sensitivity of the parasites to 1, suggesting that TgPrxII is not the invasion-relevant target of 1. However, we showed that 1 binds covalently to the peroxidatic cysteine of TgPrxII, inhibiting its enzymatic activity in vitro. Studies with human epithelial cells showed that 1 also inhibits hyperoxidation of human PrxII. These data identify Conoidin A as a novel inhibitor of this important class of antioxidant and redox signaling enzymes.
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Affiliation(s)
- Jeralyn D Haraldsen
- Department of Microbiology and Molecular Genetics, 316 Stafford Hall, University of Vermont, 95 Carrigan Drive, Burlington VT 05405, USA
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50
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Oke M, Ching RTY, Carter LG, Johnson KA, Liu H, McMahon SA, White MF, Bloch C, Botting CH, Walsh MA, Latiff AA, Kennedy MW, Cooper A, Naismith JH. Unusual chromophore and cross-links in ranasmurfin: a blue protein from the foam nests of a tropical frog. Angew Chem Int Ed Engl 2008; 47:7853-6. [PMID: 18781570 DOI: 10.1002/anie.200802901] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [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)
- Muse Oke
- Centre for Biomolecular Science and The Scottish Structural Proteomics Facility, The University, St Andrews, UK
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