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Lamelas L, Valledor L, López-Hidalgo C, Cañal MJ, Meijón M. Nucleus and chloroplast: A necessary understanding to overcome heat stress in Pinus radiata. Plant Cell Environ 2022; 45:446-458. [PMID: 34855991 DOI: 10.1111/pce.14238] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
The recovery and maintenance of plant homeostasis under stressful environments are complex processes involving organelle crosstalk for a coordinated cellular response. Here, we revealed through nuclear and chloroplast subcellular proteomics, biochemical cell profiles and targeted transcriptomics how chloroplasts and nuclei developed their responses under increased temperatures in a long-lived species (Pinus radiata). Parallel to photosynthetic impairment and reactive oxygen species production in the chloroplast, a DNA damage response was triggered in the nucleus followed by an altered chromatin conformation. In addition, in the nuclei, we found several proteins, such as HEMERA or WHIRLY, which change their locations from the chloroplasts to the nuclei carrying the stress message. Additionally, our data showed a deep rearrangement of RNA metabolism in both organelles, revealing microRNAs and AGO1 as potential regulators of the acclimation mechanisms. Altogether, our study highlights the synchronisation among the different stages required for thermotolerance acquisition in P. radiata, pointing out the role of chromatin conformation and posttranscriptional gene regulation in overcoming heat stress and assuring plant survival for the following years.
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Affiliation(s)
- Laura Lamelas
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
| | - Cristina López-Hidalgo
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
| | - María Jesús Cañal
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
| | - Mónica Meijón
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
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Pérez-Sánchez R, Carnero-Morán A, Luz Valero M, Oleaga A. A proteomics informed by transcriptomics insight into the proteome of Ornithodoros erraticus adult tick saliva. Parasit Vectors 2022; 15:1. [PMID: 34980218 PMCID: PMC8722417 DOI: 10.1186/s13071-021-05118-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/06/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The argasid tick Ornithodoros erraticus is the main vector of tick-borne human relapsing fever (TBRF) and African swine fever (ASF) in the Mediterranean Basin. The prevention and control of these diseases would greatly benefit from the elimination of O. erraticus populations, and anti-tick vaccines are envisaged as an effective and sustainable alternative to chemical acaricide usage for tick control. Ornithodoros erraticus saliva contains bioactive proteins that play essential functions in tick feeding and host defence modulation, which may contribute to host infection by tick-borne pathogens. Hence, these proteins could be candidate antigen targets for the development of vaccines aimed at the control and prevention of O. erraticus infestations and the diseases this tick transmits. The objective of the present work was to obtain and characterise the proteome of the saliva of O. erraticus adult ticks as a means to identify and select novel salivary antigen targets. METHODS A proteomics informed by transcriptomics (PIT) approach was applied to analyse samples of female and male saliva separately using the previously obtained O. erraticus sialotranscriptome as a reference database and two different mass spectrometry techniques, namely liquid chromatography-tandem mass spectrometry (LC-MS/MS) in data-dependent acquisition mode and sequential window acquisition of all theoretical fragment ion spectra MS (SWATH-MS). RESULTS Up to 264 and 263 proteins were identified by LC-MS/MS in the saliva of O. erraticus female and male ticks, respectively, totalling 387 non-redundant proteins. Of these, 224 were further quantified by SWATH-MS in the saliva of both male and female ticks. Quantified proteins were classified into 23 functional categories and their abundance compared between sexes. Heme/iron-binding proteins, protease inhibitors, proteases, lipocalins and immune-related proteins were the categories most abundantly expressed in females, while glycolytic enzymes, protease inhibitors and lipocalins were the most abundantly expressed in males. Ninety-seven proteins were differentially expressed between the sexes, of which 37 and 60 were overexpressed in females and males, respectively. CONCLUSIONS The PIT approach demonstrated its usefulness for proteomics studies of O. erraticus, a non-model organism without genomic sequences available, allowing the publication of the first comprehensive proteome of the saliva of O. erraticus reported to date. These findings confirm important quantitative differences between sexes in the O. erraticus saliva proteome, unveil novel salivary proteins and functions at the tick-host feeding interface and improve our understanding of the physiology of feeding in O. erraticus ticks. The integration of O. erraticus sialoproteomic and sialotranscriptomic data will drive a more rational selection of salivary candidates as antigen targets for the development of vaccines aimed at the control of O. erraticus infestations and the diseases it transmits.
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Affiliation(s)
- Ricardo Pérez-Sánchez
- Parasitology Laboratory, Spanish National Research Council Institute of Natural Resources and Agrobiology (CSIC-IRNASA), Cordel de Merinas, 40-52, 37008 Salamanca, Spain
| | - Angel Carnero-Morán
- Parasitology Laboratory, Spanish National Research Council Institute of Natural Resources and Agrobiology (CSIC-IRNASA), Cordel de Merinas, 40-52, 37008 Salamanca, Spain
| | - M. Luz Valero
- Proteomics Section, Central Service for Experimental Research, University of Valencia, Carrer del Dr. Moliner, 50, 46100 Burjassot, Spain
| | - Ana Oleaga
- Parasitology Laboratory, Spanish National Research Council Institute of Natural Resources and Agrobiology (CSIC-IRNASA), Cordel de Merinas, 40-52, 37008 Salamanca, Spain
- Proteomics Section, Central Service for Experimental Research, University of Valencia, Carrer del Dr. Moliner, 50, 46100 Burjassot, Spain
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Zhao Y, Zhang F, Mickan B, Wang D, Wang W. Physiological, proteomic, and metabolomic analysis provide insights into Bacillus sp.-mediated salt tolerance in wheat. Plant Cell Rep 2022; 41:95-118. [PMID: 34546426 DOI: 10.1007/s00299-021-02788-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/09/2021] [Indexed: 05/15/2023]
Abstract
Herein, the inoculation with strain wp-6 promoted the growth of wheat seedlings by improving the energy production and conversion of wheat seedlings and alleviating salt stress. Soil salinization decreases crop productivity due to high toxicity of sodium ions to plants. Plant growth-promoting rhizobacteria (PGPR) have been demonstrated to alleviate salinity stress. However, the mechanism of PGPR in improving plant salt tolerance remains unclear. In this study, physiological analysis, proteomics, and metabolomics were applied to investigate the changes in wheat seedlings under salt stress (150 mM NaCl), both with and without plant root inoculation with wp-6 (Bacillus sp.). Under salt stress, root inoculation with strain wp-6 increased plant biomass (57%) and root length (25%). The Na+ content was reduced, while the K+ content and K+/Na+ ratio were increased. The content of malondialdehyde was decreased by 31.94% after inoculation of wp-6 under salt stress, while the content of proline, soluble sugar, and soluble protein were increased by 7.48%, 12.34%, and 4.12%, respectively. The peroxidase, catalase, and superoxide dismutase activities were increased after inoculation of wp-6 under salt stress. Galactose metabolism, phenylalanine metabolism, caffeine metabolism, ubiquinone and other terpenoid-quinone biosynthesis, and glutathione metabolism might play an important role in promoting the growth of salt-stressed wheat seedlings after the inoculation with wp-6. Interaction analysis of differentially expressed proteins and metabolites found that energy production and transformation-related proteins and six metabolites (D-arginine, palmitoleic acid, chlorophyllide b, rutin, pheophorbide a, and vanillylamine) were mainly involved in the growth of wheat seedlings after the inoculation with wp-6 under salt stress. Furthermore, correlation analysis found that inoculation with wp-6 promotes the growth of salt-stressed wheat seedlings mainly through regulating amino acid metabolism and porphyrin and chlorophyll metabolism. This study provides an eco-friendly method to increase agricultural productivity and paves a way to sustainable agriculture.
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Affiliation(s)
- Yaguang Zhao
- Key Laboratory of Oasis Ecology Agriculture of Xinjiang Bingtuan, Shihezi University, North 4th Street No. 221, Shihezi, 832003, Xinjiang, China
| | - Fenghua Zhang
- Key Laboratory of Oasis Ecology Agriculture of Xinjiang Bingtuan, Shihezi University, North 4th Street No. 221, Shihezi, 832003, Xinjiang, China.
| | - Bede Mickan
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6001, Australia
| | - Dan Wang
- Key Laboratory of Oasis Ecology Agriculture of Xinjiang Bingtuan, Shihezi University, North 4th Street No. 221, Shihezi, 832003, Xinjiang, China
| | - Weichao Wang
- Key Laboratory of Oasis Ecology Agriculture of Xinjiang Bingtuan, Shihezi University, North 4th Street No. 221, Shihezi, 832003, Xinjiang, China
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Demichev V, Tober-Lau P, Lemke O, Nazarenko T, Thibeault C, Whitwell H, Röhl A, Freiwald A, Szyrwiel L, Ludwig D, Correia-Melo C, Aulakh SK, Helbig ET, Stubbemann P, Lippert LJ, Grüning NM, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Mittermaier M, Machleidt F, Garcia C, Ruwwe-Glösenkamp C, Lingscheid T, Bosquillon de Jarcy L, Stegemann MS, Pfeiffer M, Jürgens L, Denker S, Zickler D, Enghard P, Zelezniak A, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Müller-Redetzky H, Zoller H, Löffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, Witzenrath M, Suttorp N, Lilley K, Mülleder M, Sander LE, Ralser M, Kurth F. A time-resolved proteomic and prognostic map of COVID-19. Cell Syst 2021; 12:780-794.e7. [PMID: 34139154 PMCID: PMC8201874 DOI: 10.1016/j.cels.2021.05.005] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/24/2021] [Accepted: 05/07/2021] [Indexed: 12/14/2022]
Abstract
COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma proteomes at 687 sampling points. We report an initial spike in a systemic inflammatory response, which is gradually alleviated and followed by a protein signature indicative of tissue repair, metabolic reconstitution, and immunomodulation. We identify prognostic marker signatures for devising risk-adapted treatment strategies and use machine learning to classify therapeutic needs. We show that the machine learning models based on the proteome are transferable to an independent cohort. Our study presents a map linking routinely used clinical diagnostic parameters to plasma proteomes and their dynamics in an infectious disease.
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Affiliation(s)
- Vadim Demichev
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK; The University of Cambridge, Department of Biochemistry and Cambridge Centre for Proteomics, Cambridge CB21GA, UK
| | - Pinkus Tober-Lau
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Oliver Lemke
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Tatiana Nazarenko
- University College London, Department of Mathematics, London WC1E 6BT, UK; University College London, Department of Women's Cancer, EGA Institute for Women'S Health, London WC1E 6BT, UK
| | - Charlotte Thibeault
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Harry Whitwell
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW72AZ, UK; Lobachevsky University, Department of Applied Mathematics, Nizhny Novgorod 603105, Russia; Imperial College London, Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, London SW7 2AZ, UK
| | - Annika Röhl
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Anja Freiwald
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Lukasz Szyrwiel
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Daniela Ludwig
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Clara Correia-Melo
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Simran Kaur Aulakh
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Elisa T Helbig
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Paula Stubbemann
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Lena J Lippert
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Nana-Maria Grüning
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Oleg Blyuss
- Lobachevsky University, Department of Applied Mathematics, Nizhny Novgorod 603105, Russia; University of Hertfordshire, School of Physics, Astronomy and Mathematics, Hatfield AL10 9AB, UK; Sechenov First Moscow State Medical University, Department of Paediatrics and Paediatric Infectious Diseases, Moscow 119435, Russia
| | - Spyros Vernardis
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Matthew White
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Christoph B Messner
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Michael Joannidis
- Medical University Innsbruck, Division of Intensive Care and Emergency Medicine, Department of Internal Medicine, 6020 Innsbruck, Austria
| | - Thomas Sonnweber
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - Sebastian J Klein
- Medical University Innsbruck, Division of Intensive Care and Emergency Medicine, Department of Internal Medicine, 6020 Innsbruck, Austria
| | - Alex Pizzini
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - Yvonne Wohlfarter
- Medical University of Innsbruck, Institute of Human Genetics, 6020 Innsbruck, Austria
| | - Sabina Sahanic
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - Richard Hilbe
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - Benedikt Schaefer
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, 6020 Innsbruck, Austria
| | - Sonja Wagner
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, 6020 Innsbruck, Austria
| | - Mirja Mittermaier
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Berlin Institute of Health, 10178 Berlin, Germany
| | - Felix Machleidt
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Carmen Garcia
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Christoph Ruwwe-Glösenkamp
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Tilman Lingscheid
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Laure Bosquillon de Jarcy
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Miriam S Stegemann
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Moritz Pfeiffer
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Linda Jürgens
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Sophy Denker
- Charité Universitätsmedizin Berlin, Medical Department of Hematology, Oncology & Tumor Immunology, Virchow Campus & Molekulares Krebsforschungszentrum, 13353 Berlin, Germany; Berlin Institute of Health, 10178 Berlin, Germany
| | - Daniel Zickler
- Charité Universitätsmedizin Berlin, Department of Nephrology and Internal Intensive Care Medicine, 10117 Berlin, Germany
| | - Philipp Enghard
- Charité Universitätsmedizin Berlin, Department of Nephrology and Internal Intensive Care Medicine, 10117 Berlin, Germany
| | - Aleksej Zelezniak
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK; Chalmers Tekniska Högskola, Department of Biology and Biological Engineering, SE-412 96 Gothenburg, Sweden
| | - Archie Campbell
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, Edinburgh EH4 2XU, UK; University of Edinburgh, Usher Institute, Edinburgh EH16 4UX, UK
| | - Caroline Hayward
- University of Edinburgh, MRC Human Genetics Unit, Institute of Genetics and Cancer, Edinburgh EH4 2XU, UK
| | - David J Porteous
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, Edinburgh EH4 2XU, UK; University of Edinburgh, Usher Institute, Edinburgh EH16 4UX, UK
| | - Riccardo E Marioni
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, Edinburgh EH4 2XU, UK
| | - Alexander Uhrig
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Holger Müller-Redetzky
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Heinz Zoller
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, 6020 Innsbruck, Austria
| | - Judith Löffler-Ragg
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - Markus A Keller
- Medical University of Innsbruck, Institute of Human Genetics, 6020 Innsbruck, Austria
| | - Ivan Tancevski
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - John F Timms
- University College London, Department of Women's Cancer, EGA Institute for Women'S Health, London WC1E 6BT, UK
| | - Alexey Zaikin
- University College London, Department of Mathematics, London WC1E 6BT, UK; University College London, Department of Women's Cancer, EGA Institute for Women'S Health, London WC1E 6BT, UK; Lobachevsky University, Laboratory of Systems Medicine of Healthy Ageing, Nizhny Novgorod 603105, Russia
| | - Stefan Hippenstiel
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; German Centre for Lung Research, 35392 Gießen, Germany
| | - Michael Ramharter
- Bernhard Nocht Institute for Tropical Medicine, Department of Tropical Medicine, and University Medical Center Hamburg-Eppendorf, Department of Medicine, 20359 Hamburg, Germany
| | - Martin Witzenrath
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; German Centre for Lung Research, 35392 Gießen, Germany
| | - Norbert Suttorp
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; German Centre for Lung Research, 35392 Gießen, Germany
| | - Kathryn Lilley
- The University of Cambridge, Department of Biochemistry and Cambridge Centre for Proteomics, Cambridge CB21GA, UK
| | - Michael Mülleder
- Charité - Universitätsmedizin Berlin, Core Facility - High-Throughput Mass Spectrometry, 10117 Berlin, Germany
| | - Leif Erik Sander
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; German Centre for Lung Research, 35392 Gießen, Germany
| | - Markus Ralser
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK.
| | - Florian Kurth
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Bernhard Nocht Institute for Tropical Medicine, Department of Tropical Medicine, and University Medical Center Hamburg-Eppendorf, Department of Medicine, 20359 Hamburg, Germany
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Takemon Y, Chick JM, Gerdes Gyuricza I, Skelly DA, Devuyst O, Gygi SP, Churchill GA, Korstanje R. Proteomic and transcriptomic profiling reveal different aspects of aging in the kidney. eLife 2021; 10:e62585. [PMID: 33687326 PMCID: PMC8096428 DOI: 10.7554/elife.62585] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [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: 09/01/2020] [Accepted: 03/06/2021] [Indexed: 01/10/2023] Open
Abstract
Little is known about the molecular changes that take place in the kidney during the aging process. In order to better understand these changes, we measured mRNA and protein levels in genetically diverse mice at different ages. We observed distinctive change in mRNA and protein levels as a function of age. Changes in both mRNA and protein are associated with increased immune infiltration and decreases in mitochondrial function. Proteins show a greater extent of change and reveal changes in a wide array of biological processes including unique, organ-specific features of aging in kidney. Most importantly, we observed functionally important age-related changes in protein that occur in the absence of corresponding changes in mRNA. Our findings suggest that mRNA profiling alone provides an incomplete picture of molecular aging in the kidney and that examination of changes in proteins is essential to understand aging processes that are not transcriptionally regulated.
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Affiliation(s)
| | - Joel M Chick
- Harvard Medical SchoolBostonUnited States
- VividionTherapeuticsSan DiegoUnited States
| | | | | | - Olivier Devuyst
- Institute of Physiology, University of ZurichZurichSwitzerland
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Du W, Ruan C, Li J, Li H, Ding J, Zhao S, Jiang X. Quantitative proteomic analysis of Xanthoceras sorbifolium Bunge seedlings in response to drought and heat stress. Plant Physiol Biochem 2021; 160:8-17. [PMID: 33445043 DOI: 10.1016/j.plaphy.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Yellowhorn (Xanthoceras sorbifolium Bunge) is a woody oil species that is widely distributed in northwestern China. To investigate the molecular mechanisms underlying the drought and heat tolerance response of yellowhorn seedlings, changes in protein abundance were analyzed via comparative proteomics. Drought and heat treatment of seedlings was applied in growth chamber, and the leaves were harvested after 7 days of treatment. The total protein was extracted, and comparative proteomic analysis was performed via isobaric tag for relative and absolute quantitation (iTRAQ). The abundance of most of the proteins associated with oxidative phosphorylation, NADH dehydrogenase and superoxide dismutase (SOD) was reduced. The differential proteins associated with photosynthesis enzymes indicated that stress had different effects on photosystem I (PSI) and photosystem II (PSII). After comprehensively analyzing the results, we speculated that drought and heat stress could hinder the synthesis of riboflavin, reducing NADH dehydrogenase content, which might further have an impact on energy utilization. Yellowhorn seedlings relied on Fe-Mn SOD enzymes rather than Cu/Zn SOD enzymes to remove reactive oxygen species (ROS). In addition, heat-shock proteins (HSPs) had significant increase and played a key role in stress response, which could be divided into two categories according to their transcription and translation efficiency. Over all, the results can provide a basis for understanding the molecular mechanism underlying resistance to drought and heat stress in yellowhorn and for subsequent research of posttranslational modification-related omics of key proteins.
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Affiliation(s)
- Wei Du
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian Nationalities University, Dalian, 116600, China
| | - Chengjiang Ruan
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian Nationalities University, Dalian, 116600, China.
| | - Jingbin Li
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian Nationalities University, Dalian, 116600, China
| | - He Li
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian Nationalities University, Dalian, 116600, China
| | - Jian Ding
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian Nationalities University, Dalian, 116600, China
| | - Siyang Zhao
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian Nationalities University, Dalian, 116600, China
| | - Xin Jiang
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian Nationalities University, Dalian, 116600, China
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Abstract
Platelets rapidly undergo responsive transitions in form and function to repair vascular endothelium and mediate hemostasis. In contrast, heterogeneous platelet subpopulations with a range of primed or refractory phenotypes gradually arise in chronic inflammatory and other conditions in a manner that may indicate or support disease. Qualitatively distinguishable platelet phenotypes are increasingly associated with a variety of physiological and pathological circumstances; however, the origins and significance of platelet phenotypic variation remain unclear and conceptually vague. As changes in platelet function in disease exhibit many similarities to platelets following the activation of platelet agonist receptors, the intracellular responses of platelets common to hemostasis and inflammation may provide insights to the molecular basis of platelet phenotype. Here, we review concepts around how protein-level relations-from platelet receptors through intracellular signaling events-may help to define platelet phenotypes in inflammation, immune responses, aging, and other conditions. We further discuss how representing systems-wide platelet proteomics data profiles as circuit-like networks of causally related intracellular events, or, pathway maps, may inform molecular definitions of platelet phenotype. In addition to offering insights into platelets as druggable targets, maps of causally arranged intracellular relations underlying platelet function can also advance precision and interceptive medicine efforts by leveraging platelets as accessible, dynamic, endogenous, circulating biomarkers of vascular wellness and disease. Graphic Abstract: A graphic abstract is available for this article.
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Affiliation(s)
- Joseph E. Aslan
- Knight Cardiovascular Institute, School of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Chemical Physiology and Biochemistry and School of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, Oregon, USA
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Flannery SE, Hepworth C, Wood WHJ, Pastorelli F, Hunter CN, Dickman MJ, Jackson PJ, Johnson MP. Developmental acclimation of the thylakoid proteome to light intensity in Arabidopsis. Plant J 2021; 105:223-244. [PMID: 33118270 PMCID: PMC7898487 DOI: 10.1111/tpj.15053] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 10/13/2020] [Accepted: 10/21/2020] [Indexed: 05/03/2023]
Abstract
Photosynthetic acclimation, the ability to adjust the composition of the thylakoid membrane to optimise the efficiency of electron transfer to the prevailing light conditions, is crucial to plant fitness in the field. While much is known about photosynthetic acclimation in Arabidopsis, to date there has been no study that combines both quantitative label-free proteomics and photosynthetic analysis by gas exchange, chlorophyll fluorescence and P700 absorption spectroscopy. Using these methods we investigated how the levels of 402 thylakoid proteins, including many regulatory proteins not previously quantified, varied upon long-term (weeks) acclimation of Arabidopsis to low (LL), moderate (ML) and high (HL) growth light intensity and correlated these with key photosynthetic parameters. We show that changes in the relative abundance of cytb6 f, ATP synthase, FNR2, TIC62 and PGR6 positively correlate with changes in estimated PSII electron transfer rate and CO2 assimilation. Improved photosynthetic capacity in HL grown plants is paralleled by increased cyclic electron transport, which positively correlated with NDH, PGRL1, FNR1, FNR2 and TIC62, although not PGR5 abundance. The photoprotective acclimation strategy was also contrasting, with LL plants favouring slowly reversible non-photochemical quenching (qI), which positively correlated with LCNP, while HL plants favoured rapidly reversible quenching (qE), which positively correlated with PSBS. The long-term adjustment of thylakoid membrane grana diameter positively correlated with LHCII levels, while grana stacking negatively correlated with CURT1 and RIQ protein abundance. The data provide insights into how Arabidopsis tunes photosynthetic electron transfer and its regulation during developmental acclimation to light intensity.
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Affiliation(s)
- Sarah E. Flannery
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldFirth CourtWestern BankSheffieldUK
| | - Christopher Hepworth
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldFirth CourtWestern BankSheffieldUK
| | - William H. J. Wood
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldFirth CourtWestern BankSheffieldUK
| | - Federica Pastorelli
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldFirth CourtWestern BankSheffieldUK
| | - Christopher N. Hunter
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldFirth CourtWestern BankSheffieldUK
| | - Mark J. Dickman
- Department of Chemical and Biological EngineeringChELSI InstituteUniversity of SheffieldSheffieldUK
| | - Philip J. Jackson
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldFirth CourtWestern BankSheffieldUK
- Department of Chemical and Biological EngineeringChELSI InstituteUniversity of SheffieldSheffieldUK
| | - Matthew P. Johnson
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldFirth CourtWestern BankSheffieldUK
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9
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He Y, Peng X, Liu Y, Wu Q, Zhou Q, Hu L, Fang Z, Lin Y, Xu S, Feng B, Li J, Zhuo Y, Wu D, Che L. Effects of Maternal Fiber Intake on Intestinal Morphology, Bacterial Profile and Proteome of Newborns Using Pig as Model. Nutrients 2020; 13:E42. [PMID: 33375592 PMCID: PMC7823571 DOI: 10.3390/nu13010042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
Dietary fiber intake during pregnancy may improve offspring intestinal development. The aim of this study was to evaluate the effect of maternal high fiber intake during late gestation on intestinal morphology, microbiota, and intestinal proteome of newborn piglets. Sixteen sows were randomly allocated into two groups receiving the control diet (CD) and high-fiber diet (HFD) from day 90 of gestation to farrowing. Newborn piglets were selected from each litter, named as CON and Fiber group, respectively. Maternal high fiber intake did not markedly improve the birth weight, but increased the body length, the ileal crypt depth and colonic acetate level. In addition, maternal high fiber intake increased the -diversity indices (Observed species, Simpson, and ACE), and the abundance of Acidobacteria and Bacteroidetes at phylum level, significantly increased the abundance of Bradyrhizobium and Phyllobacterium at genus level in the colon of newborn piglets. Moreover, maternal high fiber intake markedly altered the ileal proteome, increasing the abundances of proteins associated with oxidative status, energy metabolism, and immune and inflammatory responses, and decreasing abundances of proteins related to cellular apoptosis, cell structure, and motility. These findings indicated that maternal high fiber intake could alter intestinal morphology, along with the altered intestinal microbiota composition and proteome of offspring.
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Affiliation(s)
- Ying He
- Key Laboratory for Animal Disease-Resistant Nutrition of the Ministry of Education of China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.H.); (X.P.); (Y.L.); (Q.W.); (Q.Z.); (Z.F.); (Y.L.); (S.X.); (B.F.); (J.L.); (Y.Z.); (D.W.)
| | - Xie Peng
- Key Laboratory for Animal Disease-Resistant Nutrition of the Ministry of Education of China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.H.); (X.P.); (Y.L.); (Q.W.); (Q.Z.); (Z.F.); (Y.L.); (S.X.); (B.F.); (J.L.); (Y.Z.); (D.W.)
| | - Yang Liu
- Key Laboratory for Animal Disease-Resistant Nutrition of the Ministry of Education of China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.H.); (X.P.); (Y.L.); (Q.W.); (Q.Z.); (Z.F.); (Y.L.); (S.X.); (B.F.); (J.L.); (Y.Z.); (D.W.)
| | - Qing Wu
- Key Laboratory for Animal Disease-Resistant Nutrition of the Ministry of Education of China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.H.); (X.P.); (Y.L.); (Q.W.); (Q.Z.); (Z.F.); (Y.L.); (S.X.); (B.F.); (J.L.); (Y.Z.); (D.W.)
| | - Qiang Zhou
- Key Laboratory for Animal Disease-Resistant Nutrition of the Ministry of Education of China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.H.); (X.P.); (Y.L.); (Q.W.); (Q.Z.); (Z.F.); (Y.L.); (S.X.); (B.F.); (J.L.); (Y.Z.); (D.W.)
| | - Liang Hu
- College of Food Science, Sichuan Agricultural University, Ya’an 625014, China;
| | - Zhengfeng Fang
- Key Laboratory for Animal Disease-Resistant Nutrition of the Ministry of Education of China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.H.); (X.P.); (Y.L.); (Q.W.); (Q.Z.); (Z.F.); (Y.L.); (S.X.); (B.F.); (J.L.); (Y.Z.); (D.W.)
| | - Yan Lin
- Key Laboratory for Animal Disease-Resistant Nutrition of the Ministry of Education of China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.H.); (X.P.); (Y.L.); (Q.W.); (Q.Z.); (Z.F.); (Y.L.); (S.X.); (B.F.); (J.L.); (Y.Z.); (D.W.)
| | - Shengyu Xu
- Key Laboratory for Animal Disease-Resistant Nutrition of the Ministry of Education of China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.H.); (X.P.); (Y.L.); (Q.W.); (Q.Z.); (Z.F.); (Y.L.); (S.X.); (B.F.); (J.L.); (Y.Z.); (D.W.)
| | - Bin Feng
- Key Laboratory for Animal Disease-Resistant Nutrition of the Ministry of Education of China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.H.); (X.P.); (Y.L.); (Q.W.); (Q.Z.); (Z.F.); (Y.L.); (S.X.); (B.F.); (J.L.); (Y.Z.); (D.W.)
| | - Jian Li
- Key Laboratory for Animal Disease-Resistant Nutrition of the Ministry of Education of China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.H.); (X.P.); (Y.L.); (Q.W.); (Q.Z.); (Z.F.); (Y.L.); (S.X.); (B.F.); (J.L.); (Y.Z.); (D.W.)
| | - Yong Zhuo
- Key Laboratory for Animal Disease-Resistant Nutrition of the Ministry of Education of China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.H.); (X.P.); (Y.L.); (Q.W.); (Q.Z.); (Z.F.); (Y.L.); (S.X.); (B.F.); (J.L.); (Y.Z.); (D.W.)
| | - De Wu
- Key Laboratory for Animal Disease-Resistant Nutrition of the Ministry of Education of China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.H.); (X.P.); (Y.L.); (Q.W.); (Q.Z.); (Z.F.); (Y.L.); (S.X.); (B.F.); (J.L.); (Y.Z.); (D.W.)
| | - Lianqiang Che
- Key Laboratory for Animal Disease-Resistant Nutrition of the Ministry of Education of China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China; (Y.H.); (X.P.); (Y.L.); (Q.W.); (Q.Z.); (Z.F.); (Y.L.); (S.X.); (B.F.); (J.L.); (Y.Z.); (D.W.)
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10
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Jiang L, Wang M, Lin S, Jian R, Li X, Chan J, Dong G, Fang H, Robinson AE, Snyder MP. A Quantitative Proteome Map of the Human Body. Cell 2020; 183:269-283.e19. [PMID: 32916130 PMCID: PMC7575058 DOI: 10.1016/j.cell.2020.08.036] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/14/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023]
Abstract
Determining protein levels in each tissue and how they compare with RNA levels is important for understanding human biology and disease as well as regulatory processes that control protein levels. We quantified the relative protein levels from over 12,000 genes across 32 normal human tissues. Tissue-specific or tissue-enriched proteins were identified and compared to transcriptome data. Many ubiquitous transcripts are found to encode tissue-specific proteins. Discordance of RNA and protein enrichment revealed potential sites of synthesis and action of secreted proteins. The tissue-specific distribution of proteins also provides an in-depth view of complex biological events that require the interplay of multiple tissues. Most importantly, our study demonstrated that protein tissue-enrichment information can explain phenotypes of genetic diseases, which cannot be obtained by transcript information alone. Overall, our results demonstrate how understanding protein levels can provide insights into regulation, secretome, metabolism, and human diseases.
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Affiliation(s)
- Lihua Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meng Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shin Lin
- Division of Cardiology, University of Washington, Seattle, WA 98195, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xiao Li
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joanne Chan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Guanlan Dong
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Huaying Fang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aaron E Robinson
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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11
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Abstract
Osteoporosis is a severe chronic skeletal disorder that increases the risks of disability and mortality; however, the mechanism of this disease and the protein markers for prognosis of osteoporosis have not been well characterized. This study aims to characterize the imbalanced serum proteostasis, the disturbed pathways, and potential serum markers in osteoporosis by using a set of bioinformatic analyses. In the present study, the large-scale proteomics datasets (PXD006464) were adopted from the Proteome Xchange database and processed with MaxQuant. The differentially expressed serum proteins were identified. The biological process and molecular function were analyzed. The protein-protein interactions and subnetwork modules were constructed. The signaling pathways were enriched. We identified 209 upregulated and 230 downregulated serum proteins. The bioinformatic analyses revealed a highly overlapped functional protein classification and the gene ontology terms between the upregulated and downregulated protein groups. Protein-protein interactions and pathway analyses showed a high enrichment in protein synthesis, inflammation, and immune response in the upregulated proteins, and cell adhesion and cytoskeleton regulation in the downregulated proteins. Our findings greatly expand the current view of the roles of serum proteins in osteoporosis and shed light on the understanding of its underlying mechanisms and the discovery of serum proteins as potential markers for the prognosis of osteoporosis.
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Affiliation(s)
- Mengying Lv
- Institute of Translational Medicine, Medical College, Yangzhou University
- Jiangsu Key Laboratory of Experimental and Translational Non-coding RNA Research, Yangzhou, Jiangsu, PR China
| | - Chuanlong Cui
- School of Graduate Studies, Rutgers, The State University of New Jersey, Newark, NJ
| | - Peng Chen
- No. 5 Region, The First Affiliated Hospital of Guangzhou University of Chinese Medicine
| | - Ziqi Li
- Department of Joint Diseases, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine
- Traumatology and Orthopedics Institute of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
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12
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Li H, Hu J, Pang J, Zhao L, Yang B, Kang X, Wang A, Xu T, Yang Z. Rho GTPase ROP1 Interactome Analysis Reveals Novel ROP1-Associated Pathways for Pollen Tube Polar Growth in Arabidopsis. Int J Mol Sci 2020; 21:ijms21197033. [PMID: 32987815 PMCID: PMC7582345 DOI: 10.3390/ijms21197033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 12/27/2022] Open
Abstract
ROP (Rho-like GTPases from plants) GTPases are polarly localized key regulators of polar growth in pollen tubes and other cells in plants. However, how ROP GTPases are regulated and how they control polar growth remains to be fully understood. To gain new insights into ROP-dependent mechanisms underlying polar cell growth, we characterized the interactome of ROP1 GTPase that controls Arabidopsis pollen tube (PT) tip growth, an extreme form of polar cell growth. We established an efficient method for culturing Arabidopsis pollen tubes in liquid medium, which was used for immunoprecipitation/mass spectrometry-based identification of ROP1-associated proteins. A total of 654 candidates were isolated from the ROP1 interactome in Arabidopsis pollen tubes, and GO (Gene Ontology) classification and pathway analysis revealed multiple uncharacterized ROP1-dependent processes including translation, cell wall modification, post transcriptional modification, and ion homeostasis, in addition to known ROP1-dependent pathways. The ROP1-interactome data was further supported by the co-expression of the candidate interactors in highly mature pollen with PT germination and growth defects being discovered in 25% (8/32) of the candidate mutant genes. Taken together, our work uncovers valuable information for the identification and functional elucidation of ROP-associated proteins in the regulation of polar growth, and provides a reliable reference to identify critical regulators of polar cell growth in the future.
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Affiliation(s)
- Hui Li
- CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 201602, China; (J.H.); (L.Z.); (B.Y.); (X.K.); (T.X.)
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, and Department of Botany and Plant Sciences, University of California, Riverside, CA 92508, USA;
- Correspondence:
| | - Jinbo Hu
- CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 201602, China; (J.H.); (L.Z.); (B.Y.); (X.K.); (T.X.)
- Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Pang
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (J.P.); (A.W.)
| | - Liangtao Zhao
- CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 201602, China; (J.H.); (L.Z.); (B.Y.); (X.K.); (T.X.)
| | - Bing Yang
- CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 201602, China; (J.H.); (L.Z.); (B.Y.); (X.K.); (T.X.)
| | - Xinlei Kang
- CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 201602, China; (J.H.); (L.Z.); (B.Y.); (X.K.); (T.X.)
| | - Aimin Wang
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (J.P.); (A.W.)
| | - Tongda Xu
- CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 201602, China; (J.H.); (L.Z.); (B.Y.); (X.K.); (T.X.)
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhenbiao Yang
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, and Department of Botany and Plant Sciences, University of California, Riverside, CA 92508, USA;
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13
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Wang ZQ, Zhao QM, Zhong X, Xiao L, Ma LX, Wu CF, Zhang Z, Zhang LQ, Tian Y, Fan W. Comparative analysis of maca (Lepidium meyenii) proteome profiles reveals insights into response mechanisms of herbal plants to high-temperature stress. BMC Plant Biol 2020; 20:431. [PMID: 32938390 PMCID: PMC7493174 DOI: 10.1186/s12870-020-02645-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/10/2020] [Indexed: 05/14/2023]
Abstract
BACKGROUND High-temperature stress (HTS) is one of the main environmental stresses that limit plant growth and crop production in agricultural systems. Maca (Lepidium meyenii) is an important high-altitude herbaceous plant adapted to a wide range of environmental stimuli such as cold, strong wind and UV-B exposure. However, it is an extremely HTS-sensitive plant species. Thus far, there is limited information about gene/protein regulation and signaling pathways related to the heat stress responses in maca. In this study, proteome profiles of maca seedlings exposed to HTS for 12 h were investigated using a tandem mass tag (TMT)-based proteomic approach. RESULTS In total, 6966 proteins were identified, of which 300 showed significant alterations in expression following HTS. Bioinformatics analyses indicated that protein processing in endoplasmic reticulum was the most significantly up-regulated metabolic pathway following HTS. Quantitative RT-PCR (qRT-PCR) analysis showed that the expression levels of 19 genes encoding proteins mapped to this pathway were significantly up-regulated under HTS. These results show that protein processing in the endoplasmic reticulum may play a crucial role in the responses of maca to HTS. CONCLUSIONS Our proteomic data can be a good resource for functional proteomics of maca and our results may provide useful insights into the molecular response mechanisms underlying herbal plants to HTS.
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Affiliation(s)
- Zhan Qi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Qi Ming Zhao
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
| | - Xueting Zhong
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Li Xiao
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Li Xuan Ma
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Chou Fei Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Zhongshan Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Li Qin Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
- Huzhou central hospital, Huzhou University, Huzhou, 313000 China
| | - Yang Tian
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Wei Fan
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
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14
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Boll I, Jensen P, Schwämmle V, Larsen MR. Depolarization-dependent Induction of Site-specific Changes in Sialylation on N-linked Glycoproteins in Rat Nerve Terminals. Mol Cell Proteomics 2020; 19:1418-1435. [PMID: 32518069 PMCID: PMC8143646 DOI: 10.1074/mcp.ra119.001896] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 06/08/2020] [Indexed: 12/11/2022] Open
Abstract
Synaptic transmission leading to release of neurotransmitters in the nervous system is a fast and highly dynamic process. Previously, protein interaction and phosphorylation have been thought to be the main regulators of synaptic transmission. Here we show that sialylation of N-linked glycosylation is a novel potential modulator of neurotransmitter release mechanisms by investigating depolarization-dependent changes of formerly sialylated N-linked glycopeptides. We suggest that negatively charged sialic acids can be modulated, similarly to phosphorylation, by the action of sialyltransferases and sialidases thereby changing local structure and function of membrane glycoproteins. We characterized site-specific alteration in sialylation on N-linked glycoproteins in isolated rat nerve terminals after brief depolarization using quantitative sialiomics. We identified 1965 formerly sialylated N-linked glycosites in synaptic proteins and found that the abundances of 430 glycosites changed after 5 s depolarization. We observed changes on essential synaptic proteins such as synaptic vesicle proteins, ion channels and transporters, neurotransmitter receptors and cell adhesion molecules. This study is to our knowledge the first to describe ultra-fast site-specific modulation of the sialiome after brief stimulation of a biological system.
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Affiliation(s)
- Inga Boll
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Pia Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark.
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15
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Sepil I, Hopkins BR, Dean R, Bath E, Friedman S, Swanson B, Ostridge HJ, Harper L, Buehner NA, Wolfner MF, Konietzny R, Thézénas ML, Sandham E, Charles PD, Fischer R, Steinhauer J, Kessler BM, Wigby S. Male reproductive aging arises via multifaceted mating-dependent sperm and seminal proteome declines, but is postponable in Drosophila. Proc Natl Acad Sci U S A 2020; 117:17094-17103. [PMID: 32611817 PMCID: PMC7382285 DOI: 10.1073/pnas.2009053117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Declining ejaculate performance with male age is taxonomically widespread and has broad fitness consequences. Ejaculate success requires fully functional germline (sperm) and soma (seminal fluid) components. However, some aging theories predict that resources should be preferentially diverted to the germline at the expense of the soma, suggesting differential impacts of aging on sperm and seminal fluid and trade-offs between them or, more broadly, between reproduction and lifespan. While harmful effects of male age on sperm are well known, we do not know how much seminal fluid deteriorates in comparison. Moreover, given the predicted trade-offs, it remains unclear whether systemic lifespan-extending interventions could ameliorate the declining performance of the ejaculate as a whole. Here, we address these problems using Drosophila melanogaster. We demonstrate that seminal fluid deterioration contributes to male reproductive decline via mating-dependent mechanisms that include posttranslational modifications to seminal proteins and altered seminal proteome composition and transfer. Additionally, we find that sperm production declines chronologically with age, invariant to mating activity such that older multiply mated males become infertile principally via reduced sperm transfer and viability. Our data, therefore, support the idea that both germline and soma components of the ejaculate contribute to male reproductive aging but reveal a mismatch in their aging patterns. Our data do not generally support the idea that the germline is prioritized over soma, at least, within the ejaculate. Moreover, we find that lifespan-extending systemic down-regulation of insulin signaling results in improved late-life ejaculate performance, indicating simultaneous amelioration of both somatic and reproductive aging.
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Affiliation(s)
- Irem Sepil
- Department of Zoology, University of Oxford, OX1 3SZ Oxford, United Kingdom;
| | - Ben R Hopkins
- Department of Zoology, University of Oxford, OX1 3SZ Oxford, United Kingdom
- Department of Ecology and Evolution, University of California, Davis, CA 95616
| | - Rebecca Dean
- Department of Genetics, Evolution and Environment, University College London, WC1E 6BT London, United Kingdom
| | - Eleanor Bath
- Department of Zoology, University of Oxford, OX1 3SZ Oxford, United Kingdom
| | | | - Ben Swanson
- Department of Zoology, University of Oxford, OX1 3SZ Oxford, United Kingdom
| | - Harrison J Ostridge
- Department of Zoology, University of Oxford, OX1 3SZ Oxford, United Kingdom
- Department of Genetics, Evolution and Environment, University College London, WC1E 6BT London, United Kingdom
| | - Lucy Harper
- Department of Zoology, University of Oxford, OX1 3SZ Oxford, United Kingdom
- School of Biology, University of St Andrews, KY16 9ST St Andrews, United Kingdom
| | - Norene A Buehner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Rebecca Konietzny
- Nuffield Department of Medicine, TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of Oxford, OX3 7FZ Oxford, United Kingdom
| | - Marie-Laëtitia Thézénas
- Nuffield Department of Medicine, TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of Oxford, OX3 7FZ Oxford, United Kingdom
| | - Elizabeth Sandham
- Department of Zoology, University of Oxford, OX1 3SZ Oxford, United Kingdom
| | - Philip D Charles
- Nuffield Department of Medicine, TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of Oxford, OX3 7FZ Oxford, United Kingdom
| | - Roman Fischer
- Nuffield Department of Medicine, TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of Oxford, OX3 7FZ Oxford, United Kingdom
| | | | - Benedikt M Kessler
- Nuffield Department of Medicine, TDI Mass Spectrometry Laboratory, Target Discovery Institute, University of Oxford, OX3 7FZ Oxford, United Kingdom
| | - Stuart Wigby
- Department of Zoology, University of Oxford, OX1 3SZ Oxford, United Kingdom
- Faculty Biology, Applied Zoology, Technische Universität Dresden, 01069 Dresden, Germany
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7ZB Liverpool, United Kingdom
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16
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Santos-Lozano A, Fiuza-Luces C, Fernández-Moreno D, Llavero F, Arenas J, López JA, Vázquez J, Escribano-Subías P, Zugaza JL, Lucia A. Exercise Benefits in Pulmonary Hypertension. J Am Coll Cardiol 2020; 73:2906-2907. [PMID: 31171100 DOI: 10.1016/j.jacc.2019.03.489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 03/20/2019] [Accepted: 03/20/2019] [Indexed: 11/30/2022]
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17
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Barros D, Pradhan A, Pascoal C, Cássio F. Proteomic responses to silver nanoparticles vary with the fungal ecotype. Sci Total Environ 2020; 704:135385. [PMID: 31787274 DOI: 10.1016/j.scitotenv.2019.135385] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/03/2019] [Accepted: 11/03/2019] [Indexed: 06/10/2023]
Abstract
Enhanced commercial application of silver nanoparticles (AgNPs) is increasing the chance of their release into aquatic environments, potentially putting non-target microorganisms at risk. Impacts of AgNPs and Ag+ on two fungal ecotypes of Articulospora tetracladia, collected from a metal-polluted (At61) and a non-polluted (At72) stream, were assessed based on antioxidant enzymatic and proteomic responses. At61 showed more tolerance to AgNPs than At72 (EC20, 158.9 vs 7.5 µg L-1, respectively). Antioxidant enzyme activities were induced by AgNPs or Ag+ in both fungal ecotypes. Proteomic responses to AgNPs or Ag+ revealed that 41.3% of the total altered proteins were common in At72, while 27.3% were common in At61. In At72, gene ontology enrichment analyses indicated that Ag+ increased mainly the content of proteins involved in proteostasis and decreased the content of those related to vesicle-mediated transport; whereas the key group of proteins induced by AgNPs had functions in DNA repair and energy production. In At61, AgNPs induced proteins involved in energy production and protein biosynthesis, while both Ag forms induced proteins related to cell-redox and protein homeostasis, ascospore formation, fatty acid biosynthesis and nucleic acids metabolism. Both Ag forms induced stress-responsive proteins, and this was consistent with the responses of antioxidant enzymes. The negligible quantity of Ag+ released from AgNPs (<0.2 μg L-1) supported a minor role of dissolved ionic form in AgNP-induced toxicity to both fungal ecotypes. Overall, results unraveled distinct mechanisms of toxicity and cellular targets of nanoparticulate and ionic silver in aquatic fungi with different environmental background, and constitutes a proof of concept that toxicants induce adaptive responses in microbes to face emergent contaminants.
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Affiliation(s)
- Diana Barros
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Arunava Pradhan
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal.
| | - Cláudia Pascoal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Fernanda Cássio
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
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18
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Ray S, Valekunja UK, Stangherlin A, Howell SA, Snijders AP, Damodaran G, Reddy AB. Circadian rhythms in the absence of the clock gene Bmal1. Science 2020; 367:800-806. [PMID: 32054765 DOI: 10.1126/science.aaw7365] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 07/18/2019] [Accepted: 01/14/2020] [Indexed: 12/14/2022]
Abstract
Circadian (~24 hour) clocks have a fundamental role in regulating daily physiology. The transcription factor BMAL1 is a principal driver of a molecular clock in mammals. Bmal1 deletion abolishes 24-hour activity patterning, one measure of clock output. We determined whether Bmal1 function is necessary for daily molecular oscillations in skin fibroblasts and liver slices. Unexpectedly, in Bmal1 knockout mice, both tissues exhibited 24-hour oscillations of the transcriptome, proteome, and phosphoproteome over 2 to 3 days in the absence of any exogenous drivers such as daily light or temperature cycles. This demonstrates a competent 24-hour molecular pacemaker in Bmal1 knockouts. We suggest that such oscillations might be underpinned by transcriptional regulation by the recruitment of ETS family transcription factors, and nontranscriptionally by co-opting redox oscillations.
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Affiliation(s)
- Sandipan Ray
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Utham K Valekunja
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessandra Stangherlin
- Institute of Metabolic Science, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | | | | | | | - Akhilesh B Reddy
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Chronobiology and Sleep institute (CSI), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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19
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Noronha Souza PF, Abreu Oliveira JT, Vasconcelos IM, Magalhães VG, Albuquerque Silva FD, Guedes Silva RG, Oliveira KS, Franco OL, Gomes Silveira JA, Leite Carvalho FE. H 2O 2Accumulation, Host Cell Death and Differential Levels of Proteins Related to Photosynthesis, Redox Homeostasis, and Required for Viral Replication Explain the Resistance of EMS-mutagenized Cowpea to Cowpea Severe Mosaic Virus. J Plant Physiol 2020; 245:153110. [PMID: 31918353 DOI: 10.1016/j.jplph.2019.153110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 06/10/2023]
Abstract
Infection with Cowpea severe mosaic virus (CPSMV) represents one of the main limitations for cowpea (Vigna unguiculata L. Walp.) productivity due to the severity of the disease symptoms, frequency of incidence, and difficulties in dissemination control. This study aimed to identify the proteins and metabolic pathways associated with the susceptibility and resistance of cowpea plants to CPSMV. Therefore, we treated the seeds of a naturally susceptible cowpea genotype (CE-31) with the mutagenic agent ethyl methane sulfonate (EMS) and compared the secondary leaf proteomic profile of the mutagenized resistant plants inoculated with CPSMV (MCPI plant group) to those of the naturally susceptible cowpea genotype CE-31 inoculated (CPI) and noninoculated (CPU) with CPSMV. MCPI responded to CPSMV by accumulating proteins involved in the oxidative burst, increasing H2O2 generation, promoting leaf cell death (LCD), increasing the synthesis of defense proteins, and decreasing host factors important for the establishment of CPSMV infection. In contrast, CPI accumulated several host factors that favor CPSMV infection and did not accumulate H2O2 or present LCD, which allowed CPSMV replication and systemic dissemination. Based on these results, we propose that the differential abundance of defense proteins and proteins involved in the oxidative burst, LCD, and the decrease in cowpea protein factors required for CPSMV replication are associated with the resistance trait acquired by the MCPI plant group.
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Affiliation(s)
| | | | | | | | | | | | - Kleber Sousa Oliveira
- Proteomics Analysis and Biochemical Center, Catholic University of Brasilia, Brasilia, Brazil
| | - Octavio Luis Franco
- Proteomics Analysis and Biochemical Center, Catholic University of Brasilia, Brasilia, Brazil; S-Inova Biotech, Catholic University Dom Bosco, Campo Grande, MS, Brazil.
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20
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Skupien-Rabian B, Jankowska U, Kedracka-Krok S. Analysis of a Nuclear Intrinsically Disordered Proteome. Methods Mol Biol 2020; 2175:181-196. [PMID: 32681491 DOI: 10.1007/978-1-0716-0763-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Intrinsically disordered proteins (IDPs) play crucial roles in cell functioning, although they do not possess defined three-dimensional architecture. They are highly abundant in the cell nucleus, and the vast majority of transcription factors (TFs) contain extended regions of intrinsic disorder. IDPs do not respond to denaturing conditions in a standard manner, and this can be used for their separation from structured proteins. Here we describe a protocol for the isolation and characterization of nuclear IDPs in which heat treatment is used for enrichment of IDPs in samples. The whole workflow comprises the following steps: nuclei isolation from HEK293 (human embryonic kidney) cells, protein extraction, enrichment of IDPs, sample preparation for mass spectrometric analysis, liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, in silico assessment of protein disorder, and Gene Ontology analysis.
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Affiliation(s)
- Bozena Skupien-Rabian
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Urszula Jankowska
- Laboratory of Proteomics and Mass Spectrometry, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Sylwia Kedracka-Krok
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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21
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Sun CQ, Chen FD, Teng NJ, Yao YM, Shan X, Dai ZL. Transcriptomic and proteomic analysis reveals mechanisms of low pollen-pistil compatibility during water lily cross breeding. BMC Plant Biol 2019; 19:542. [PMID: 31805858 PMCID: PMC6896271 DOI: 10.1186/s12870-019-2166-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/26/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND In water lily (Nymphaea) hybrid breeding, breeders often encounter non-viable seeds, which make it difficult to transfer desired or targeted genes of different Nymphaea germplasm. We found that pre-fertilization barriers were the main factor in the failure of the hybridization of Nymphaea. The mechanism of low compatibility between the pollen and stigma remains unclear; therefore, we studied the differences of stigma transcripts and proteomes at 0, 2, and 6 h after pollination (HAP). Moreover, some regulatory genes and functional proteins that may cause low pollen-pistil compatibility in Nymphaea were identified. RESULTS RNA-seq was performed for three comparisons (2 vs 0 HAP, 6 vs 2 HAP, 6 vs 0 HAP), and the number of differentially expressed genes (DEGs) was 8789 (4680 were up-regulated), 6401 (3020 were up-regulated), and 11,284 (6148 were up-regulated), respectively. Using label-free analysis, 75 (2 vs 0 HAP) proteins (43 increased and 32 decreased), nine (6 vs 2 HAP) proteins (three increased and six decreased), and 90 (6 vs 0 HAP) proteins (52 increased and 38 decreased) were defined as differentially expressed proteins (DEPs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the DEGs and DEPs were mainly involved in cell wall organization or biogenesis, S-adenosylmethionine (SAM) metabolism, hydrogen peroxide decomposition and metabolism, reactive oxygen species (ROS) metabolism, secondary metabolism, secondary metabolite biosynthesis, and phenylpropanoid biosynthesis. CONCLUSIONS Our transcriptomic and proteomic analysis highlighted specific genes, incuding those in ROS metabolism, biosynthesis of flavonoids, SAM metabolism, cell wall organization or biogenesis and phenylpropanoid biosynthesis that warrant further study in investigations of the pollen-stigma interaction of water lily. This study strengthens our understanding of the mechanism of low pollen-pistil compatibility in Nymphaea at the molecular level, and provides a theoretical basis for overcoming the pre-fertilization barriers in Nymphaea in the future.
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Affiliation(s)
- Chun-Qing Sun
- Zhenjiang Institute of Agricultural Science in Jiangsu Hilly Areas, Jurong, 212400, China
| | - Fa-Di Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nian-Jun Teng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yue-Mei Yao
- Zhenjiang Institute of Agricultural Science in Jiangsu Hilly Areas, Jurong, 212400, China
| | - Xi Shan
- Zhenjiang Institute of Agricultural Science in Jiangsu Hilly Areas, Jurong, 212400, China
| | - Zhong-Liang Dai
- Zhenjiang Institute of Agricultural Science in Jiangsu Hilly Areas, Jurong, 212400, China.
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22
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Chang L, Wang L, Peng C, Tong Z, Wang D, Ding G, Xiao J, Guo A, Wang X. The chloroplast proteome response to drought stress in cassava leaves. Plant Physiol Biochem 2019; 142:351-362. [PMID: 31422174 DOI: 10.1016/j.plaphy.2019.07.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 07/30/2019] [Accepted: 07/30/2019] [Indexed: 06/10/2023]
Abstract
Cassava is an important tropical crop with strong resistance to drought stress. The chloroplast, the site of photosynthesis, is sensitive to stress, and the drought-response proteins in cassava chloroplasts are worthy of investigation. In this study, cassava leaves were collected for ultra-structure observation from plants subjected to different drought stress conditions. Our results showed that drought stress can promote starch accumulation in cassava chloroplasts. To evaluate changes in chloroplast proteins under different drought conditions, two-dimensional electrophoresis was performed using purified chloroplasts, which resulted in the identification of 26 unique chloroplast proteins responsive to drought stress. These drought-responsive proteins are predominantly related to photosynthesis, carbon and nitrogen metabolism, and amino acid metabolism. Among them, most photosynthesis-related proteins are downregulated, with decreases in photosynthetic parameters upon drought stress. Several proteins associated with carbon and nitrogen metabolism, including rubisco and carbonic anhydrase, were upregulated, which might promote drought tolerance in cassava by enhancing the carbohydrate conversion efficiency and protecting the plant from oxidative stress. Our proteomic data not only provide insight into the complement of proteins in cassava chloroplasts but also further our overall understanding of drought-responsive proteins in cassava chloroplasts.
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Affiliation(s)
- Lili Chang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Limin Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China; College of Agriculture, Ludong University, Yantai, Shandong, 264025, China
| | - Cunzhi Peng
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Zheng Tong
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Dan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Guohua Ding
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Junhan Xiao
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Anping Guo
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Xuchu Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China; College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, Hainan, 571158, China.
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23
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Devani RS, Chirmade T, Sinha S, Bendahmane A, Dholakia BB, Banerjee AK, Banerjee J. Flower bud proteome reveals modulation of sex-biased proteins potentially associated with sex expression and modification in dioecious Coccinia grandis. BMC Plant Biol 2019; 19:330. [PMID: 31337343 PMCID: PMC6651928 DOI: 10.1186/s12870-019-1937-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/11/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND Dioecy is an important sexual system wherein, male and female flowers are borne on separate unisexual plants. Knowledge of sex-related differences can enhance our understanding in molecular and developmental processes leading to unisexual flower development. Coccinia grandis is a dioecious species belonging to Cucurbitaceae, a family well-known for diverse sexual forms. Male and female plants have 22A + XY and 22A + XX chromosomes, respectively. Previously, we have reported a gynomonoecious form (22A + XX) of C. grandis bearing morphologically hermaphrodite flowers (GyM-H) and female flowers (GyM-F). Also, we have showed that foliar spray of AgNO3 on female plant induces morphologically hermaphrodite bud development (Ag-H) despite the absence of Y-chromosome. RESULTS To identify sex-related differences, total proteomes from male, female, GyM-H and Ag-H flower buds at early and middle stages of development were analysed by label-free proteomics. Protein search against the cucumber protein sequences (Phytozome) as well as in silico translated C. grandis flower bud transcriptome database, resulted in the identification of 2426 and 3385 proteins (FDR ≤ 1%), respectively. The latter database was chosen for further analysis as it led to the detection of higher number of proteins. Identified proteins were annotated using BLAST2GO pipeline. SWATH-MS-based comparative abundance analysis between Female_Early_vs_Male_Early, Ag_Early_vs_Female_Early, GyM-H_Middle_vs_Male_Middle and Ag_Middle_vs_ Male_Middle led to the identification of 650, 1108, 905 and 805 differentially expressed proteins, respectively, at fold change ≥1.5 and P ≤ 0.05. Ethylene biosynthesis-related candidates as highlighted in protein interaction network were upregulated in female buds compared to male buds. AgNO3 treatment on female plant induced proteins related to pollen development in Ag-H buds. Additionally, a few proteins governing pollen germination and tube growth were highly enriched in male buds compared to Ag-H and GyM-H buds. CONCLUSION Overall, current proteomic analysis provides insights in the identification of key proteins governing dioecy and unisexual flower development in cucurbitaceae, the second largest horticultural family in terms of economic importance. Also, our results suggest that the ethylene-mediated stamen inhibition might be conserved in dioecious C. grandis similar to its monoecious cucurbit relatives. Further, male-biased proteins associated with pollen germination and tube growth identified here can help in understanding pollen fertility.
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Affiliation(s)
- Ravi Suresh Devani
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune, 411008 India
- IPS2, INRA, CNRS, University Paris Sud, University of Evry, University of Paris Diderot, University of Paris Saclay, Batiment 630, 91405 Orsay, France
| | - Tejas Chirmade
- Biochemical Science Division National Chemical laboratory (CSIR-NCL), Pune, 411008 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Sangram Sinha
- Department of Botany, Tripura University, Suryamaninagar, Tripura 799022 India
| | - Abdelhafid Bendahmane
- IPS2, INRA, CNRS, University Paris Sud, University of Evry, University of Paris Diderot, University of Paris Saclay, Batiment 630, 91405 Orsay, France
| | - Bhushan B. Dholakia
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune, 411008 India
- Biochemical Science Division National Chemical laboratory (CSIR-NCL), Pune, 411008 India
- Department of Molecular Biology & Bioinformatics, Tripura University, Suryamaninagar, Tripura 799022 India
| | - Anjan Kumar Banerjee
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune, 411008 India
| | - Jayeeta Banerjee
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune, 411008 India
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24
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Morrison EJ, Champagne DP, Dzieciatkowska M, Nemkov T, Zimring JC, Hansen KC, Guan F, Huffman DM, Santambrogio L, D'Alessandro A. Parabiosis Incompletely Reverses Aging-Induced Metabolic Changes and Oxidant Stress in Mouse Red Blood Cells. Nutrients 2019; 11:nu11061337. [PMID: 31207887 PMCID: PMC6627295 DOI: 10.3390/nu11061337] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/03/2019] [Accepted: 06/12/2019] [Indexed: 12/19/2022] Open
Abstract
Mature red blood cells (RBCs) not only account for ~83% of the total host cells in the human body, but they are also exposed to all body tissues during their circulation in the bloodstream. In addition, RBCs are devoid of de novo protein synthesis capacity and, as such, they represent a perfect model to investigate system-wide alterations of cellular metabolism in the context of aging and age-related oxidant stress without the confounding factor of gene expression. In the present study, we employed ultra-high-pressure liquid chromatography coupled with mass spectrometry (UHPLC–MS)-based metabolomics and proteomics to investigate RBC metabolism across age in male mice (6, 15, and 25 months old). We report that RBCs from aging mice face a progressive decline in the capacity to cope with oxidant stress through the glutathione/NADPH-dependent antioxidant systems. Oxidant stress to tryptophan and purines was accompanied by declines in late glycolysis and methyl-group donors, a potential compensatory mechanism to repair oxidatively damaged proteins. Moreover, heterochronic parabiosis experiments demonstrated that the young environment only partially rescued the alterations in one-carbon metabolism in old mice, although it had minimal to no impact on glutathione homeostasis, the pentose phosphate pathway, and oxidation of purines and tryptophan, which were instead aggravated in old heterochronic parabionts.
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Affiliation(s)
- Evan J Morrison
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, 12801 East 17th Ave RC1 South, Aurora, CO 80045, USA.
| | - Devin P Champagne
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, 12801 East 17th Ave RC1 South, Aurora, CO 80045, USA.
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, 12801 East 17th Ave RC1 South, Aurora, CO 80045, USA.
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, 12801 East 17th Ave RC1 South, Aurora, CO 80045, USA.
| | | | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, 12801 East 17th Ave RC1 South, Aurora, CO 80045, USA.
| | - Fangxia Guan
- Departments of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, New York, NY 10461, USA.
- Institute for Aging Research, Albert Einstein College of Medicine, 1300 Morris Park Avenue, New York, NY 10461, USA.
| | - Derek M Huffman
- Departments of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, New York, NY 10461, USA.
- Institute for Aging Research, Albert Einstein College of Medicine, 1300 Morris Park Avenue, New York, NY 10461, USA.
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, New York, NY 10461, USA.
| | - Laura Santambrogio
- Department of Pathology, Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, New York, NY 10461, USA.
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, 12801 East 17th Ave RC1 South, Aurora, CO 80045, USA.
- Department of Medicine-Division of Hematology, University of Colorado Denver-Anschutz Medical Campus, 12469 East 17th Ave RC2, Aurora, CO 80045, USA.
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25
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Zhao Y, Wilmarth PA, Cheng C, Limi S, Fowler VM, Zheng D, David LL, Cvekl A. Proteome-transcriptome analysis and proteome remodeling in mouse lens epithelium and fibers. Exp Eye Res 2019; 179:32-46. [PMID: 30359574 PMCID: PMC6360118 DOI: 10.1016/j.exer.2018.10.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 08/31/2018] [Accepted: 10/20/2018] [Indexed: 12/21/2022]
Abstract
Epithelial cells and differentiated fiber cells represent distinct compartments in the ocular lens. While previous studies have revealed proteins that are preferentially expressed in epithelial vs. fiber cells, a comprehensive proteomics library comparing the molecular compositions of epithelial vs. fiber cells is essential for understanding lens formation, function, disease and regenerative potential, and for efficient differentiation of pluripotent stem cells for modeling of lens development and pathology in vitro. To compare protein compositions between the lens epithelium and fibers, we employed tandem mass spectrometry (2D-LC/MS) analysis of microdissected mouse P0.5 lenses. Functional classifications of the top 525 identified proteins into gene ontology categories by molecular processes and subcellular localizations, were adapted for the lens. Expression levels of both epithelial and fiber proteomes were compared with whole lens proteome and mRNA levels using E14.5, E16.5, E18.5, and P0.5 RNA-Seq data sets. During this developmental time window, multiple complex biosynthetic and catabolic processes generate the molecular and structural foundation for lens transparency. As expected, crystallins showed a high correlation between their mRNA and protein levels. Comprehensive data analysis confirmed and/or predicted roles for transcription factors (TFs), RNA-binding proteins (e.g. Carhsp1), translational apparatus including ribosomal heterogeneity and initiation factors, microtubules, cytoskeletal [e.g. non-muscle myosin IIA heavy chain (Myh9) and βB2-spectrin (Sptbn2)] and membrane proteins in lens formation and maturation. Our data highlighted many proteins with unknown functions in the lens that were preferentially enriched in epithelium or fibers, setting the stage for future studies to further dissect the roles of these proteins in fiber cell differentiation vs. epithelial cell maintenance. In conclusion, the present proteomic datasets represent the first mouse lens epithelium and fiber cell proteomes, establish comparative analyses of protein and RNA-Seq data, and characterize the major proteome remodeling required to form the mature lens fiber cells.
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Affiliation(s)
- Yilin Zhao
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Phillip A Wilmarth
- Department of Biochemistry & Molecular Biology, Oregon Health Sciences University, 3181 Southwest Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Catherine Cheng
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Saima Limi
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Velia M Fowler
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Deyou Zheng
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Neurology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Neuroscience, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Larry L David
- Department of Biochemistry & Molecular Biology, Oregon Health Sciences University, 3181 Southwest Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Ales Cvekl
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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Abstract
Some of the most challenging stress conditions that organisms encounter during their lifetime involve the transient accumulation of reactive oxygen and chlorine species. Extremely reactive to amino acid side chains, these oxidants cause widespread protein unfolding and aggregation. It is therefore not surprising that cells draw on a variety of different strategies to counteract the damage and maintain a healthy proteome. Orchestrated largely by direct changes in the thiol oxidation status of key proteins, the response strategies involve all layers of protein protection. Reprogramming of basic biological functions helps decrease nascent protein synthesis and restore redox homeostasis. Mobilization of oxidative stress-activated chaperones and production of stress-resistant non-proteinaceous chaperones prevent irreversible protein aggregation. Finally, redox-controlled increase in proteasome activity removes any irreversibly damaged proteins. Together, these systems pave the way to restore protein homeostasis and enable organisms to survive stress conditions that are inevitable when living an aerobic lifestyle.
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Affiliation(s)
- Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Wilhelm Voth
- Department of Molecular, Cellular, and Developmental Biology and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Ursula Jakob
- Department of Molecular, Cellular, and Developmental Biology and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-1048, USA.
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27
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Deng X, Zhen S, Liu D, Liu Y, Li M, Liu N, Yan Y. Integrated proteome analyses of wheat glume and awn reveal central drought response proteins under water deficit conditions. J Plant Physiol 2019; 232:270-283. [PMID: 30540969 DOI: 10.1016/j.jplph.2018.11.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 06/09/2023]
Abstract
Integrated proteome analyses revealed differentially accumulated proteins in the non-leaf green organs in wheat glume and awn that play important roles in photosynthesis and drought resistance. Two non-leaf green organs in wheat, glume and awn, have photosynthetic potential, contribute to grain yield, and also play roles in resistance to adverse conditions. We performed the first integrated proteome analysis of wheat glume and awn in response to water deficit. Water deficit caused a significant decrease in important agronomic traits and grain yield. A total of 120 and 77 differentially accumulated protein (DAP) spots, representing 100 and 67 unique proteins responsive to water deficit, were identified by two-dimensional difference gel electrophoresis (2D-DIGE) in glumes and awns, respectively, of the elite Chinese bread wheat cultivar Zhongmai 175. The DAPs of both organs showed similar functional classification and proportion and were mainly involved in photosynthesis, detoxification/defense, carbon/energy metabolism, and proteometabolism. Comparative proteome analyses revealed many more drought-responsive DAP spots in glumes than in awns, which indicate that glumes underwent more proteome changes in response to water deficit. The main DAPs involved in photosynthesis and carbon metabolism were significantly downregulated, whereas those related to detoxification/defense and energy metabolism were markedly upregulated under water deficit. The potential functions of the identified DAPs revealed an intricate interaction network that responds synergistically to drought stress during grain development. Our results from the proteome perspective illustrate the potential roles of wheat non-leaf green organs glume and awn in photosynthetic and defensive responses under drought stress.
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Affiliation(s)
- Xiong Deng
- College of Life Science, Capital Normal University, 100048, Beijing, China.
| | - Shoumin Zhen
- College of Life Science, Capital Normal University, 100048, Beijing, China.
| | - Dongmiao Liu
- College of Life Science, Capital Normal University, 100048, Beijing, China.
| | - Yue Liu
- College of Life Science, Capital Normal University, 100048, Beijing, China.
| | - Mengfei Li
- College of Life Science, Capital Normal University, 100048, Beijing, China.
| | - Nannan Liu
- College of Life Science, Capital Normal University, 100048, Beijing, China.
| | - Yueming Yan
- College of Life Science, Capital Normal University, 100048, Beijing, China.
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Elguero B, Gonilski Pacin D, Cárdenas Figueroa C, Fuertes M, Arzt E. Modifications in the cellular proteome and their clinical application. Medicina (B Aires) 2019; 79:570-575. [PMID: 31864228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023] Open
Abstract
Post-translational modifications (PTMs) are covalent modifications in proteins during or after their synthesis. Among them, the best known are phosphorylation, methylation, acetylation, and also cleavage or binding of small peptides (ubiquitination, SUMOylation and NEDDylation). Often the protein is modified in multiple sites and these modifications are coordinated generating a PTMs crosstalk. Altered patterns of PTMs have been related to several pathologies. Currently, advances in mass spectrometry have made it possible to study multiple PTMs simultaneously. Oncology is one of the disciplines that incorporated these technologies for the need to better characterize tumors. In cancer, several alterations related to the ubiquitinlike PTMs have been described, such as SUMOylation. In particular, the interaction between different PTMs with SUMOylation has been studied in the context of the von Hippel Lindau (VHL) multitumoral syndrome, generating new putative biomarkers for the evolution of these tumors. RSUME or RWDD3, an enhancer of SUMOylation that acts on VHL and HIF proteins, shows a correlation with malignant parameters in this type of tumors, such as angiogenesis. Regulators of PTMs are becoming relevant as biomarkers in cancer.
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Affiliation(s)
- Belén Elguero
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Argentina
| | - David Gonilski Pacin
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Argentina
| | - Carolina Cárdenas Figueroa
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Argentina
| | - Mariana Fuertes
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Argentina
| | - Eduardo Arzt
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Argentina
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina. E-mail:
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29
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Barua P, Lande NV, Subba P, Gayen D, Pinto S, Keshava Prasad TS, Chakraborty S, Chakraborty N. Dehydration-responsive nuclear proteome landscape of chickpea (Cicer arietinum L.) reveals phosphorylation-mediated regulation of stress response. Plant Cell Environ 2019; 42:230-244. [PMID: 29749054 DOI: 10.1111/pce.13334] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 04/27/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
Nonavailability of water or dehydration remains recurring climatic disorder affecting yield of major food crops, legumes in particular. Nuclear proteins (NPs) and phosphoproteins (NPPs) execute crucial cellular functions that form the regulatory hub for coordinated stress response. Phosphoproteins hold enormous influence over cellular signalling. Four-week-old seedlings of a grain legume, chickpea, were subjected to gradual dehydration, and NPs were extracted from unstressed control and from 72- and 144-hr stressed tissues. We identified 4,832 NPs and 478 phosphosites, corresponding to 299 unique NPPs involved in multivariate cellular processes including protein modification and gene expression regulation, among others. The identified proteins included several novel kinases, phosphatases, and transcription factors, besides 660 uncharacterized proteins. Spliceosome complex and splicing related proteins were dominant among differentially regulated NPPs, indicating their dehydration modulated regulation. Phospho-motif analysis revealed stress-induced enrichment of proline-directed serine phosphorylation. Association mapping of NPPs revealed predominance of differential phosphorylation of spliceosome and splicing associated proteins. Also, regulatory proteins of key processes viz., protein degradation, regulation of flowering time, and circadian clock were observed to undergo dehydration-induced dephosphorylation. The characterization of novel regulatory proteins would provide new insights into stress adaptation and enable directed genetic manipulations for developing climate-resilient crops.
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Affiliation(s)
- Pragya Barua
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna, Asaf Ali Marg, New Delhi, 110067, India
| | - Nilesh Vikram Lande
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna, Asaf Ali Marg, New Delhi, 110067, India
| | - Pratigya Subba
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575 018, India
| | - Dipak Gayen
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna, Asaf Ali Marg, New Delhi, 110067, India
| | - Sneha Pinto
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575 018, India
| | - T S Keshava Prasad
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575 018, India
- International Technology Park, Institute of Bioinformatics, Bengaluru, 560066, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna, Asaf Ali Marg, New Delhi, 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna, Asaf Ali Marg, New Delhi, 110067, India
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30
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Kolbert Z, Molnár Á, Feigl G, Van Hoewyk D. Plant selenium toxicity: Proteome in the crosshairs. J Plant Physiol 2019; 232:291-300. [PMID: 30544054 DOI: 10.1016/j.jplph.2018.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/02/2018] [Accepted: 11/02/2018] [Indexed: 05/23/2023]
Abstract
The metalloid element, selenium (Se) is in many ways special and perhaps because of this its research in human and plant systems is of great interest. Despite its non-essentiality, higher plants take it up and metabolize it via sulfur pathways, but higher amounts of Se cause toxic symptoms in plants. However, the molecular mechanisms of selenium phytotoxicity have been only partly revealed; the data obtained so far point out that Se toxicity targets the plant proteome. Besides seleno- and oxyproteins, nitroproteins are also formed due to Se stress. In order to minimize proteomic damages induced by Se, certain plants are able to redirect selenocysteine away from protein synthesis thus preventing Se-protein formation. Additionally, the damaged or malformed selenoproteins, oxyproteins and nitroproteins may be removed by proteasomes. Based on the literature this review sets Se toxicity mechanisms into a new concept and it draws attention to the importance of Se-induced protein-level changes.
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Affiliation(s)
- Z Kolbert
- Department of Plant Biology, University of Szeged, 6726 Szeged Közép fasor 52, Hungary.
| | - Á Molnár
- Department of Plant Biology, University of Szeged, 6726 Szeged Közép fasor 52, Hungary.
| | - G Feigl
- Department of Plant Biology, University of Szeged, 6726 Szeged Közép fasor 52, Hungary.
| | - D Van Hoewyk
- Department of Biology, Coastal Carolina University, Conway, SC 29526, USA.
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31
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Wei S, Wang X, Jiang D, Dong S. Physiological and proteome studies of maize (Zea mays L.) in response to leaf removal under high plant density. BMC Plant Biol 2018; 18:378. [PMID: 30594144 PMCID: PMC6310946 DOI: 10.1186/s12870-018-1607-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 12/17/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND Under high plant density, intensifying competition among individual plants led to overconsumption of energy and nutrients and resulted in an almost dark condition in the lower strata of the canopy, which suppressed the photosynthetic potential of the shaded leaves. Leaf removal could help to ameliorate this problem and increase crop yields. To reveal the mechanism of leaf removal in maize, tandem mass tags label-based quantitative analysis coupled with liquid chromatography-tandem mass spectrometry were used to capture the differential protein expression profiles of maize subjected to the removal of the two uppermost leaves (S2), the four uppermost leaves (S4), and with no leaf removal as control (S0). RESULTS Excising leaves strengthened the light transmission rate of the canopy and increased the content of malondialdehyde, whereas decreased the activities of superoxide dismutase and peroxidase. Two leaves removal increased the photosynthetic capacity of ear leaves and the grain yield significantly, whereas S4 decreased the yield markedly. Besides, 239 up-accumulated proteins and 99 down-accumulated proteins were identified between S2 and S0, which were strongly enriched into 30 and 23 functional groups; 71 increased proteins and 42 decreased proteins were identified between S4 and S0, which were strongly enriched into 22 and 23 functional groups, for increased and decreased proteins, respectively. CONCLUSIONS Different defoliation levels had contrastive effects on maize. The canopy light transmission rate was strengthened and proteins related to photosynthetic electron-transfer reaction were up-regulated significantly for treatment S2, which improved the leaf photosynthetic capacity, and obtained a higher grain yield consequently. In contrast, S4 decreased the grain yield and increased the expressions of proteins and genes associated with fatty acid metabolism. Besides, both S2 and S4 exaggerated the defensive response of maize in physiological and proteomic level. Although further studies are required, the results in our study provide new insights to the further improvement in maize grain yield by leaf removal.
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Affiliation(s)
- Shanshan Wei
- College of Agriculture/Key Laboratory of Crop Physiology, Ecology and Management, Ministry of Agriculture/Hi-Tech Key Laboratory of Information Agriculture of Jiangsu Province, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province People’s Republic of China
- State Key Laboratory of Crop Biology, College of Agriculture, Shandong Agricultural University, Tai’an, 271018 Shandong Province People’s Republic of China
| | - Xiangyu Wang
- State Key Laboratory of Crop Biology, College of Agriculture, Shandong Agricultural University, Tai’an, 271018 Shandong Province People’s Republic of China
- College of Life Science, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province People’s Republic of China
| | - Dong Jiang
- College of Agriculture/Key Laboratory of Crop Physiology, Ecology and Management, Ministry of Agriculture/Hi-Tech Key Laboratory of Information Agriculture of Jiangsu Province, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province People’s Republic of China
| | - Shuting Dong
- State Key Laboratory of Crop Biology, College of Agriculture, Shandong Agricultural University, Tai’an, 271018 Shandong Province People’s Republic of China
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32
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Schroll MM, Ludwig KR, LaBonia GJ, Herring EL, Hummon AB. Combined Short-Term Glucose Starvation and Chemotherapy in 3D Colorectal Cancer Cell Culture Decreases 14-3-3 Family Protein Expression and Phenotypic Response to Therapy. J Am Soc Mass Spectrom 2018; 29:2012-2022. [PMID: 30019162 PMCID: PMC9366728 DOI: 10.1007/s13361-018-2013-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/31/2018] [Accepted: 06/21/2018] [Indexed: 05/16/2023]
Abstract
Short-term glucose starvation prior to chemotherapy has the potential to preferentially weaken cancer cells, making them more likely to succumb to treatment, while protecting normal cells. In this study, we used 3D cell cultures of colorectal cancer and assessed the effects of short-term glucose starvation and chemotherapy compared to treatment of either individually. We evaluated both phenotypic changes and protein expression levels. Our findings indicate that the combined treatment results in more significant phenotypic responses, including decreased cell viability and clonogenicity. These phenotypic responses can be explained by the decreased expression of LDHA and 14-3-3 family proteins, which were found only in the combined treatment groups. This study indicates that short-term glucose starvation has the potential to increase the efficacy of current cancer treatment regimes. Graphical Abstract ᅟ.
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Affiliation(s)
- Monica M Schroll
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Katelyn R Ludwig
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Gabriel J LaBonia
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Emily L Herring
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, Comprehensive Cancer Center, The Ohio State University, 414 Biomedical Research Tower, Columbus, OH, 43201, USA.
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Watson SJ, Sowden RG, Jarvis P. Abiotic stress-induced chloroplast proteome remodelling: a mechanistic overview. J Exp Bot 2018; 69:2773-2781. [PMID: 29547945 DOI: 10.1093/jxb/ery053] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/08/2018] [Indexed: 05/22/2023]
Abstract
The chloroplast houses photosynthesis in all green plants, and is therefore of fundamental importance to the viability and productivity of plants, ecosystems, and agriculture. Chloroplasts are, however, extremely vulnerable to environmental stress, on account of the inherent volatility of oxygenic photosynthesis. To counteract this sensitivity, sophisticated systems of chloroplast stress acclimation have evolved, and many of these involve broad proteome changes. Here, we provide an overview of the interlocking and mutually dependent mechanisms of abiotic stress-induced chloroplast proteome remodelling. Topics that are covered in this context include: nucleus to chloroplast signalling mechanisms, with a particular emphasis on the nuclear control of the chloroplast genome; chloroplast to nucleus signalling; and the roles of chloroplast pre-protein import regulation and chloroplast proteases.
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Affiliation(s)
- Samuel J Watson
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Robert G Sowden
- Department of Plant Sciences, University of Oxford, Oxford, UK
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34
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Viganó C, von Schubert C, Ahrné E, Schmidt A, Lorber T, Bubendorf L, De Vetter JRF, Zaman GJR, Storchova Z, Nigg EA. Quantitative proteomic and phosphoproteomic comparison of human colon cancer DLD-1 cells differing in ploidy and chromosome stability. Mol Biol Cell 2018; 29:1031-1047. [PMID: 29496963 PMCID: PMC5921571 DOI: 10.1091/mbc.e17-10-0577] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 02/15/2018] [Accepted: 02/21/2018] [Indexed: 11/11/2022] Open
Abstract
Although aneuploidy is poorly tolerated during embryogenesis, aneuploidy and whole chromosomal instability (CIN) are common hallmarks of cancer, raising the question of how cancer cells can thrive in spite of chromosome aberrations. Here we present a comprehensive and quantitative proteomics analysis of isogenic DLD-1 colorectal adenocarcinoma cells lines, aimed at identifying cellular responses to changes in ploidy and/or CIN. Specifically, we compared diploid (2N) and tetraploid (4N) cells with posttetraploid aneuploid (PTA) clones and engineered trisomic clones. Our study provides a comparative data set on the proteomes and phosphoproteomes of the above cell lines, comprising several thousand proteins and phosphopeptides. In comparison to the parental 2N line, we observed changes in proteins associated with stress responses and with interferon signaling. Although we did not detect a conspicuous protein signature associated with CIN, we observed many changes in phosphopeptides that relate to fundamental cellular processes, including mitotic progression and spindle function. Most importantly, we found that most changes detectable in PTA cells were already present in the 4N progenitor line. This suggests that activation of mitotic pathways through hyper-phosphorylation likely constitutes an important response to chromosomal burden. In line with this conclusion, cells with extensive chromosome gains showed differential sensitivity toward a number of inhibitors targeting cell cycle kinases, suggesting that the efficacy of anti-mitotic drugs may depend on the karyotype of cancer cells.
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Affiliation(s)
| | | | - Erik Ahrné
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | - Thomas Lorber
- Institute of Pathology, University Hospital Basel, University of Basel, 4056 Basel, Switzerland
| | - Lukas Bubendorf
- Institute of Pathology, University Hospital Basel, University of Basel, 4056 Basel, Switzerland
| | | | - Guido J. R. Zaman
- Netherlands Translational Research Center B.V., 5340 Oss, The Netherlands
| | | | - Erich A. Nigg
- Biozentrum, University of Basel, 4056 Basel, Switzerland
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35
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Chen GX, Zhen SM, Liu YL, Yan X, Zhang M, Yan YM. In vivo phosphoproteome characterization reveals key starch granule-binding phosphoproteins involved in wheat water-deficit response. BMC Plant Biol 2017; 17:168. [PMID: 29058608 PMCID: PMC5651632 DOI: 10.1186/s12870-017-1118-z] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 10/09/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Drought stress during grain development causes significant yield loss in cereal production. The phosphorylated modification of starch granule-binding proteins (SGBPs) is an important mechanism regulating wheat starch biosynthesis. In this study, we performed the first proteomics and phosphoproteomics analyses of SGBPs in elite Chinese bread wheat (Triticum aestivum L.) cultivar Jingdong 17 under well-watered and water-stress conditions. RESULTS Water stress treatment caused significant reductions in spike grain numbers and weight, total starch and amylopectin content, and grain yield. Two-dimensional gel electrophoresis revealed that the quantity of SGBPs was reduced significantly by water-deficit treatment. Phosphoproteome characterization of SGBPs under water-deficit treatment demonstrated a reduced level of phosphorylation of main starch synthesis enzymes, particularly for granule-bound starch synthase (GBSS I), starch synthase II-a (SS II-a), and starch synthase III (SS III). Specifically, the Ser34 site of the GBSSI protein, the Tyr358 site of SS II-a, and the Ser837 site of SS III-a exhibited significant less phosphorylation under water-deficit treatment than well-watered treatment. Furthermore, the expression levels of several key genes related with starch biosynthesis detected by qRT-PCR were decreased significantly at 15 days post-anthesis under water-deficit treatment. Immunolocalization showed a clear movement of GBSS I from the periphery to the interior of starch granules during grain development, under both water-deficit and well-watered conditions. CONCLUSIONS Our results demonstrated that the reduction in gene expression or transcription level, protein expression and phosphorylation levels of starch biosynthesis related enzymes under water-deficit conditions is responsible for the significant decrease in total starch content and grain yield.
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Affiliation(s)
- Guan-Xing Chen
- College of Life Science, Capital Normal University, Xisanhuan Beilu No. 105, 100048 Beijing, People’s Republic of China
| | - Shou-Min Zhen
- College of Life Science, Capital Normal University, Xisanhuan Beilu No. 105, 100048 Beijing, People’s Republic of China
| | - Yan-Lin Liu
- College of Life Science, Capital Normal University, Xisanhuan Beilu No. 105, 100048 Beijing, People’s Republic of China
| | - Xing Yan
- College of Life Science, Capital Normal University, Xisanhuan Beilu No. 105, 100048 Beijing, People’s Republic of China
| | - Ming Zhang
- College of Life Science, Capital Normal University, Xisanhuan Beilu No. 105, 100048 Beijing, People’s Republic of China
| | - Yue-Ming Yan
- College of Life Science, Capital Normal University, Xisanhuan Beilu No. 105, 100048 Beijing, People’s Republic of China
- Hubei Collaborative Innovation Center for Grain Industry/Yangtze University, Jingzhou, 434025 China
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36
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Aguilar-Hernández V, Kim DY, Stankey RJ, Scalf M, Smith LM, Vierstra RD. Mass Spectrometric Analyses Reveal a Central Role for Ubiquitylation in Remodeling the Arabidopsis Proteome during Photomorphogenesis. Mol Plant 2017; 10:846-865. [PMID: 28461270 PMCID: PMC5695678 DOI: 10.1016/j.molp.2017.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/17/2017] [Accepted: 04/18/2017] [Indexed: 05/21/2023]
Abstract
The switch from skotomorphogenesis to photomorphogenesis is a key developmental transition in the life of seed plants. While much of the underpinning proteome remodeling is driven by light-induced changes in gene expression, the proteolytic removal of specific proteins by the ubiquitin-26S proteasome system is also likely paramount. Through mass spectrometric analysis of ubiquitylated proteins affinity-purified from etiolated Arabidopsis seedlings before and after red-light irradiation, we identified a number of influential proteins whose ubiquitylation status is modified during this switch. We observed a substantial enrichment for proteins involved in auxin, abscisic acid, ethylene, and brassinosteroid signaling, peroxisome function, disease resistance, protein phosphorylation and light perception, including the phytochrome (Phy) A and phototropin photoreceptors. Soon after red-light treatment, PhyA becomes the dominant ubiquitylated species, with ubiquitin attachment sites mapped to six lysines. A PhyA mutant protected from ubiquitin addition at these sites is substantially more stable in planta upon photoconversion to Pfr and is hyperactive in driving photomorphogenesis. However, light still stimulates ubiquitylation and degradation of this mutant, implying that other attachment sites and/or proteolytic pathways exist. Collectively, we expand the catalog of ubiquitylation targets in Arabidopsis and show that this post-translational modification is central to the rewiring of plants for photoautotrophic growth.
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Affiliation(s)
- Victor Aguilar-Hernández
- Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Drive, St. Louis, MO 63130, USA; Department of Genetics, 425-G Henry Mall, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Do-Young Kim
- Department of Genetics, 425-G Henry Mall, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Robert J Stankey
- Department of Genetics, 425-G Henry Mall, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Mark Scalf
- Department of Chemistry, 1101 University Avenue, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lloyd M Smith
- Department of Chemistry, 1101 University Avenue, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Drive, St. Louis, MO 63130, USA; Department of Genetics, 425-G Henry Mall, University of Wisconsin-Madison, Madison, WI 53706, USA.
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37
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Abstract
The anterior pituitary gland (AP) secretes six established hormones that collectively control hundreds of biological and behavioral functions. Because of advances in mass spectrometry (MS), protein labeling, and bioinformatics, it is now possible to characterize, compare, and quantify the AP hormones together with large numbers of nonhormonal AP proteins. For example, by using high-performance liquid chromatography in line with tandem MS we characterized 145 proteins in subcellular fractions of the AP of young adult male Golden Syrian hamsters and 115 proteins in subcellular fractions of the AP of young adult male mice. These included hormones, proteins involved in hormone synthesis and release, and housekeeping proteins. We also used difference gel electrophoresis in conjunction with MS and peptide mass fingerprinting to quantify the effects of estrogen on the AP-soluble protein fraction in rats. Ovarlectomized rats were administered 50 μg of estradiol valerate subcutaneously and studied 48 hrs later, before the onset of the anticipated surges of gonadotropins in blood. Following DeCyder image analysis, we Identified by MS and peptide mass fingerprinting 26 protein spots that were upregulated and 19 protein spots that were downregulated. Estrogen increased levels of acidic isoforms of growth hormone and Prolactin, several proteins involved in protein synthesis, folding and secretion, and several metabolic enzymes. Most of the downregulated proteins are involved in RNA or DNA interactions. We followed up on the results with RT-PCR and immunohistochemical techniques to demonstrate that one protein identified by MS in hamster AP, fertility protein SP22, is synthesized in the AP and localized primarily in somatotropes and thyrotropes. These experiments demonstrate the efficacy of our proteomics approach to characterize AP proteins and quantify changes in them. The approaches used to study the AP could serve as a model to investigate other heterogeneous organs.
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Affiliation(s)
- Charles A Blake
- Department of Cell and Developmental Biology and Anatomy, University of South Carolina School of Medicine, Columbia, South Carolina 29208, USA.
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Abstract
Estrogen Is known to affect the regulation of all six of the established anterior pituitary gland (AP) hormones, but little is known of the specifics of its regulation of the AP hormones, their isoforms, and nonhormonal AP proteins. We used difference gel electrophoresis in conjunction with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and peptide mass fingerprinting to quantify the effects of estrogen on the AP-soluble protein fraction in rats. Two-month-old rats were ovariectomized and used at 6 months of age. They were injected subcutaneously with sesame oil vehicle or 50 μg estradiol valerate in vehicle and studied 48 hrs later, approximately 3 hrs before the time of the anticipated onset of the estrogen-induced surges of gonadotropins in blood. The APs were pooled, and the soluble protein fraction was examined in replicate analyses. After DeCyder software analysis, we identified 26 protein spots that had a 1.5-fold or greater average increase in the experimental group relative to the controls. Nineteen showed a 1.5-fold or greater decrease. Estrogen increased levels of the more acidic isoforms of growth hormone and prolactin and of proteins involved in protein synthesis, folding, and secretion (e.g., eukaryotic translation elongation factor 2, ERp57, ERp29, Hsc70-ps1, calreticulin, coatomer delta subunit, and secretogranin II) and of some metabolic enzymes (e.g., arginosuccinate synthetase, enolase 1, creatine kinase B, phosphoglycerate mutase, malate dehydrogenase, pyruvate kinase, and aldolase A). The majority of the downregulated proteins were involved in RNA or DNA interactions (e.g., five heterogeneous nuclear ribonucleoproteins, DEAD-box proteins 17 and 48, ssDNA binding protein PUR-alpha, PTB-associated splicing factor, and Pigpen protein), but isovaleryl coenzyme A dehydrogenase, mitochondrial aldehyde dehydrogenase, stathmin 1, vinculin, radixin, and secretogranin III were also reduced. Our results indicate that estrogen acts in vivo within 48 hrs to modulate levels of a significant number of AP proteins.
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Affiliation(s)
- Charles A Blake
- Department of Cell and Developmental Biology and Anatomy, University of South Carolina School of Medicine, Columbia, SC 29208, USA.
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Parada C, Orruño M, Kaberdin V, Bravo Z, Barcina I, Arana I. Changes in the Vibrio harveyi Cell Envelope Subproteome During Permanence in Cold Seawater. Microb Ecol 2016; 72:549-558. [PMID: 27324654 DOI: 10.1007/s00248-016-0802-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 06/13/2016] [Indexed: 06/06/2023]
Abstract
Previous work demonstrated that physiological, morphological, and gene expression changes as well as the time-dependent entry into the viable but not culturable (VBNC) state are used by Vibrio species to survive and cope with diverse stress conditions including seasonal temperature downshifts and starvation. To learn more about the nature and specific contribution of membrane proteins to cell adaptation and survival, we analyzed variations in the protein composition of cell envelope and related them to morphological and physiological changes that were taking place during the long-term permanence of Vibrio harveyi in seawater microcosm at 4 °C. We found that after 21 days of permanence, nearly all population (ca. 99 %) of V. harveyi acquired the VBNC phenotype. Although the size of V. harveyi cells gradually decreased during the incubation time, we found that this morphological change was not directly related to their entry into the VBNC state. Our proteomic study revealed that the level of membrane proteins playing key roles in cellular transport, maintenance of cell structure, and in bioenergetics processes remained unchanged along starvation at low temperature, thus suggesting that V. harveyi might need these proteins for the long-term survival and/or for the resuscitation process. On a contrary, the level of two proteins, elongation factor Tu (EF-TU) and bacterioferritin, greatly increased reaching the maximal values by the end of the incubation period. We further discuss the above data with respect to the putative roles likely exerted by membrane proteins during transition to and maintaining of the VBNC state.
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Affiliation(s)
- Claudia Parada
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Bilbao, Spain
| | - Maite Orruño
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of Basque Country (UPV/EHU), Bilbao, Spain
| | - Vladimir Kaberdin
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Bilbao, Spain
- Department of Immunology, Microbiology and Parasitology, IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Zaloa Bravo
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Bilbao, Spain
| | - Isabel Barcina
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Bilbao, Spain
| | - Inés Arana
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Bilbao, Spain.
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Machado D, Herrgård MJ, Rocha I. Stoichiometric Representation of Gene-Protein-Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction. PLoS Comput Biol 2016; 12:e1005140. [PMID: 27711110 PMCID: PMC5053500 DOI: 10.1371/journal.pcbi.1005140] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/13/2016] [Indexed: 12/05/2022] Open
Abstract
Genome-scale metabolic reconstructions are currently available for hundreds of organisms. Constraint-based modeling enables the analysis of the phenotypic landscape of these organisms, predicting the response to genetic and environmental perturbations. However, since constraint-based models can only describe the metabolic phenotype at the reaction level, understanding the mechanistic link between genotype and phenotype is still hampered by the complexity of gene-protein-reaction associations. We implement a model transformation that enables constraint-based methods to be applied at the gene level by explicitly accounting for the individual fluxes of enzymes (and subunits) encoded by each gene. We show how this can be applied to different kinds of constraint-based analysis: flux distribution prediction, gene essentiality analysis, random flux sampling, elementary mode analysis, transcriptomics data integration, and rational strain design. In each case we demonstrate how this approach can lead to improved phenotype predictions and a deeper understanding of the genotype-to-phenotype link. In particular, we show that a large fraction of reaction-based designs obtained by current strain design methods are not actually feasible, and show how our approach allows using the same methods to obtain feasible gene-based designs. We also show, by extensive comparison with experimental 13C-flux data, how simple reformulations of different simulation methods with gene-wise objective functions result in improved prediction accuracy. The model transformation proposed in this work enables existing constraint-based methods to be used at the gene level without modification. This automatically leverages phenotype analysis from reaction to gene level, improving the biological insight that can be obtained from genome-scale models.
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Affiliation(s)
- Daniel Machado
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Markus J. Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Horsølm, Denmark
| | - Isabel Rocha
- Centre of Biological Engineering, University of Minho, Braga, Portugal
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Abstract
Sperm is highly differentiated cell that can be easily obtained and purified. Mature sperm is considered to be transcriptionally and translationally silent and incapable of protein synthesis. Recently, a large number of proteins have been identified in sperm from different species by using the proteomic approaches. Clinically, sperm proteins can be used as markers for male infertility due to different protein profiles identified in sperm from fertile and infertile male animals. Recent evidences have shown that the conditions of sperm preservation in vitro can also change the sperm protein profiles. This paper reviews the recent scientific publications available to address sperm proteome and their relationship with sperm cryopreservation, capacitation, fertilization, and separation of X and Y sperm. Future directions in the application of sperm proteomics to develop or optimize reproductive technologies in mammals are also discussed.
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Affiliation(s)
- Chun-Jin Li
- College of Animal Sciences, Jilin University, 5333 Xian Road, Changchun 130062, PR China
| | - Dong Wang
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agriculture Sciences, Beijing 100193, PR China
| | - Xu Zhou
- College of Animal Sciences, Jilin University, 5333 Xian Road, Changchun 130062, PR China.
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Echevarría-Zomeño S, Fernández-Calvino L, Castro-Sanz AB, López JA, Vázquez J, Castellano MM. Dissecting the proteome dynamics of the early heat stress response leading to plant survival or death in Arabidopsis. Plant Cell Environ 2016; 39:1264-78. [PMID: 26580143 DOI: 10.1111/pce.12664] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/14/2015] [Accepted: 10/16/2015] [Indexed: 05/18/2023]
Abstract
In many plant species, an exposure to a sublethal temperature triggers an adaptative response called acclimation. This response involves an extensive molecular reprogramming that allows the plant to further survive to an otherwise lethal increase of temperature. A related response is also launched under an abrupt and lethal heat stress that, in this case, is unable to successfully promote thermotolerance and therefore ends up in plant death. Although these molecular programmes are expected to have common players, the overlapping degree and the specific regulators of each process are currently unknown. We have carried out a high-throughput comparative proteomics analysis during acclimation and during the early stages of the plant response to a severe heat stress that lead Arabidopsis seedlings either to survival or death. This analysis dissects these responses, unravels the common players and identifies the specific proteins associated with these different fates. Thermotolerance assays of mutants in genes with an uncharacterized role in heat stress demonstrate the relevance of this study to uncover both positive and negative heat regulators and pinpoint a pivotal role of JR1 and BAG6 in heat tolerance.
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Affiliation(s)
- Sira Echevarría-Zomeño
- Centro de Biotecnología y Genómica de Plantas, INIA-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | | | - Ana B Castro-Sanz
- Centro de Biotecnología y Genómica de Plantas, INIA-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Juan Antonio López
- Centro Nacional de Investigaciones Cardiovasculares, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Jesús Vázquez
- Centro Nacional de Investigaciones Cardiovasculares, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - M Mar Castellano
- Centro de Biotecnología y Genómica de Plantas, INIA-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
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Dineshram R, Chandramouli K, Ko GWK, Zhang H, Qian PY, Ravasi T, Thiyagarajan V. Quantitative analysis of oyster larval proteome provides new insights into the effects of multiple climate change stressors. Glob Chang Biol 2016; 22:2054-2068. [PMID: 26990129 DOI: 10.1111/gcb.13249] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 01/26/2016] [Accepted: 01/27/2016] [Indexed: 06/05/2023]
Abstract
The metamorphosis of planktonic larvae of the Pacific oyster (Crassostrea gigas) underpins their complex life-history strategy by switching on the molecular machinery required for sessile life and building calcite shells. Metamorphosis becomes a survival bottleneck, which will be pressured by different anthropogenically induced climate change-related variables. Therefore, it is important to understand how metamorphosing larvae interact with emerging climate change stressors. To predict how larvae might be affected in a future ocean, we examined changes in the proteome of metamorphosing larvae under multiple stressors: decreased pH (pH 7.4), increased temperature (30 °C), and reduced salinity (15 psu). Quantitative protein expression profiling using iTRAQ-LC-MS/MS identified more than 1300 proteins. Decreased pH had a negative effect on metamorphosis by down-regulating several proteins involved in energy production, metabolism, and protein synthesis. However, warming switched on these down-regulated pathways at pH 7.4. Under multiple stressors, cell signaling, energy production, growth, and developmental pathways were up-regulated, although metamorphosis was still reduced. Despite the lack of lethal effects, significant physiological responses to both individual and interacting climate change related stressors were observed at proteome level. The metamorphosing larvae of the C. gigas population in the Yellow Sea appear to have adequate phenotypic plasticity at the proteome level to survive in future coastal oceans, but with developmental and physiological costs.
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Affiliation(s)
- Ramadoss Dineshram
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong Island, Hong Kong SAR, China
| | - Kondethimmanahalli Chandramouli
- Division of Biological, Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences and KAUST Environmental Epigenetic Program (KEEP), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ginger Wai Kuen Ko
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong Island, Hong Kong SAR, China
| | - Huoming Zhang
- Division of Biological, Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences and KAUST Environmental Epigenetic Program (KEEP), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Timothy Ravasi
- Division of Biological, Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences and KAUST Environmental Epigenetic Program (KEEP), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong Island, Hong Kong SAR, China
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Pawłowski TA, Staszak AM. Analysis of the embryo proteome of sycamore (Acer pseudoplatanus L.) seeds reveals a distinct class of proteins regulating dormancy release. J Plant Physiol 2016; 195:9-22. [PMID: 26970688 DOI: 10.1016/j.jplph.2016.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 06/05/2023]
Abstract
Acer pseudoplatanus seeds are characterized by a deep physiological embryo dormancy that requires a few weeks of cold stratification in order to promote germination. Understanding the function of proteins and their related metabolic pathways, in conjunction with the plant hormones implicated in the breaking of seed dormancy, would expand our knowledge pertaining to this process. In this study, a proteomic approach was used to analyze the changes occurring in seeds in response to cold stratification, which leads to dormancy release. In addition, the involvement of abscisic (ABA) and gibberellic acids (GA) was also examined. Fifty-three proteins showing significant changes were identified by mass spectrometry. An effect of ABA on protein variation was observed at the beginning of stratification, while the influence of GA on protein abundance was observed during the middle phase of stratification. The majority of proteins associated with dormancy breaking in the presence of only water, and also ABA or GA, were classified as being involved in metabolism and genetic information processing. For metabolic-related proteins, the effect of ABA on protein abundance was stimulatory for half of the proteins and inhibitory for half of the proteins. On the other hand, the effect on genetic information processing related proteins was stimulatory. GA was found to upregulate both metabolic-related and genetic information processing-related proteins. While seed dormancy breaking depends on proteins involved in a variety of processes, proteins associated with methionine metabolism (adenosine kinase, methionine synthase) and glycine-rich RNA binding proteins appear to be of particular importance.
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Vincent M, Whidden M, Schnell S. Quantitative proteome-based guidelines for intrinsic disorder characterization. Biophys Chem 2016; 213:6-16. [PMID: 27085142 DOI: 10.1016/j.bpc.2016.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/08/2016] [Accepted: 03/29/2016] [Indexed: 11/19/2022]
Abstract
Intrinsically disordered proteins fail to adopt a stable three-dimensional structure under physiological conditions. It is now understood that many disordered proteins are not dysfunctional, but instead engage in numerous cellular processes, including signaling and regulation. Disorder characterization from amino acid sequence relies on computational disorder prediction algorithms. While numerous large-scale investigations of disorder have been performed using these algorithms, and have offered valuable insight regarding the prevalence of protein disorder in many organisms, critical proteome-based descriptive statistical guidelines that would enable the objective assessment of intrinsic disorder in a protein of interest remain to be established. Here we present a quantitative characterization of numerous disorder features using a rigorous non-parametric statistical approach, providing expected values and percentile cutoffs for each feature in ten eukaryotic proteomes. Our estimates utilize multiple ab initio disorder prediction algorithms grounded on physicochemical principles. Furthermore, we present novel threshold values, specific to both the prediction algorithms and the proteomes, defining the longest primary sequence length in which the significance of a continuous disordered region can be evaluated on the basis of length alone. The guidelines presented here are intended to improve the interpretation of disorder content and continuous disorder predictions from the proteomic point of view.
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Affiliation(s)
- Michael Vincent
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mark Whidden
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Santiago Schnell
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, MI, USA; Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, MI, USA.
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46
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Teixeira-Gomes AP, Harichaux G, Gennetay D, Skipor J, Thiery JC, Labas V, Dufourny L. Photoperiod affects the cerebrospinal fluid proteome: a comparison between short day- and long day-treated ewes. Domest Anim Endocrinol 2015; 53:1-8. [PMID: 26046803 DOI: 10.1016/j.domaniend.2015.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/10/2015] [Accepted: 04/19/2015] [Indexed: 12/21/2022]
Abstract
Photoperiod is the main physical synchronizer of seasonal functions and a key factor in the modulation of molecule access to cerebrospinal fluid (CSF) in animals. Previous work has shown that photoperiod affects the transfer rate of steroids and protein hormones from blood to CSF and modulates choroid plexus tight junction protein content. We hypothesized that the CSF proteome would also be modified by photoperiod. We tested this hypothesis by comparing CSF obtained from the third ventricle of mature, ovariectomized, estradiol-replaced ewes exposed to long day length (LD) or short day length (SD). Variations in CSF protein expression between SD- or LD-treated ewes were studied in pools of CSF collected for 48 h. Proteins were precipitated, concentrated, and included in a polyacrylamide gel without protein fractionation. After in-gel tryptic digestion of total protein samples, we analyzed the resulting peptides by nanoliquid chromatography coupled with high-resolution tandem mass spectrometry (GeLC-MS/MS). Quantitative analysis was performed using 2 methods based on spectral counting and extracted ion chromatograms. Among 103 identified proteins, 41 were differentially expressed between LD and SD ewes (with P < 0.05 and at least a 1.5-fold difference). Of the 41 differentially expressed proteins, 22 were identified by both methods and 19 using extracted ion chromatograms only. Eighteen proteins were more abundant in LD ewes and 23 were more abundant in SD ewes. These proteins are involved in numerous functions including hormone transport, immune system activity, metabolism, and angiogenesis. To confirm proteomic results, 2 proteins, pigment epithelium-derived factor (PEDF) and gelsolin, for each individual sample of CSF collected under SD or LD were analyzed with Western blots. These results suggest an important photoperiod-dependent change in CSF proteome composition. Nevertheless, additional studies are required to assess the role of each protein in seasonal functions.
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Affiliation(s)
- A-P Teixeira-Gomes
- Laboratoire de Spectrométrie de Masse, Plate-forme d'Analyse Intégrative des Biomolécules, INRA, F-37380 Nouzilly, France; Unité Mixte de Recherches 1282, Infectiologie et Santé Publique, INRA, F-37380 Nouzilly, France; Université François Rabelais de Tours, F-37000 Tours, France
| | - G Harichaux
- Laboratoire de Spectrométrie de Masse, Plate-forme d'Analyse Intégrative des Biomolécules, INRA, F-37380 Nouzilly, France; Université François Rabelais de Tours, F-37000 Tours, France; Unité Mixte de Recherches 85, Physiologie de la Reproduction et des Comportements, INRA, 37380 Nouzilly, France; Unité Mixte de Recherches 7247, CNRS, 37380 Nouzilly, France; Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France
| | - D Gennetay
- Université François Rabelais de Tours, F-37000 Tours, France; Unité Mixte de Recherches 85, Physiologie de la Reproduction et des Comportements, INRA, 37380 Nouzilly, France; Unité Mixte de Recherches 7247, CNRS, 37380 Nouzilly, France; Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France
| | - J Skipor
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - J-C Thiery
- Université François Rabelais de Tours, F-37000 Tours, France; Unité Mixte de Recherches 85, Physiologie de la Reproduction et des Comportements, INRA, 37380 Nouzilly, France; Unité Mixte de Recherches 7247, CNRS, 37380 Nouzilly, France; Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France
| | - V Labas
- Laboratoire de Spectrométrie de Masse, Plate-forme d'Analyse Intégrative des Biomolécules, INRA, F-37380 Nouzilly, France; Université François Rabelais de Tours, F-37000 Tours, France; Unité Mixte de Recherches 85, Physiologie de la Reproduction et des Comportements, INRA, 37380 Nouzilly, France; Unité Mixte de Recherches 7247, CNRS, 37380 Nouzilly, France; Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France
| | - L Dufourny
- Université François Rabelais de Tours, F-37000 Tours, France; Unité Mixte de Recherches 85, Physiologie de la Reproduction et des Comportements, INRA, 37380 Nouzilly, France; Unité Mixte de Recherches 7247, CNRS, 37380 Nouzilly, France; Institut Français du Cheval et de l'Equitation, F-37380 Nouzilly, France.
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Fitzgerald GA, Yang G, Paschos GK, Liang X, Skarke C. Molecular clocks and the human condition: approaching their characterization in human physiology and disease. Diabetes Obes Metab 2015; 17 Suppl 1:139-42. [PMID: 26332979 PMCID: PMC4562067 DOI: 10.1111/dom.12526] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 05/11/2015] [Indexed: 01/06/2023]
Abstract
Molecular clockworks knit together diverse biological networks and compelling evidence from model systems infers their importance in metabolism, immunological and cardiovascular function. Despite this and the diurnal variation in many aspects of human physiology and the phenotypic expression of disease, our understanding of the role and importance of clock function and dysfunction in humans is modest. There are tantalizing hints of connection across the translational divide and some correlative evidence of gene variation and human disease but most of what we know derives from forced desynchrony protocols in controlled environments. We now have the ability to monitor quantitatively ex vivo or in vivo the genome, metabolome, proteome and microbiome of humans in the wild. Combining this capability, with the power of mobile telephony and the evolution of remote sensing, affords a new opportunity for deep phenotyping, including the characterization of diurnal behaviour and the assessment of the impact of the clock on approved drug function.
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Affiliation(s)
- G A Fitzgerald
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School Of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - G Yang
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School Of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - G K Paschos
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School Of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - X Liang
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School Of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - C Skarke
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School Of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Takemoto K, Kawakami Y. The proportion of genes in a functional category is linked to mass-specific metabolic rate and lifespan. Sci Rep 2015; 5:10008. [PMID: 25943793 PMCID: PMC4421859 DOI: 10.1038/srep10008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/26/2015] [Indexed: 11/08/2022] Open
Abstract
Metabolic rate and lifespan are important biological parameters that are studied in a wide range of research fields. They are known to correlate with body mass, but their association with gene (protein) functions is poorly understood. In this study, we collected data on the metabolic rate and lifespan of various organisms and investigated the relationship of these parameters with their genomes. We showed that the proportion of genes in a functional category, but not genome size, was correlated with mass-specific metabolic rate and maximal lifespan. In particular, the proportion of genes in oxic reactions (which occur in the presence of oxygen) was significantly associated with these two biological parameters. Additionally, we found that temperature, taxonomy, and mode-of-life traits had little effect on the observed associations. Our findings emphasize the importance of considering the biological functions of genes when investigating the relationships between genome, metabolic rate, and lifespan. Moreover, this provides further insights into these relationships, and may be useful for estimating metabolic rate and lifespan in individuals and the ecosystem using a combination of body mass measurements and genomic data.
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Affiliation(s)
- Kazuhiro Takemoto
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Yuko Kawakami
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
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Jarocki VM, Tacchi JL, Djordjevic SP. Non-proteolytic functions of microbial proteases increase pathological complexity. Proteomics 2015; 15:1075-88. [PMID: 25492846 PMCID: PMC7167786 DOI: 10.1002/pmic.201400386] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/26/2014] [Accepted: 12/05/2014] [Indexed: 12/26/2022]
Abstract
Proteases are enzymes that catalyse hydrolysis of peptide bonds thereby controlling the shape, size, function, composition, turnover and degradation of other proteins. In microbes, proteases are often identified as important virulence factors and as such have been targets for novel drug design. It is emerging that some proteases possess additional non‐proteolytic functions that play important roles in host epithelia adhesion, tissue invasion and in modulating immune responses. These additional “moonlighting” functions have the potential to obfuscate data interpretation and have implications for therapeutic design. Moonlighting enzymes comprise a subcategory of multifunctional proteins that possess at least two distinct biological functions on a single polypeptide chain. Presently, identifying moonlighting proteins relies heavily on serendipitous empirical data with clues arising from proteins lacking signal peptides that are localised to the cell surface. Here, we describe examples of microbial proteases with additional non‐proteolytic functions, including streptococcal pyrogenic exotoxin B, PepO and C5a peptidases, mycoplasmal aminopeptidases, mycobacterial chaperones and viral papain‐like proteases. We explore how these non‐proteolytic functions contribute to host cell adhesion, modulate the coagulation pathway, assist in non‐covalent folding of proteins, participate in cell signalling, and increase substrate repertoire. We conclude by describing how proteomics has aided in moonlighting protein discovery, focusing attention on potential moonlighters in microbial exoproteomes.
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Affiliation(s)
- Veronica M. Jarocki
- The ithree instituteProteomics Core Facility, University of TechnologySydneyNSWAustralia
| | - Jessica L. Tacchi
- The ithree instituteProteomics Core Facility, University of TechnologySydneyNSWAustralia
| | - Steven P. Djordjevic
- The ithree instituteProteomics Core Facility, University of TechnologySydneyNSWAustralia
- Proteomics Core FacilityUniversity of TechnologySydneyNSWAustralia
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Cabral V, Znaidi S, Walker LA, Martin-Yken H, Dague E, Legrand M, Lee K, Chauvel M, Firon A, Rossignol T, Richard ML, Munro CA, Bachellier-Bassi S, d'Enfert C. Targeted changes of the cell wall proteome influence Candida albicans ability to form single- and multi-strain biofilms. PLoS Pathog 2014; 10:e1004542. [PMID: 25502890 PMCID: PMC4263760 DOI: 10.1371/journal.ppat.1004542] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 10/28/2014] [Indexed: 12/29/2022] Open
Abstract
Biofilm formation is an important virulence trait of the pathogenic yeast Candida albicans. We have combined gene overexpression, strain barcoding and microarray profiling to screen a library of 531 C. albicans conditional overexpression strains (∼10% of the genome) for genes affecting biofilm development in mixed-population experiments. The overexpression of 16 genes increased strain occupancy within a multi-strain biofilm, whereas overexpression of 4 genes decreased it. The set of 16 genes was significantly enriched for those encoding predicted glycosylphosphatidylinositol (GPI)-modified proteins, namely Ihd1/Pga36, Phr2, Pga15, Pga19, Pga22, Pga32, Pga37, Pga42 and Pga59; eight of which have been classified as pathogen-specific. Validation experiments using either individually- or competitively-grown overexpression strains revealed that the contribution of these genes to biofilm formation was variable and stage-specific. Deeper functional analysis of PGA59 and PGA22 at a single-cell resolution using atomic force microscopy showed that overexpression of either gene increased C. albicans ability to adhere to an abiotic substrate. However, unlike PGA59, PGA22 overexpression led to cell cluster formation that resulted in increased sensitivity to shear forces and decreased ability to form a single-strain biofilm. Within the multi-strain environment provided by the PGA22-non overexpressing cells, PGA22-overexpressing cells were protected from shear forces and fitter for biofilm development. Ultrastructural analysis, genome-wide transcript profiling and phenotypic analyses in a heterologous context suggested that PGA22 affects cell adherence through alteration of cell wall structure and/or function. Taken together, our findings reveal that several novel predicted GPI-modified proteins contribute to the cooperative behaviour between biofilm cells and are important participants during C. albicans biofilm formation. Moreover, they illustrate the power of using signature tagging in conjunction with gene overexpression for the identification of novel genes involved in processes pertaining to C. albicans virulence. Candida albicans is the most prevalent human fungal pathogen. Its ability to cause disease relies, in part, on the formation of biofilms, a protective structure of highly adherent cells tolerant to antifungal agents and the host immune response. The biofilm is considered as a persistent root of infection, disseminating infectious cells to other locations. In this study, we performed large-scale phenotypic analyses aimed at identifying genes whose overexpression affects biofilm development in C. albicans. Our screen relied on a collection of 531 C. albicans strains, each conditionally overexpressing one given gene and carrying one specific molecular tag allowing the quantification of strain abundance in mixed-population experiments. Our results strikingly revealed the enrichment of strains overproducing poorly-characterized surface proteins called Pgas (Putative GPI-Anchored proteins), within a 531-strain-containing biofilm model. We show that these PGA genes differentially contribute to single-strain and multi-strain biofilm formation and are involved in specific stages of the biofilm developmental process. Taken together, our results reveal the importance of C. albicans cell surface proteins during biofilm formation and reflect the powerful use of strain barcoding in combination with gene overexpression to identify genes and/or pathways involved in processes pertaining to virulence of pathogenic microbes.
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Affiliation(s)
- Vitor Cabral
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
- Univ. Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Sadri Znaidi
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
| | - Louise A. Walker
- School of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Hélène Martin-Yken
- INSA, UPS, INP, ISAE, LAAS, Université de Toulouse, Toulouse, France
- UMR792 Ingénierie des Systèmes Biologiques et des Procédés, INRA, Toulouse, France
- UMR5504, CNRS, Toulouse, France
| | - Etienne Dague
- INSA, UPS, INP, ISAE, LAAS, Université de Toulouse, Toulouse, France
- LAAS, CNRS, Toulouse, France
| | - Mélanie Legrand
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
| | - Keunsook Lee
- School of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Murielle Chauvel
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
| | - Arnaud Firon
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
| | - Tristan Rossignol
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
| | - Mathias L. Richard
- INRA, UMR1319 Micalis, Jouy-en-Josas, France
- AgroParisTech, UMR Micalis, Thiverval Grignon, France
| | - Carol A. Munro
- School of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Sophie Bachellier-Bassi
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
| | - Christophe d'Enfert
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France
- INRA, USC2019, Paris, France
- * E-mail:
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