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Nikolovski N, Fongwoo TA, Di Salvo AN. From strength to stamina: an examination of subsequent resistance and endurance training impact on mitochondrial adaptations and endurance performance. J Physiol 2023; 601:4487-4489. [PMID: 37712567 DOI: 10.1113/jp285369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023] Open
Affiliation(s)
- Nino Nikolovski
- Department of Kinesiology, University of Toronto, Toronto, ON, Canada
| | | | - Adam N Di Salvo
- Department of Kinesiology, University of Toronto, Toronto, ON, Canada
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Anders N, Wilson LFL, Sorieul M, Nikolovski N, Dupree P. β-1,4-Xylan backbone synthesis in higher plants: How complex can it be? Front Plant Sci 2023; 13:1076298. [PMID: 36714768 PMCID: PMC9874913 DOI: 10.3389/fpls.2022.1076298] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Xylan is a hemicellulose present in the cell walls of all land plants. Glycosyltransferases of the GT43 (IRX9/IRX9L and IRX14/IRX14L) and GT47 (IRX10/IRX10L) families are involved in the biosynthesis of its β-1,4-linked xylose backbone, which can be further modified by acetylation and sugar side chains. However, it remains unclear how the different enzymes work together to synthesize the xylan backbone. A xylan synthesis complex (XSC) has been described in the monocots wheat and asparagus, and co-expression of asparagus AoIRX9, AoIRX10 and AoIRX14A is required to form a catalytically active complex for secondary cell wall xylan biosynthesis. Here, we argue that an equivalent XSC exists for the synthesis of the primary cell wall of the eudicot Arabidopsis thaliana, consisting of IRX9L, IRX10L and IRX14. This would suggest the existence of distinct XSCs for primary and secondary cell wall xylan synthesis, reminiscent of the distinct cellulose synthesis complexes (CSCs) of the primary and secondary cell wall. In contrast to the CSC, in which each CESA protein has catalytic activity, the XSC seems to contain proteins with non-catalytic function with each component bearing potentially unique but crucial roles. Moreover, the core XSC formed by a combination of IRX9/IRX9L, IRX10/IRX10L and IRX14/IRX14L might not be stable in its composition during transit from the endoplasmic reticulum to the Golgi apparatus. Instead, potential dynamic changes of the XSC might be a means of regulating xylan biosynthesis to facilitate coordinated deposition of tailored polysaccharides in the plant cell wall.
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Zhang Y, Nikolovski N, Sorieul M, Vellosillo T, McFarlane HE, Dupree R, Kesten C, Schneider R, Driemeier C, Lathe R, Lampugnani E, Yu X, Ivakov A, Doblin MS, Mortimer JC, Brown SP, Persson S, Dupree P. Golgi-localized STELLO proteins regulate the assembly and trafficking of cellulose synthase complexes in Arabidopsis. Nat Commun 2016; 7:11656. [PMID: 27277162 PMCID: PMC4906169 DOI: 10.1038/ncomms11656] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/15/2016] [Indexed: 01/24/2023] Open
Abstract
As the most abundant biopolymer on Earth, cellulose is a key structural component of the plant cell wall. Cellulose is produced at the plasma membrane by cellulose synthase (CesA) complexes (CSCs), which are assembled in the endomembrane system and trafficked to the plasma membrane. While several proteins that affect CesA activity have been identified, components that regulate CSC assembly and trafficking remain unknown. Here we show that STELLO1 and 2 are Golgi-localized proteins that can interact with CesAs and control cellulose quantity. In the absence of STELLO function, the spatial distribution within the Golgi, secretion and activity of the CSCs are impaired indicating a central role of the STELLO proteins in CSC assembly. Point mutations in the predicted catalytic domains of the STELLO proteins indicate that they are glycosyltransferases facing the Golgi lumen. Hence, we have uncovered proteins that regulate CSC assembly in the plant Golgi apparatus.
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Affiliation(s)
- Yi Zhang
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Nino Nikolovski
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Mathias Sorieul
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Tamara Vellosillo
- Energy Biosciences Institute, and Plant and Microbial Biology Department, University of California, Berkeley, California 94720, USA
| | - Heather E McFarlane
- School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ray Dupree
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Christopher Kesten
- School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - René Schneider
- School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Carlos Driemeier
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, Campinas, São Paulo CEP 13083-970, Brazil
| | - Rahul Lathe
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Edwin Lampugnani
- School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia.,ARC Centre of Excellence in Plant Cell Walls, School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Xiaolan Yu
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Alexander Ivakov
- School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Monika S Doblin
- School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia.,ARC Centre of Excellence in Plant Cell Walls, School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jenny C Mortimer
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Staffan Persson
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany.,School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia.,ARC Centre of Excellence in Plant Cell Walls, School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
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Nikolovski N, Shliaha PV, Gatto L, Dupree P, Lilley KS. Label-free protein quantification for plant Golgi protein localization and abundance. Plant Physiol 2014; 166:1033-43. [PMID: 25122472 PMCID: PMC4213074 DOI: 10.1104/pp.114.245589] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The proteomic composition of the Arabidopsis (Arabidopsis thaliana) Golgi apparatus is currently reasonably well documented; however, little is known about the relative abundances between different proteins within this compartment. Accurate quantitative information of Golgi resident proteins is of great importance: it facilitates a better understanding of the biochemical processes that take place within this organelle, especially those of different polysaccharide synthesis pathways. Golgi resident proteins are challenging to quantify because the abundance of this organelle is relatively low within the cell. In this study, an organelle fractionation approach targeting the Golgi apparatus was combined with a label-free quantitative mass spectrometry (data-independent acquisition method using ion mobility separation known as LC-IMS-MS(E) [or HDMS(E)]) to simultaneously localize proteins to the Golgi apparatus and assess their relative quantity. In total, 102 Golgi-localized proteins were quantified. These data show that organelle fractionation in conjunction with label-free quantitative mass spectrometry is a powerful and relatively simple tool to access protein organelle localization and their relative abundances. The findings presented open a unique view on the organization of the plant Golgi apparatus, leading toward unique hypotheses centered on the biochemical processes of this organelle.
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Affiliation(s)
- Nino Nikolovski
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (N.N., P.V.S., L.G., P.D., K.S.L.); Computational Proteomics Unit (L.G.), and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre (N.N., P.S., L.G., K.L.), Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, United Kingdom
| | - Pavel V Shliaha
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (N.N., P.V.S., L.G., P.D., K.S.L.); Computational Proteomics Unit (L.G.), and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre (N.N., P.S., L.G., K.L.), Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, United Kingdom
| | - Laurent Gatto
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (N.N., P.V.S., L.G., P.D., K.S.L.); Computational Proteomics Unit (L.G.), and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre (N.N., P.S., L.G., K.L.), Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, United Kingdom
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (N.N., P.V.S., L.G., P.D., K.S.L.); Computational Proteomics Unit (L.G.), and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre (N.N., P.S., L.G., K.L.), Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, United Kingdom
| | - Kathryn S Lilley
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (N.N., P.V.S., L.G., P.D., K.S.L.); Computational Proteomics Unit (L.G.), and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre (N.N., P.S., L.G., K.L.), Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, United Kingdom
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Busse-Wicher M, Gomes TCF, Tryfona T, Nikolovski N, Stott K, Grantham NJ, Bolam DN, Skaf MS, Dupree P. The pattern of xylan acetylation suggests xylan may interact with cellulose microfibrils as a twofold helical screw in the secondary plant cell wall of Arabidopsis thaliana. Plant J 2014; 79:492-506. [PMID: 24889696 PMCID: PMC4140553 DOI: 10.1111/tpj.12575] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [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: 04/19/2014] [Revised: 05/16/2014] [Accepted: 05/27/2014] [Indexed: 05/17/2023]
Abstract
The interaction between xylan and cellulose microfibrils is important for secondary cell wall properties in vascular plants; however, the molecular arrangement of xylan in the cell wall and the nature of the molecular bonding between the polysaccharides are unknown. In dicots, the xylan backbone of β-(1,4)-linked xylosyl residues is decorated by occasional glucuronic acid, and approximately one-half of the xylosyl residues are O-acetylated at C-2 or C-3. We recently proposed that the even, periodic spacing of GlcA residues in the major domain of dicot xylan might allow the xylan backbone to fold as a twofold helical screw to facilitate alignment along, and stable interaction with, cellulose fibrils; however, such an interaction might be adversely impacted by random acetylation of the xylan backbone. Here, we investigated the arrangement of acetyl residues in Arabidopsis xylan using mass spectrometry and NMR. Alternate xylosyl residues along the backbone are acetylated. Using molecular dynamics simulation, we found that a twofold helical screw conformation of xylan is stable in interactions with both hydrophilic and hydrophobic cellulose faces. Tight docking of xylan on the hydrophilic faces is feasible only for xylan decorated on alternate residues and folded as a twofold helical screw. The findings suggest an explanation for the importance of acetylation for xylan-cellulose interactions, and also have implications for our understanding of cell wall molecular architecture and properties, and biological degradation by pathogens and fungi. They will also impact strategies to improve lignocellulose processing for biorefining and bioenergy.
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Affiliation(s)
- Marta Busse-Wicher
- Department of Biochemistry, University Of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK
| | - Thiago C F Gomes
- Institute of Chemistry, University of Campinas-UNICAMPPO Box 6154, Campinas, SP, 13084-862, Brazil
| | - Theodora Tryfona
- Department of Biochemistry, University Of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK
| | - Nino Nikolovski
- Department of Biochemistry, University Of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK
| | - Katherine Stott
- Department of Biochemistry, University Of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK
| | - Nicholas J Grantham
- Department of Biochemistry, University Of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK
| | - David N Bolam
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle UniversityNewcastle upon Tyne, NE2 4HH, UK
| | - Munir S Skaf
- Institute of Chemistry, University of Campinas-UNICAMPPO Box 6154, Campinas, SP, 13084-862, Brazil
| | - Paul Dupree
- Department of Biochemistry, University Of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK
- *For correspondence (e-mail )
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Gatto L, Breckels LM, Burger T, Nightingale DJH, Groen AJ, Campbell C, Nikolovski N, Mulvey CM, Christoforou A, Ferro M, Lilley KS. A foundation for reliable spatial proteomics data analysis. Mol Cell Proteomics 2014; 13:1937-52. [PMID: 24846987 DOI: 10.1074/mcp.m113.036350] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Quantitative mass-spectrometry-based spatial proteomics involves elaborate, expensive, and time-consuming experimental procedures, and considerable effort is invested in the generation of such data. Multiple research groups have described a variety of approaches for establishing high-quality proteome-wide datasets. However, data analysis is as critical as data production for reliable and insightful biological interpretation, and no consistent and robust solutions have been offered to the community so far. Here, we introduce the requirements for rigorous spatial proteomics data analysis, as well as the statistical machine learning methodologies needed to address them, including supervised and semi-supervised machine learning, clustering, and novelty detection. We present freely available software solutions that implement innovative state-of-the-art analysis pipelines and illustrate the use of these tools through several case studies involving multiple organisms, experimental designs, mass spectrometry platforms, and quantitation techniques. We also propose sound analysis strategies for identifying dynamic changes in subcellular localization by comparing and contrasting data describing different biological conditions. We conclude by discussing future needs and developments in spatial proteomics data analysis.
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Affiliation(s)
- Laurent Gatto
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom; §Computational Proteomics Unit, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
| | - Lisa M Breckels
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom; §Computational Proteomics Unit, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
| | - Thomas Burger
- ¶Université Grenoble-Alpes, CEA (iRSTV/BGE), INSERM (U1038), CNRS (FR3425), F-38054 Grenoble, France
| | - Daniel J H Nightingale
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
| | - Arnoud J Groen
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
| | - Callum Campbell
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
| | - Nino Nikolovski
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
| | - Claire M Mulvey
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
| | - Andy Christoforou
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
| | - Myriam Ferro
- ¶Université Grenoble-Alpes, CEA (iRSTV/BGE), INSERM (U1038), CNRS (FR3425), F-38054 Grenoble, France
| | - Kathryn S Lilley
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom;
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Nikolovski N, Rubtsov D, Segura MP, Miles GP, Stevens TJ, Dunkley TP, Munro S, Lilley KS, Dupree P. Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics. Plant Physiol 2012; 160:1037-51. [PMID: 22923678 PMCID: PMC3461528 DOI: 10.1104/pp.112.204263] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 08/22/2012] [Indexed: 05/18/2023]
Abstract
The Golgi apparatus is the central organelle in the secretory pathway and plays key roles in glycosylation, protein sorting, and secretion in plants. Enzymes involved in the biosynthesis of complex polysaccharides, glycoproteins, and glycolipids are located in this organelle, but the majority of them remain uncharacterized. Here, we studied the Arabidopsis (Arabidopsis thaliana) membrane proteome with a focus on the Golgi apparatus using localization of organelle proteins by isotope tagging. By applying multivariate data analysis to a combined data set of two new and two previously published localization of organelle proteins by isotope tagging experiments, we identified the subcellular localization of 1,110 proteins with high confidence. These include 197 Golgi apparatus proteins, 79 of which have not been localized previously by a high-confidence method, as well as the localization of 304 endoplasmic reticulum and 208 plasma membrane proteins. Comparison of the hydrophobic domains of the localized proteins showed that the single-span transmembrane domains have unique properties in each organelle. Many of the novel Golgi-localized proteins belong to uncharacterized protein families. Structure-based homology analysis identified 12 putative Golgi glycosyltransferase (GT) families that have no functionally characterized members and, therefore, are not yet assigned to a Carbohydrate-Active Enzymes database GT family. The substantial numbers of these putative GTs lead us to estimate that the true number of plant Golgi GTs might be one-third above those currently annotated. Other newly identified proteins are likely to be involved in the transport and interconversion of nucleotide sugar substrates as well as polysaccharide and protein modification.
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Abstract
BACKGROUND Osseous "bone-derived" myxoma is a benign, slow-growing, locally invasive tumor that is found exclusively in the facial skeleton. Although recurrence is frequent, uncontrolled growth is not classic. METHODS AND RESULTS We report the case of a patient with myxoma of the maxilla in which the growth of the myxoma was so invasive that it resulted in destruction and deformation of the facial skeleton even after repeated resections. Eventually, destruction and infiltration of the skull base with a fatal outcome was the result. CONCLUSIONS This case of locally aggressive myxoma of the maxilla illustrates the need for a correct primary treatment of this benign tumor. Although complete resection may result in a significant functional and aesthetic mutilation, incomplete primary removal results in high recurrence rates. Therefore, a radical primary resection of the tumor with maximal preservation of surrounding anatomic structures is necessary. Follow-up should be meticulous and based upon regular clinical and radiographic examinations.
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Affiliation(s)
- P B Deron
- Department of Otorhinolaryngology, Head & Neck Surgery, Erasmus University Rotterdam, The Netherlands
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