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McFarlane HE. Open questions in plant cell wall synthesis. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad110. [PMID: 36961357 DOI: 10.1093/jxb/erad110] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Indexed: 06/18/2023]
Abstract
Plant cells are surrounded by strong yet flexible polysaccharide-based cell walls that support the cell while also allowing growth by cell expansion. Plant cell wall research has advanced tremendously in recent years. Sequenced genomes of many model and crop plants have facilitated cataloging and characterization of many enzymes involved in cell wall synthesis. Structural information has been generated for several important cell wall synthesizing enzymes. Important tools have been developed including antibodies raised against a variety of cell wall polysaccharides and glycoproteins, collections of enzyme clones and synthetic glycan arrays for characterizing enzymes, herbicides that specifically affect cell wall synthesis, live-cell imaging probes to track cell wall synthesis, and an inducible secondary cell wall synthesis system. Despite these advances, and often because of the new information they provide, many open questions about plant cell wall polysaccharide synthesis persist. This article highlights some of the key questions that remain open, reviews the data supporting different hypotheses that address these questions, and discusses technological developments that may answer these questions in the future.
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Affiliation(s)
- Heather E McFarlane
- Department of Cell & Systems Biology, University of Toronto, 25 Harbord St., Toronto, ON, M5S 3G5, Canada
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2
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Cuttler K, de Swardt D, Engelbrecht L, Kriel J, Cloete R, Bardien S. Neurexin 2 p.G849D variant, implicated in Parkinson's disease, increases reactive oxygen species, and reduces cell viability and mitochondrial membrane potential in SH-SY5Y cells. J Neural Transm (Vienna) 2022; 129:1435-1446. [PMID: 36242655 DOI: 10.1007/s00702-022-02548-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/10/2022] [Indexed: 01/20/2023]
Abstract
Parkinson's disease (PD) is a neurodegenerative movement disorder, affecting 1-2% of the human population over 65. A previous study by our group identified a p.G849D variant in neurexin 2α (NRXN2) co-segregating with PD, prompting validation of its role using experimental methods. This novel variant had been found in a South African family with autosomal dominant PD. NRXN2α is an essential synaptic maintenance protein with multiple functional roles at the synaptic cleft. The aim of the present study was to investigate the potential role of the translated protein NRXN2α and the observed mutant in PD by performing functional studies in an in vitro model. Wild-type and mutant NRXN2α plasmids were transfected into SH-SY5Y cells to assess the effect of the mutant on cell viability and apoptosis [(3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) Assay; ApoTox-Glo™ Triplex Assay)], mitochondrial membrane potential (MMP; MitoProbe™ JC-1 Assay), mitochondrial network analysis (MitoTracker®) and reactive oxygen species (ROS; ROS-Glo™ H2O2 Assay). Cells transfected with the mutant NRXN2α plasmid showed decreased cell viability and MMP. They also exhibited increased ROS production. However, these cells showed no changes in mitochondrial fragmentation. Our findings led us to speculate that the p.G849D variant may be involved in a toxic feedback loop leading to neuronal death in PD. Mitochondrial dysfunction and synaptic dysfunction have been linked to PD. Therefore, findings from this exploratory study are in line with previous studies connecting these two processes and warrants further investigation into the role of this variant in other cellular and animal models.
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Affiliation(s)
- Katelyn Cuttler
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Dalene de Swardt
- Central Analytical Facilities, Stellenbosch University, Cape Town, South Africa
| | - Lize Engelbrecht
- Central Analytical Facilities, Stellenbosch University, Cape Town, South Africa
| | - Jurgen Kriel
- Central Analytical Facilities, Stellenbosch University, Cape Town, South Africa
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Cape Town, South Africa.
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Wood Formation under Changing Environment: Omics Approaches to Elucidate the Mechanisms Driving the Early-to-Latewood Transition in Conifers. FORESTS 2022. [DOI: 10.3390/f13040608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The global change scenarios highlight the urgency of clarifying the mechanisms driving the determination of wood traits in forest trees. Coniferous xylem is characterized by the alternation between earlywood (EW) and latewood (LW), on which proportions the wood density depend, one of the most important mechanical xylem qualities. However, the molecular mechanisms triggering the transition between the production of cells with the typical features of EW to the LW are still far from being completely elucidated. The increasing availability of omics resources for conifers, e.g., genomes and transcriptomes, would lay the basis for the comprehension of wood formation dynamics, boosting both breeding and gene-editing approaches. This review is intended to introduce the importance of wood formation dynamics and xylem traits of conifers in a changing environment. Then, an up-to-date overview of the omics resources available for conifers was reported, focusing on both genomes and transcriptomes. Later, an analysis of wood formation studies using omics approaches was conducted, with the aim of elucidating the main metabolic pathways involved in EW and LW determination. Finally, the future perspectives and the urgent needs on this research topic were highlighted.
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Islinger M, Wildgruber R, Völkl A. Preparative free-flow electrophoresis, a versatile technology complementing gradient centrifugation in the isolation of highly purified cell organelles. Electrophoresis 2018; 39:2288-2299. [DOI: 10.1002/elps.201800187] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 05/01/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Markus Islinger
- Institute for Neuroanatomy, Centre for Biomedicine and Medical Technology Mannheim, Medical Faculty Mannheim; University of Heidelberg; Heidelberg Germany
| | | | - Alfred Völkl
- Department of Medical Cell Biology; Institute of Anatomy; University of Heidelberg; Heidelberg Germany
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Lao J, Smith-Moritz AM, Mortimer JC, Heazlewood JL. Enrichment of the Plant Cytosolic Fraction. Methods Mol Biol 2017; 1511:213-232. [PMID: 27730614 DOI: 10.1007/978-1-4939-6533-5_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The cytosol is at the core of cellular metabolism and contains many important metabolic pathways, including glycolysis, gluconeogenesis, and the pentose phosphate pathway. Despite the importance of this matrix, few attempts have sought to specifically enrich this compartment from plants. Although a variety of biochemical pathways and signaling cascades pass through the cytosol, much of the focus has usually been targeted at the reactions that occur within membrane-bound organelles of the plant cell. In this chapter, we outline a method for the enrichment of the cytosol from rice suspension cell cultures which includes sample preparation and enrichment as well as validation using immunoblotting and fluorescence-tagged proteins.
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Affiliation(s)
- Jeemeng Lao
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94702, USA
| | - Andreia M Smith-Moritz
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94702, USA
| | - Jennifer C Mortimer
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94702, USA
| | - Joshua L Heazlewood
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94702, USA.
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia.
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Abstract
The Golgi apparatus is an essential component in the plant secretory pathway. The enrichment of Golgi membranes from plant tissue is fundamental to the study of this structurally complex organelle. The utilization of density centrifugation for the enrichment of Golgi membranes is still the most widely employed isolation technique. Generally, the procedure requires optimization depending on the plant tissue being employed. Here we provide a detailed enrichment procedure that has previously been used to characterize cell wall biosynthetic complexes from wheat seedlings. We also outline several downstream analyses procedures, including nucleoside diphosphatase assays, immunoblotting, and finally localization of putative Golgi proteins by fluorescent tags.
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Ford KL, Chin T, Srivastava V, Zeng W, Doblin MS, Bulone V, Bacic A. Comparative "Golgi" Proteome Study of Lolium multiflorum and Populus trichocarpa. Proteomes 2016; 4:proteomes4030023. [PMID: 28248233 PMCID: PMC5217351 DOI: 10.3390/proteomes4030023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/08/2016] [Accepted: 07/08/2016] [Indexed: 01/01/2023] Open
Abstract
The Golgi apparatus (GA) is a crucial organelle in the biosynthesis of non-cellulosic polysaccharides, glycoproteins and proteoglycans that are primarily destined for secretion to the cell surface (plasma membrane, cell wall and apoplast). Only a small proportion of the proteins involved in these processes have been identified in plants, with the majority of their functions still unknown. The availability of a GA proteome would greatly assist plant biochemists, cell and molecular biologists in determining the precise function of the cell wall-related proteins. There has been some progress towards defining the GA proteome in the model plant system Arabidopsis thaliana, yet in commercially important species, such as either the cereals or woody species there has been relatively less progress. In this study, we applied discontinuous sucrose gradient centrifugation to partially enrich GA from suspension cell cultures (SCCs) and combined this with stable isotope labelling (iTRAQ) to determine protein sub-cellular locations. Results from a representative grass species, Italian ryegrass (Lolium multiflorum) and a dicot species, black cottonwood (Populus trichocarpa) are compared. The results confirm that membrane fractionation approaches that provide effective GA-enriched fractions for proteomic analyses in Arabidopsis are much less effective in the species examined here and highlight the complexity of the GA, both within and between species.
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Affiliation(s)
- Kristina L Ford
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria 3010, Australia.
| | - Tony Chin
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria 3010, Australia.
| | - Vaibhav Srivastava
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden.
| | - Wei Zeng
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria 3010, Australia.
| | - Monika S Doblin
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria 3010, Australia.
| | - Vincent Bulone
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden.
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia.
| | - Antony Bacic
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria 3010, Australia.
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Abstract
Unconventional protein secretion (UPS) describes secretion pathways that bypass one or several of the canonical secretion pit-stops on the way to the plasma membrane, and/or involve the secretion of leaderless proteins. So far, alternatives to conventional secretion were primarily observed and studied in yeast and animal cells. The sessile lifestyle of plants brings with it unique restraints on how they adapt to adverse conditions and environmental challenges. Recently, attention towards unconventional secretion pathways in plant cells has substantially increased, with the large number of leaderless proteins identified through proteomic studies. While UPS pathways in plants are certainly not yet exhaustively researched, an emerging notion is that induction of UPS pathways is correlated with pathogenesis and stress responses. Given the multitude UPS events observed, comprehensively organizing the routes proteins take to the apoplast in defined UPS categories is challenging. With the establishment of a larger collection of studied plant proteins taking these UPS pathways, a clearer picture of endomembrane trafficking as a whole will emerge. There are several novel enabling technologies, such as vesicle proteomics and chemical genomics, with great potential for dissecting secretion pathways, providing information about the cargo that travels along them and the conditions that induce them.
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Affiliation(s)
- Destiny J Davis
- Department of Plant Sciences, University of California, Asmundson Hall, One Shields Avenue, Davis, CA, 95616, USA
| | - Byung-Ho Kang
- Center for Organelle Biogenesis and Function, School of Life Sciences, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Angelo S Heringer
- Department of Plant Sciences, University of California, Asmundson Hall, One Shields Avenue, Davis, CA, 95616, USA
| | - Thomas E Wilkop
- Department of Plant Sciences, University of California, Asmundson Hall, One Shields Avenue, Davis, CA, 95616, USA.
| | - Georgia Drakakaki
- Department of Plant Sciences, University of California, Asmundson Hall, One Shields Avenue, Davis, CA, 95616, USA.
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Hansen SF, Ebert B, Rautengarten C, Heazlewood JL. Proteomic Characterization of Golgi Membranes Enriched from Arabidopsis Suspension Cell Cultures. Methods Mol Biol 2016; 1496:91-109. [PMID: 27632004 DOI: 10.1007/978-1-4939-6463-5_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The plant Golgi apparatus has a central role in the secretory pathway and is the principal site within the cell for the assembly and processing of macromolecules. The stacked membrane structure of the Golgi apparatus along with its interactions with the cytoskeleton and endoplasmic reticulum has historically made the isolation and purification of this organelle difficult. Density centrifugation has typically been used to enrich Golgi membranes from plant microsomal preparations, and aside from minor adaptations, the approach is still widely employed. Here we outline the enrichment of Golgi membranes from an Arabidopsis cell suspension culture that can be used to investigate the proteome of this organelle. We also provide a useful workflow for the examination of proteomic data as the result of multiple analyses. Finally, we highlight a simple technique to validate the subcellular localization of proteins by fluorescent tags after their identification by tandem mass spectrometry.
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Affiliation(s)
- Sara Fasmer Hansen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94702, USA
| | - Berit Ebert
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Carsten Rautengarten
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Joshua L Heazlewood
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94702, USA.
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
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Agostino FJ, Krylov SN. Advances in steady-state continuous-flow purification by small-scale free-flow electrophoresis. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.03.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Puangpila C, Mayadunne E, El Rassi Z. Liquid phase based separation systems for depletion, prefractionation, and enrichment of proteins in biological fluids and matrices for in-depth proteomics analysis-An update covering the period 2011-2014. Electrophoresis 2015; 36:238-52. [PMID: 25287967 PMCID: PMC4485988 DOI: 10.1002/elps.201400434] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 09/25/2014] [Accepted: 09/26/2014] [Indexed: 11/07/2022]
Abstract
This review article expands on the previous one (S. Selvaraju and Z. El Rassi, Electrophoresis 2012, 33, 74-88) by reviewing pertinent literature in the period extending from early 2011 to present. As the previous review article, the present one is concerned with proteomic sample preparation (e.g., depletion of high-abundance proteins, reduction of the protein dynamic concentration range, enrichment of a particular subproteome), and the subsequent chromatographic and/or electrophoretic prefractionation prior to peptide separation and identification by LC-MS/MS. This review article, however, is distinguished from its earlier version by expanding on capturing/enriching subphosphoproteomes by immobilized metal affinity chromatography and metal oxide affinity chromatography. Seventy-seven papers published in the period extending from mid-2011 to the present have been reviewed. By no means this review article is exhaustive, given the fact that its aim is to give a concise treatment of the latest developments in the field.
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Affiliation(s)
- Chanida Puangpila
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA
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