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Biology Jul 2020After the discovery in 1967 of plant glyoxysomes, aconitase, one the five enzymes involved in the glyoxylate cycle, was thought to be present in the organelles, and... (Review)
Review
After the discovery in 1967 of plant glyoxysomes, aconitase, one the five enzymes involved in the glyoxylate cycle, was thought to be present in the organelles, and although this was found not to be the case around 25 years ago, it is still suggested in some textbooks and recent scientific articles. Genetic research (including the study of mutants and transcriptomic analysis) is becoming increasingly important in plant biology, so metabolic pathways must be presented correctly to avoid misinterpretation and the dissemination of bad science. The focus of our study is therefore aconitase, from its first localization inside the glyoxysomes to its relocation. We also examine data concerning the role of the enzyme malate dehydrogenase in the glyoxylate cycle and data of the expression of aconitase genes in Arabidopsis and other selected higher plants. We then propose a new model concerning the interaction between glyoxysomes, mitochondria and cytosol in cotyledons or endosperm during the germination of oil-rich seeds.
PubMed: 32664680
DOI: 10.3390/biology9070162 -
Current Opinion in Cell Biology Aug 2012Peroxisomes are essential organelles responsible for many metabolic reactions, such as the oxidation of very long chain and branched fatty acids, D-amino acids and... (Review)
Review
Peroxisomes are essential organelles responsible for many metabolic reactions, such as the oxidation of very long chain and branched fatty acids, D-amino acids and polyamines, as well as the production and turnover of hydrogen peroxide. They comprise a class of organelles called microbodies, including glycosomes, glyoxysomes and Woronin bodies. Dysfunction of human peroxisomes causes severe and often fatal peroxisome biogenesis disorders (PBDs). Peroxisomal matrix protein import is mediated by receptors that shuttle between the cytosol and peroxisomal matrix using ubiquitination/deubiquitination reactions and ATP hydrolysis for receptor recycling. We focus on the machinery involved in the peroxisomal matrix protein import cycle, highlighting recent advances in peroxisomal matrix protein import, cargo release and receptor recycling/degradation.
Topics: Cytosol; Glyoxysomes; Humans; Intracellular Membranes; Peroxisomes; Protein Sorting Signals; Protein Transport; Proteins; Ubiquitination
PubMed: 22683191
DOI: 10.1016/j.ceb.2012.05.003 -
Antioxidants (Basel, Switzerland) Apr 2019Reactive oxygen species (ROS) have been recognized as important signaling compoundsof major importance in a number of developmental and physiological processes in... (Review)
Review
Reactive oxygen species (ROS) have been recognized as important signaling compoundsof major importance in a number of developmental and physiological processes in plants. Theexistence of cellular compartments enables efficient redox compartmentalization and ensuresproper functioning of ROS-dependent signaling pathways. Similar to other organisms, theproduction of individual ROS in plant cells is highly localized and regulated bycompartment-specific enzyme pathways on transcriptional and post-translational level. ROSmetabolism and signaling in specific compartments are greatly affected by their chemicalinteractions with other reactive radical species, ROS scavengers and antioxidant enzymes. Adysregulation of the redox status, as a consequence of induced ROS generation or decreasedcapacity of their removal, occurs in plants exposed to diverse stress conditions. During stresscondition, strong induction of ROS-generating systems or attenuated ROS scavenging can lead tooxidative or nitrosative stress conditions, associated with potential damaging modifications of cellbiomolecules. Here, we present an overview of compartment-specific pathways of ROS productionand degradation and mechanisms of ROS homeostasis control within plant cell compartments.
PubMed: 30999668
DOI: 10.3390/antiox8040105 -
The Journal of Cell Biology Nov 1991Glyoxysomes in cotyledons of cotton (Gossypium hirsutum, L.) seedlings enlarge dramatically within 48 h after seed imbibition (Kunce, C.M., R.N. Trelease, and D.C....
Glyoxysomes in cotyledons of cotton (Gossypium hirsutum, L.) seedlings enlarge dramatically within 48 h after seed imbibition (Kunce, C.M., R.N. Trelease, and D.C. Doman. 1984. Planta (Berl.). 161:156-164) to effect mobilization of stored cotton-seed oil. We discovered that the membranes of enlarging glyoxysomes at all stages examined contained a large percentage (36-62% by weight) of nonpolar lipid, nearly all of which were triacylglycerols (TAGs) and TAG metabolites. Free fatty acids comprised the largest percentage of these nonpolar lipids. Six uncommon (and as yet unidentified) fatty acids constituted the majority (51%) of both the free fatty acids and the fatty acids in TAGs of glyoxysome membranes; the same six uncommon fatty acids were less than 7% of the acyl constituents in TAGs extracted from cotton-seed storage lipid bodies. TAGs of lipid bodies primarily were composed of palmitic, oleic, and linoleic acids (together 70%). Together, these three major storage fatty acids were less than 10% of both the free fatty acids and fatty acids in TAGs of glyoxysome membranes. Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) constituted a major portion of glyoxysome membrane phospholipids (together 61% by weight). Pulse-chase radiolabeling experiments in vivo clearly demonstrated that 14C-PC and 14C-PE were synthesized from 14C-choline and 14C-ethanolamine, respectively, in ER of cotyledons, and then transported to mitochondria; however, these lipids were not transported to enlarging glyoxysomes. The lack of ER involvement in glyoxysome membrane phospholipid synthesis, and the similarities in lipid compositions between lipid bodies and membranes of glyoxysomes, led us to formulate and test a new hypothesis whereby lipid bodies serve as the dynamic source of nonpolar lipids and phospholipids for membrane expansion of enlarging glyoxysomes. In a cell-free system, 3H-triolein (TO) and 3H-PC were indeed transferred from lipid bodies to glyoxysomes. 3H-PC, but not 3H-TO, also was transferred to mitochondria in vitro. The amount of lipid transferred increased linearly with respect to time and amount of acceptor organelle protein, and transfer occurred only when lipid body membrane proteins were associated with the donor lipid bodies. 3H-TO was transferred to and incorporated into glyoxysome membranes, and then hydrolyzed to free fatty acids. 3H-PC was transferred to and incorporated into glyoxysome and mitochondria membranes without subsequent hydrolysis. Our data are inconsistent with the hypothesis that ER contributes membrane lipids to glyoxysomes during postgerminative seedling growth.(ABSTRACT TRUNCATED AT 400 WORDS)
Topics: Biological Transport; Cell Differentiation; Chromatography, Gas; Endoplasmic Reticulum; Gossypium; In Vitro Techniques; Intracellular Membranes; Kinetics; Membrane Lipids; Microbodies; Microscopy, Electron; Phospholipids
PubMed: 1955468
DOI: 10.1083/jcb.115.4.995 -
Genome Biology May 2023Plants memorize previous pathogen attacks and are "primed" to produce a faster and stronger defense response, which is critical for defense against pathogens. In plants,...
BACKGROUND
Plants memorize previous pathogen attacks and are "primed" to produce a faster and stronger defense response, which is critical for defense against pathogens. In plants, cytosines in transposons and gene bodies are reported to be frequently methylated. Demethylation of transposons can affect disease resistance by regulating the transcription of nearby genes during defense response, but the role of gene body methylation (GBM) in defense responses remains unclear.
RESULTS
Here, we find that loss of the chromatin remodeler decrease in DNA methylation 1 (ddm1) synergistically enhances resistance to a biotrophic pathogen under mild chemical priming. DDM1 mediates gene body methylation at a subset of stress-responsive genes with distinct chromatin properties from conventional gene body methylated genes. Decreased gene body methylation in loss of ddm1 mutant is associated with hyperactivation of these gene body methylated genes. Knockout of glyoxysomal protein kinase 1 (gpk1), a hypomethylated gene in ddm1 loss-of-function mutant, impairs priming of defense response to pathogen infection in Arabidopsis. We also find that DDM1-mediated gene body methylation is prone to epigenetic variation among natural Arabidopsis populations, and GPK1 expression is hyperactivated in natural variants with demethylated GPK1.
CONCLUSIONS
Based on our collective results, we propose that DDM1-mediated GBM provides a possible regulatory axis for plants to modulate the inducibility of the immune response.
Topics: Arabidopsis; DNA Methylation; Transcription Factors; DNA-Binding Proteins; Arabidopsis Proteins; Chromatin; Gene Expression Regulation, Plant
PubMed: 37147734
DOI: 10.1186/s13059-023-02952-7 -
Plant Physiology Feb 1977Glyoxysome, endoplasmic reticulum, mitochondria, and proplastid fractions were isolated from endosperm of castor beans (Ricinus communis) germinated for 5 days at 30 C....
Glyoxysome, endoplasmic reticulum, mitochondria, and proplastid fractions were isolated from endosperm of castor beans (Ricinus communis) germinated for 5 days at 30 C. Samples from sucrose density gradients were diluted with 0.15 m KCI and the membranes pelleted. Lipid extracts of these membranes were analyzed for phosphoglyceride, acyl lipid, and sterol content. The endoplasmic reticulum contains 1.24 mumol of phosphoglyceride per mg of protein; the mitochondria, 0.65 mumol/mg; and the glyoxysome membranes, 0.55 mumol/mg. Phosphatidyl choline and phosphatidyl ethanolamine are the most abundant lipids in all membranes studied, accounting for 70% or more of the lipid phosphorus and 50% or more of the fatty acid. Glyoxysome membranes and endoplasmic reticulum also contain phosphatidyl inositol (respectively, 9 and 17% of the lipid phosphorus) and free fatty acids (13% of the total fatty acid in each). Compared with other organelles, mitochondrial membranes have more phosphatidyl ethanolamine relative to phosphatidyl choline and are characterized by the presence of cardiolipin, in which 80% of the fatty acid is linoleate. The relative amounts of linoleate, palmitate, oleate, stearate, and linolenate in each of the phosphotoglycerides are constant regardless of the membrane source. Stimasgasterol and beta-sitosterol are present in the membranes (1-9 nmol each/mg protein).The data provide further evidence that glyoxysome membranes are derived from the endoplasmic reticulum but at the same time indicate some differentiation.
PubMed: 16659829
DOI: 10.1104/pp.59.2.259 -
Plant Physiology Jan 2018Oil bodies have multiple functions: oleosin-mediated freezing tolerance of seeds, direct interaction with glyoxysomes for lipid degradation in seedlings, and antifungal... (Review)
Review
Oil bodies have multiple functions: oleosin-mediated freezing tolerance of seeds, direct interaction with glyoxysomes for lipid degradation in seedlings, and antifungal compound production in leaves.
Topics: Cell Membrane; Glyoxysomes; Lipid Droplets; Membrane Proteins; Plant Leaves; Seeds
PubMed: 29203559
DOI: 10.1104/pp.17.01522 -
Journal of Bacteriology Jan 1985An inducible beta-oxidation system was demonstrated in a particulate fraction from Neurospora crassa. The activities of all individual beta-oxidation enzymes were...
An inducible beta-oxidation system was demonstrated in a particulate fraction from Neurospora crassa. The activities of all individual beta-oxidation enzymes were enhanced in cells after a shift from a sucrose to an acetate medium. The induction was even more pronounced in transfer to a medium containing oleate as sole carbon and energy source. Since an acyl-coenzyme A (CoA) dehydrogenase was detected instead of acyl-CoA oxidase, the former enzyme seems to catalyze the first step of the beta-oxidation sequence in N. crassa. After isopycnic centrifugation in a linear sucrose gradient, the intracellular organelles housing the fatty acid degradation pathway cosedimented (1.21 g/cm3) with the glyoxylate bypass enzymes isocitrate lyase and malate synthase and were clearly resolved from both mitochondrial marker enzymes (1.19 g/cm3) and catalase (1.26 g/cm3). On the basis of biochemical as well as morphological properties, these particles from N. crassa have recently been designated as glyoxysome-like particles (G. Wanner and T. Theimer, Ann. N.Y. Acad. Sci. 386:269-284, 1982). The failure to detect catalase, urate oxidase, and acyl-CoA oxidase indicate that these glyoxysome-like microbodies in N. crassa lack peroxisomal function and thus are clearly different from the various microbodies reported so far to contain a beta-oxidation pathway.
Topics: 3-Hydroxyacyl CoA Dehydrogenases; Acetyl-CoA C-Acyltransferase; Centrifugation, Density Gradient; Enoyl-CoA Hydratase; Fatty Acid Desaturases; Fatty Acids; Isocitrate Lyase; Neurospora; Neurospora crassa; Oleic Acid; Oleic Acids; Organoids; Oxidation-Reduction
PubMed: 3155714
DOI: 10.1128/jb.161.1.153-157.1985 -
FEMS Yeast Research Jun 2017What follows are snapshots of my career in chicken eyes, yeast and Rhodospirillum rubrum, castor beans, Escherichia coli and finally yeast again. In contrast, only a few...
What follows are snapshots of my career in chicken eyes, yeast and Rhodospirillum rubrum, castor beans, Escherichia coli and finally yeast again. In contrast, only a few of the failures that realistically make up a career are included. It is a tale of the generosity and influences of those who shaped what I am and what I learned in a wonderful profession. The science described is only that which I was lucky enough to do or was performed in my laboratory by those who really deserve the credit for any success that I've enjoyed. Not mentioned for lack of space are the critical contributions of many impressive investigators in the field of nitrogen-responsive regulation for no scientific investigation occurs in isolation.
Topics: Biochemistry; History, 20th Century; History, 21st Century; Humans; Microbiology; Saccharomyces cerevisiae; United States; Workforce
PubMed: 28582501
DOI: 10.1093/femsyr/fox039 -
Acta Crystallographica. Section F,... Oct 2018Malate dehydrogenase (MDH), a carbohydrate and energy metabolism enzyme in eukaryotes, catalyzes the interconversion of malate to oxaloacetate (OAA) in conjunction with...
Malate dehydrogenase (MDH), a carbohydrate and energy metabolism enzyme in eukaryotes, catalyzes the interconversion of malate to oxaloacetate (OAA) in conjunction with that of nicotinamide adenine dinucleotide (NAD) to NADH. Three isozymes of MDH have been reported in Saccharomyces cerevisiae: MDH1, MDH2 and MDH3. MDH1 is a mitochondrial enzyme and a member of the tricarboxylic acid cycle, whereas MDH2 is a cytosolic enzyme that functions in the glyoxylate cycle. MDH3 is a glyoxysomal enzyme that is involved in the reoxidation of NADH, which is produced during fatty-acid β-oxidation. The affinity of MDH3 for OAA is lower than those of MDH1 and MDH2. Here, the crystal structures of yeast apo MDH3, the MDH3-NAD complex and the MDH3-NAD-OAA ternary complex were determined. The structure of the ternary complex suggests that the active-site loop is in the open conformation, differing from the closed conformations in mitochondrial and cytosolic malate dehydrogenases.
Topics: Amino Acid Sequence; Apoenzymes; Catalytic Domain; Cloning, Molecular; Crystallography, X-Ray; Escherichia coli; Gene Expression; Genetic Vectors; Glyoxysomes; Isoenzymes; Malate Dehydrogenase; Malates; Models, Molecular; NAD; Oxaloacetic Acid; Protein Binding; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Interaction Domains and Motifs; Protein Multimerization; Recombinant Proteins; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Sequence Alignment; Sequence Homology, Amino Acid; Substrate Specificity
PubMed: 30279312
DOI: 10.1107/S2053230X18011895