* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Peroxisomes: family of versatile organelles
Mitogen-activated protein kinase wikipedia , lookup
Evolution of metal ions in biological systems wikipedia , lookup
Oxidative phosphorylation wikipedia , lookup
Metalloprotein wikipedia , lookup
Amino acid synthesis wikipedia , lookup
Magnesium transporter wikipedia , lookup
Clinical neurochemistry wikipedia , lookup
Biosynthesis wikipedia , lookup
Interactome wikipedia , lookup
Fatty acid synthesis wikipedia , lookup
Lipid signaling wikipedia , lookup
Fatty acid metabolism wikipedia , lookup
Two-hybrid screening wikipedia , lookup
Protein–protein interaction wikipedia , lookup
Biochemistry wikipedia , lookup
G protein–coupled receptor wikipedia , lookup
Biochemical cascade wikipedia , lookup
Paracrine signalling wikipedia , lookup
Western blot wikipedia , lookup
Anthrax toxin wikipedia , lookup
Course: Molecular, cell biological and genetic aspects of diseases (743665S) Lecture: Peroxisomes Faculty of Biochemistry and Molecular Medicine Lecturer: Tuomo Glumoff, Ph.D. University Lecturer Acknowledgment: some materials on these lecture handouts are courtesy of Dr. Vasily Antonenkov Contents: 1. What are peroxisomes? 2. Functions associated with peroxisomes 3. Proliferation, biogenesis and maintenance of peroxisomes 4. Protein import into peroxisomes 5. Interplay of peroxisomes with other organelles Topical reading for those who are especially interested in peroxisomes: http://www.sciencedirect.com/science/journal/01674889/1863/5 Biochimica et Biophysica Acta (BBA) - Molecular Cell Research Volume 1863, Issue 5, Pages 787-1070 (May 2016) Assembly, Maintenance and Dynamics of Peroxisomes Edited by Ralf Erdmann Topics: Characterization, prediction and evolution of plant peroxisomal targeting signals type 1 (PTS1s) Structural biology of the import pathways of peroxisomal matrix proteins The first minutes in the life of a peroxisomal matrix protein Peroxisomal protein import pores Role of AAA+-proteins in peroxisome biogenesis and function Regulation of peroxisomal matrix protein import by ubiquitination Peroxisome biogenesis, protein targeting mechanisms and PEX gene functions in plants Towards the molecular mechanism of the integration of peroxisomal membrane proteins Targeting and insertion of peroxisomal membrane proteins: ER trafficking versus direct delivery to peroxisomes Multiple paths to peroxisomes: Mechanism of peroxisome maintenance in mammals De novo peroxisome biogenesis: Evolving concepts and conundrums The birth of yeast peroxisomes A role for mRNA trafficking and localized translation in peroxisome biogenesis and function? Human disorders of peroxisome metabolism and biogenesis Peroxisomes in brain development and function Hepatic dysfunction in peroxisomal disorders Proliferation and fission of peroxisomes — An update Peroxisome homeostasis: Mechanisms of division and selective degradation of peroxisomes in mammals Pexophagy in yeasts Pexophagy and peroxisomal protein turnover in plants Small GTPases in peroxisome dynamics Sharing with your children: Mechanisms of peroxisome inheritance Why do peroxisomes associate with the cytoskeleton? Regulation of peroxisome dynamics by phosphorylation Biogenesis, maintenance and dynamics of glycosomes in trypanosomatid parasites Peroxisome biogenesis in mammalian cells: The impact of genes and environment No peroxisome is an island — Peroxisome contact sites 1. What are peroxisomes? microbodies peroxisomes - liver - kidney microperoxisomes - other tissues glyoxysomes glycosomes - glyoxylate cycle enzymes (in addition) - glycolytic pathway enzymes (Trypanosoma) Woronin bodies (mushrooms) mitochondrion peroxisome Med InFoZ (medinfoz.com) • diameter: peroxisomes 0.5µm; microperoxisomes 0.1-0.2µm • single membrane • no own DNA Microperoxisomes • Most peroxisomes in plants and yeasts are with size around 0.5 µm. In contrast, peroxisomes in mammalian tissues (except for liver and kidney) are small (0.1-0.2 µm) and without nucleoid. It is difficult to recognize them on tissue slices using common transmission electron microscopy. • Method has been developed (Graham, Karnovsky staining) to detect catalase in peroxisomes by its peroxidase activity with diaminobenzidine. The product of this reaction forms an insoluble sediment which can be seen under EM. • Rat parotid exocrine glands (photo). Why such name? • First enzymes discovered in the particles: catalase and H2O2-producing oxidases (urate oxidase, D-amino acid oxidase and glycolate oxidase); • • Catalase is able to catalyze two reactions: dismutation of H2O2: 2H2O2 = 2H2O + O2 and peroxidation (if substrate is available) of some compounds (methanol, ethanol, certain phenols, formaldehyde, formic acid, and the nitrite ion): • The oxidases produce H202 that can be used by catalase to oxidize corresponding substrates; • The proposed chain of reactions gives the name to organelles: peroxisomes, i.e. particles were hydrogen peroxide is metabolized. Main metabolic pathways in peroxisomes - fatty-acyl β-oxidation: can handle different substrates, which are imported by different ABCD transporters - fatty-acyl α-oxidation of phytanic acid - plasmalogen synthesis Waterham et al. Biochim Biophys Acta. 2016 - bile acid synthesis - glyoxylate detoxification Main metabolic pathways in peroxisomes. Peroxisomal proteins involved in the different pathways are indicated by their respective gene names and boxed. Substrates and products are unboxed. The main enzymes involved in the peroxisomal fatty acid beta-oxidation pathway are indicated in light orange. The peroxisomal fatty acid beta-oxidation pathway can handle different substrates (indicated by distinct colors), including very long chain fatty acids (sVLCFA, unVLCFA (green)), dicarboxylic acids (DCA (blue)), the bile intermediates DHCA and THCA (dark red), and pristanic acid (magenta), which are imported into peroxisomes by the different ABCD transporters as indicated. The peroxisomal enzymes involved in alphaoxidation of phytanic acid (purple) are indicated in yellow. The peroxisomal enzymes involved in plasmalogen synthesis (black) are indicated in purple. The peroxisomal enzymes involved in bile acid synthesis (dark red) are indicated in bright and light orange. The peroxisomal enzyme involved in glyoxylate detoxification (brown) is indicated in red and catalase required for H2O2 degradation in green. Abbreviations: ACAA1 = 3-ketoacyl-CoA thiolase ACOX1 = Acyl-CoA oxidase 1 ACOX2 = acyl-CoA oxidase 2 ABCD1 = ABC transporter D1 ABCD2 = ABC transporter D2 ABCD3 = ABC transporter D3 AGPS = alkyl-dihydroxyacetonephosphate synthase AGT = alanine-glyoxylate aminotransferase AMACR = 2-methylacyl-CoA racemace BAAT = bile acid–CoA:amino acid N-acyltransferase brAcyl = branched-acyl CA = cholic acid CAT = catalase CDCA = chenodeoxycholic acid DBP = D-bifunctional protein DCA = dicarboxylic acids DHAP = dihydroxyacetone phosphate DHCA = dihydroxycholestanoic acid FAR1 = fatty acyl reductase 1 GNPAT = dihydroxyacetonephosphate acyltransferase HACL1 = 2-hydroxyphytanoyl-CoA lyase LBP = L-bifunctional protein PHYH = phytanoyl-CoA 2-hydoxylase PrDH = pristanal dehydrogenase SCPx = SCPx sVLCFA = saturated very long chain fatty acids THCA = trihydroxycholestanoic acid unVLCFA = unsaturated very long chain fatty acids. 2. Functions associated with peroxisomes • The main function of mammalian peroxisomes is beta-oxidation of long- and very long-chain fatty acids and a side chain of bile-acid precursors. Dual localization of the beta-oxidation in mammals (peroxisomes and mitochondria). • The peroxisomal beta-oxidation of fatty acids does not proceed to completion, i.e., complete degradation of fatty acids to acetyl (C2) groups. Instead, it produces chain-shortened fatty acids (C6-C14) which can be used inside or outside peroxisomes for synthesis of some compounds or exported to mitochondria for further oxidation down to acetyl group. • • Alpha-oxidation of branchedchain fatty acids derived from phytol – constituent of plant chloroplast; Oxidation of glycolic acid, main source of it is plant leafs and other green staff. Catabolism of purines - another example how peroxisomes participate in a complex metabolic pathway. Further functions of peroxisomes The main function of peroxisomes is oxidative degradation of compounds with poor (low) solubility in water and in lipids as well. Most of these compounds are amphipathic molecules (mostly lipids) containing a charged group and a large hydrophobic part, such as long(C16-C20) and very long- (C22 and longer) chain fatty acids, bile acids, some amino acids, etc. Some non-lipid molecules with poor solubility in water: purines and oxalates, are oxidized also in peroxisomes. Further functions of peroxisomes • Peroxisomes in plant leafs participate in photorespiration producing link between chloroplasts and mitochondria. • Photorespiration is a lightdependent uptake of O2 and release of CO2. Photorespiration regulates efficiency of photosynthesis that is important at high level of illumination. • Role of peroxisomes: prevent formation of H2O2 and glyoxylate in mitochondria and in chloroplasts Glyoxysomes in plant seeds • Plants can convert lipids to sugars using glyoxylate cycle that is short variant of the citric acid cycle. Animal cells can not carry out the net synthesis of carbohydrate from fat because they have no glyoxylate cycle. 3. Proliferation, biogenesis and maintenance of peroxisomes • Some amphipathic compounds increase amount and size of peroxisomes in liver, kidney and intestine of rodents (mice, rats), and, in less extent, in humans. Proliferation of peroxisomes leads to activation of peroxisomal beta-oxidation of long chain fatty acids in the liver for more than 10 times (rodents). • The natural peroxisome proliferators are most probably some long chain fatty acids, especially unsaturated acids. • Proliferation of peroxisomes is an adaptation mechanism to excessive consumption of lipids. It is part of more complex system for regulation of lipid metabolism. Mitochondrial beta oxidation is also increased, but at the lower level. • • Receptor concept: the cytosolic receptor binds ligand (peroxisome proliferator) and delivers it to nucleus where the complex interacts with DNA and activates transcription of peroxisomal genes. Peroxisome proliferator-activated receptor family of proteins - PPAR’s. Only PPAR alpha is responsible for proliferation of peroxisomes, other members of the family are involved in regulation of other pathways in lipid metabolism and in cell growth and differentiation. After ligand binding the PPAR forms a heterodimer with another nuclear receptor, the retinoid-X receptor (RXR), that binds retinoic acid (related to vitamin A); Next, the PPAR/RXR complex binds to DNA sequences containing repeats of hexanucleotide: AGGTCA, known as peroxisome proliferator response element (PPRE). These repeats were found in the promoter regions of PPAR target genes. Some additional proteins (co-activators) are involved in the binding. (next page) Lee & Kim PPAR Research 2015 • Biogenesis of peroxisomes is a complex process requiring more than 30 different proteins called Pex proteins; • Peroxisomes have no own DNA, therefore matrix and membrane proteins are synthesized on free (poly)ribosomes in cytoplasm and imported into peroxisomes by means of special mechanisms; • • Several steps in biogenesis: 1. Budding of a new peroxisome from special subdomain of endoplasmic reticulum 2. Growth and maturation of the peroxisome that involves delivery of the newly synthesized proteins into the particles 3. Division of the matured peroxisome into daughter peroxisomes. • • model for de novo biogenesis Hua & Kim Biochim Biophys Acta. 2016 model for the maintenance of peroxisomes: • growth and division from pre-existing peroxisomes • de novo from other organelles, like ER Hua & Kim Biochim Biophys Acta. 2016 Agrawal & Subramani Biochim Biophys Acta. 2016 Schematic representation of peroxisome biogenesis pathways. 1] PMPs are both translated in the cytosol on free ribosomes or on the ER-associated ribosomes and incorporated post-translationally or cotranslationally in the ERmembrane. The ER-translocon, Sec61, is important for the PMP incorporation process. Similarly, TA-proteins (tail-anchored) are imported into the ER-membrane via the GET pathway. 2] Subsequently, an intra-ER sorting process targets the PMPs to respective pER domains. 3] The PMPs are exported from the ER in vesicular carriers and require Pex19. Pex16 is also important for the exit of Pex3 and other PMPs from the ER in mammalian cells. 4] The vesicular carriers containing complementary sets of PMPs fuse to assemble the importomer complex. The fusion process requires peroxins Pex1 and Pex6. 5] This assembly enables the nascent peroxisome to import matrix proteins and become a metabolically active organelle. 6] Type II PMPs are imported directly into the peroxisome membrane with the assistance of Pex3 and Pex19 (inset). 7] The de novo route involving the ER also contributes to the cellular peroxisome population, thus sustaining the growth and division pathway and substituting for it when it is blocked or impaired. Using this backup pathway, in mutant cells (such as pex3∆ and pex19∆ cells) lacking functional pre-existing peroxisomes, reintroduction of the missing gene will form peroxisomes de novo and the new peroxisomes that are generated will restart growth and division pathway. Agrawal & Subramani Biochim Biophys Acta. 2016 Waterham et al. Biochim Biophys Acta. 2016 Signalling pathways that trigger peroxisome proliferation in mammals. (A) Extra- or intracellular signalling molecules such as growth factors, hypolipidemic compounds, ROS or fatty acids bind to specific nuclear receptors (e.g. PPARα) leading to PPAR-dependent and potentially to PPAR-independent signalling pathways. Schrader et al. Biochim Biophys Acta. 2016 (B) In the PPAR-dependent pathway, binding of activating ligands to PPARs and to its partner RXR induce conformational changes of the receptors resulting in transcriptional complex formation. Activation of the transcriptional complex occurs upon transcriptional cofactor binding, which then allows binding to PPREs in peroxisomal genes to initiate gene expression. PPAR-independent mechanisms have also been described which may signal through as yet unidentified receptors (indicated by “?”) Schrader et al. Biochim Biophys Acta. 2016 (C) Expression of peroxisomal biogenesis factors (e.g. Pex11) and/or β-oxidation enzymes can promote peroxisome proliferation and/or increased fatty acid metabolism. Peroxisome proliferation is initiated by membrane remodelling followed by a multi-step process of membrane elongation (growth), constriction and final membrane scission. These processes are mediated by division proteins (e.g. Pex11β, Fis1, Mff and DLP1) Schrader et al. Biochim Biophys Acta. 2016 Model of peroxisome division in mammalian cells. DHA facilitates the oligomerization of Pex11β, which leads to the formation of Pex11β-rich regions and initiates peroxisome elongation (step 1). Peroxisomes elongate there in one direction (step 2). Mff and Fis1 are localized to peroxisomes (step 3), where Mff then recruits DLP1 and the Mff–DLP1 complex translocates to the membrane-constricted regions of elongated peroxisomes. Honsho et al. Biochim Biophys Acta. 2016 The functional complex comprising Pex11β, Mff, and DLP1 promotes Mff-mediated fission during peroxisomal division (step 4). The complex may include Fis1 that also interacts with DLP1. The activated DLP1 hydrolyzes GTP, by which peroxisomal membranes are cleaved, thereby giving rise to peroxisomal fission (step 5), followed by translocation of daughter peroxisomes via microtubules (MT) (step 6). 4. Protein import into peroxisomes • Transport of folded, cofactor-bound and oligomeric proteins by shuttling receptors pex5 (PTS1) and pex7(PTS2); • Receptors recognize newly synthesized proteins in the cytosol using peroxisomal targeting signals (PTS): PTS1 is at the C-terminus with a consensus sequence (S/A/C)(K/R/H)(L/I); PTS2 is near the N-terminus with a consensus sequence (R/K)(L/V/I)-xxxxx(H/Q)(L/A) (only few proteins); • After delivering of proteins into peroxisomes, the receptors move back to cytosol. • • The problem is to deliver folded and even oligomeric protein across the membrane into the matrix. Hypothesis: Transient pore model. When Pex 5 receptor protein together with cargo protein reach the peroxisomal membrane, it forms temporal channel which allows matrix proteins penetrate the membrane. Model of peroxisomal matrix protein import. (I) Proteins harboring a peroxisomal targeting signal of type 1 (PTS1) are recognized and bound by the import receptor Pex5 in the cytosol; (II) The cargo-loaded receptor is directed to the peroxisomal membrane and binds to the docking complex (Pex13/Pex14/Pex17); (III) The import receptor assembles with Pex14 to form a transient pore; (IV) Cargo proteins are transported into the peroxisomal matrix in an unknown manner. Cargo release might involve the function of Pex8 or Pex14; (V) The import receptor is monoubiquitinated at a conserved cysteine by the E2enzyme complex Pex4/Pex22 in tandem with E3-ligases of the RINGcomplex (Pex2, Pex10, Pex12); (VI) The ubiquitinated receptor is released from the peroxisomal membrane in an ATP-dependent manner by the AAA-peroxins Pex1 and Pex6, which are anchored to the peroxisomal membrane via Pex15. As the last step of the cycle, the ubiquitin moiety is removed and the receptor enters a new round of import. The designation is based on the yeast nomenclature. Emmanouilidis et al. Biochim Biophys Acta. 2016 Import pathways of peroxisomal matrix proteins. The import of peroxisomal matrix proteins occurs via two pathways, based on the presence of distinct peroxisomal targeting signal (PTS) sequences in the cargo protein. Cargo proteins with a PTS1 motif exhibit a C-terminal tripeptide (S/A/C)–(K/R/L)–(L/M) (PTS1, left) and bind to the Pex5 receptor in the PTS1 import pathway. Cargo proteins harboring an N-terminal PTS2 motif with a consensus sequence (R/K)-(L/V/I)-X5-(H/Q)-(L/A) are recognized by Pex7/Pex21 and imported via the PTS2 pathway (right). (A) Newly made cargo proteins and peroxins are released from polyribosomes into the cytosol. (B) In the cytosol, PTS1 cargo is recognized by the soluble Pex5 receptor, while PTS2 cargo is recognized by a complex of the Pex7/Pex21 receptors leading to the formation of receptor–cargo complexes. Note, that the coreceptor of Pex7 differs depending on the species. In human a long splice isoform of Pex5 acts as a coreceptor. In yeast species Pex21/Pex18 and Pex20, act as coreceptors (C) The cargo–receptor complexes bind to a docking subcomplex comprising Pex14 and Pex13 at the peroxisomal membrane. (D) Subsequently, the receptor–cargo complexes translocate the matrix protein into the peroxisome. Note, that — although the basic steps along the pathways are similar — the peroxisomal proteins involved and their specific roles vary between organisms. Peroxisomal protein import. Schematic view of the human import machinery for peroxisomal matrix proteins and membrane proteins highlighting the roles of the different PEX proteins (peroxins). Waterham et al. Biochim Biophys Acta. 2016 (note the difference to the previous slides) PTS2 cargo recognition by the Pex7–Pex21 receptor. (A) Cartoon and surface representation of the PTS2 cargo– receptor complex. The Pex7WD domain (yellow) and the C-terminal domain of the coreceptor Pex21 (cyan) together recognize the helical PTS2 signal peptide of Fox3N (red) fused to MBP (gray). (B) Zoomed view of the PTS2 helix with side chains depicted as sticks. Emmanouilidis et al. Biochim Biophys Acta. 2016 Peroxisomal protein import receptor cycle: (1) Cargo recognition in the cytosol. (2) Docking of the receptor–cargo complex to the peroxisomal membrane via the docking complex. (3) Pore assembly and protein translocation. (4) Receptor ubiquitination. (5) Receptor export and recycling. Abbreviations: ubiquitin (Ub). Meinecke et al. Biochim Biophys Acta. 2016 5. Interplay of peroxisomes with other organelles No peroxisome is an island In order to optimize their multiple cellular functions, peroxisomes must collaborate and communicate with the surrounding organelles. A common way of communication between organelles is through physical membrane contact sites where membranes of two organelles are tethered, facilitating exchange of small molecules and intracellular signaling. In addition contact sites are important for controlling processes such as metabolism, organelle trafficking, inheritance and division. How peroxisomes rely on contact sites for their various cellular activities is only recently starting to be appreciated and explored and the extent of peroxisomal communication, their contact sites and their functions are less characterized. Shai et al. Biochim Biophys Acta. 2016 Peroxisome–mitochondria contact site. Peroxisomes can be localized adjacent to a specific mitochondrial niche near the ER-mitochondria contact site proximal to where the pyruvate dehydrogenase (PDH) complex is found in the mitochondria matrix. The proximity to the ER-mitochondria contacts may suggest a function of a three way organelle junction. The peroxisome-mitochondria tether has been suggested to be mediated by the interaction between Pex11, a key protein involved in peroxisome proliferation, and Mdm34, one of the proteins creating the ER-mitochondria tether (ERMES). Schrader et al. Biochim Biophys Acta. 2016 There is emerging evidence that the functional relationship between peroxisomes and mitochondria is the result of an organellar co-evolution originating in the early ancestors of all eukaryotes. This fundamental interconnection between peroxisomes and mitochondria is reflected by an increasing number of cooperative functions, such as fatty acid β-oxidation, innate immune response, maintenance of ROS homeostasis or even regulation of apoptosis and cell survival. Furthermore, both organelles share a significant number of proteins linked to the cellular processes. Peroxisome–lipid droplet contact site. In the budding yeast, peroxisomes stably adhere to lipid droplets (LDs) thereby stimulating the breakdown and transfer of various lipids across these organellar boundaries. Peroxisome protrusions, termed pexopodia, have been seen to invade the LD core as a result of hemifusion of the single leaflet of the lipid droplet membrane and the outer leaflet of the peroxisomal membrane. Pexopodia are believed to facilitate the flux of fatty acids into peroxisomes and the transfer of peroxisomal oxidation enzymes into LDs. Peroxisome–lysosome contact site. It was recently identified that a peroxisome–lysosome contact site occurs (termed LPMC) in human cells. The LPMC is dynamic and cholesterol dependent. The tether holding the two organelles together is the integral lysosomal membrane protein, Synaptotagmin VII (Syt7), through binding to the lipid PI(4,5)P2 on the peroxisomal membrane. This contact site facilitates the transfer of cholesterol from lysosomes to peroxisomes. Peroxisome–peroxisome interaction. In mammalian cells, peroxisomes are engaged in close self-interactions. Although such interactions are transient, peroxisomes are able to re-contact rapidly creating long-term contacts. The interaction between peroxisomes has three possible roles: (A) Movement of peroxisome populations in the cell. (B) Fusion between peroxisomes. (C) Creation of functional units to exchange metabolites or lipids. Three hypotheses as to how peroxisomes maintain such diverse contacts with other organelles: (A) Random encounters: peroxisome may contain all the necessary proteins, lipids and molecules to interact with any other organelle and even with multiple organelles at once. Random encounters enable the creation of contact sites between peroxisomes and other organelles. (B) Conditional contact sites: peroxisome contact sites are condition dependent hence forming specifically with certain organelles for specific functions. Changes in contact site partners are enabled by specific signals for the regulation of the tether/proteins/lipids. (C) Specialized peroxisomes: peroxisome sub-populations exist in the cell, each tailored to interact with a specific organelle. Each sub-population could contain a unique proteome and has the ability to interact with a specific organelle for a different function. Attachment of peroxisomes to cytoskeleton and movement along microtubular filaments and actin cables are essential and highly regulated processes enabling metabolic efficiency, biogenesis, maintenance and inheritance of this dynamic cellular compartment. Several peroxisome-associated proteins have been identified, which mediate interaction with motor proteins, adaptor proteins or other constituents of the cytoskeleton. It appears that there is a species-specific complexity of protein–protein interactions required to control directional movement and arresting. An open question is why some proteins with a specific role in peroxisomal protein import have an additional function in the regulation of cytoskeleton binding and motility of peroxisomes. Neuhaus et al. Biochim Biophys Acta. 2016