1
|
Záhonová K, Low RS, Warren CJ, Cantoni D, Herman EK, Yiangou L, Ribeiro CA, Phanprasert Y, Brown IR, Rueckert S, Baker NL, Tachezy J, Betts EL, Gentekaki E, van der Giezen M, Clark CG, Jackson AP, Dacks JB, Tsaousis AD. Evolutionary analysis of cellular reduction and anaerobicity in the hyper-prevalent gut microbe Blastocystis. Curr Biol 2023:S0960-9822(23)00620-6. [PMID: 37267944 DOI: 10.1016/j.cub.2023.05.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 03/22/2023] [Accepted: 05/11/2023] [Indexed: 06/04/2023]
Abstract
Blastocystis is the most prevalent microbial eukaryote in the human and animal gut, yet its role as commensal or parasite is still under debate. Blastocystis has clearly undergone evolutionary adaptation to the gut environment and possesses minimal cellular compartmentalization, reduced anaerobic mitochondria, no flagella, and no reported peroxisomes. To address this poorly understood evolutionary transition, we have taken a multi-disciplinary approach to characterize Proteromonas lacertae, the closest canonical stramenopile relative of Blastocystis. Genomic data reveal an abundance of unique genes in P. lacertae but also reductive evolution of the genomic complement in Blastocystis. Comparative genomic analysis sheds light on flagellar evolution, including 37 new candidate components implicated with mastigonemes, the stramenopile morphological hallmark. The P. lacertae membrane-trafficking system (MTS) complement is only slightly more canonical than that of Blastocystis, but notably, we identified that both organisms encode the complete enigmatic endocytic TSET complex, a first for the entire stramenopile lineage. Investigation also details the modulation of mitochondrial composition and metabolism in both P. lacertae and Blastocystis. Unexpectedly, we identify in P. lacertae the most reduced peroxisome-derived organelle reported to date, which leads us to speculate on a mechanism of constraint guiding the dynamics of peroxisome-mitochondrion reductive evolution on the path to anaerobiosis. Overall, these analyses provide a launching point to investigate organellar evolution and reveal in detail the evolutionary path that Blastocystis has taken from a canonical flagellated protist to the hyper-divergent and hyper-prevalent animal and human gut microbe.
Collapse
Affiliation(s)
- Kristína Záhonová
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton T6G 2G3, Canada; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, České Budějovice (Budweis) 370 05, Czech Republic; Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec 252 50, Czech Republic; Life Science Research Centre, Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava 710 00, Czech Republic
| | - Ross S Low
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Christopher J Warren
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Diego Cantoni
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Emily K Herman
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton T6G 2G3, Canada; Department of Agricultural, Food, and Nutritional Science, Faculty of Agricultural, Life, and Environmental Sciences, University of Alberta, 2-31 General Services Building, Edmonton, AB T6G 2H1, Canada
| | - Lyto Yiangou
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Cláudia A Ribeiro
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Yasinee Phanprasert
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton T6G 2G3, Canada; School of Science, Mae Fah Luang Universit, 333 Moo 1, T. Tasud, Muang District, Chiang Rai 57100, Thailand
| | - Ian R Brown
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Sonja Rueckert
- School of Applied Sciences, Sighthill Campus, Room 3.B.36, Edinburgh EH11 4BN, Scotland; Faculty of Biology, AG Eukaryotische Mikrobiologie, Universitätsstrasse 5, S05 R04 H83, Essen 45141, Germany
| | - Nicola L Baker
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec 252 50, Czech Republic
| | - Emma L Betts
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK; School of Applied Sciences, Sighthill Campus, Room 3.B.36, Edinburgh EH11 4BN, Scotland
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang Universit, 333 Moo 1, T. Tasud, Muang District, Chiang Rai 57100, Thailand; Gut Microbiome Research Group, Mae Fah Luang University, 333 Moo 1, T. Tasud, Muang District, Chiang Rai 57100, Thailand
| | - Mark van der Giezen
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger Richard Johnsens Gate 4, 4021 Stavanger, Norway; Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - C Graham Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Andrew P Jackson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton T6G 2G3, Canada; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, České Budějovice (Budweis) 370 05, Czech Republic; Centre for Life's Origin and Evolution, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.
| | - Anastasios D Tsaousis
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK.
| |
Collapse
|
2
|
Tan H, Wang L, Wang H, Cheng Y, Li X, Wan H, Liu C, Liu T, Li Q. Engineering Komagataella phaffii to biosynthesize cordycepin from methanol which drives global metabolic alterations at the transcription level. Synth Syst Biotechnol 2023; 8:242-252. [PMID: 37007278 PMCID: PMC10060148 DOI: 10.1016/j.synbio.2023.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/18/2023] Open
Abstract
Cordycepin has the potential to be an alternative to the disputed herbicide glyphosate. However, current laborious and time-consuming production strategies at low yields based on Cordyceps militaris lead to extremely high cost and restrict its application in the field of agriculture. In this study, Komagataella phaffii (syn. Pichia pastoris) was engineered to biosynthesize cordycepin from methanol, which could be converted from CO2. Combined with fermentation optimization, cordycepin content in broth reached as high as 2.68 ± 0.04 g/L within 168 h, around 15.95 mg/(L·h) in productivity. Additionally, a deaminated product of cordycepin was identified at neutral or weakly alkaline starting pH during fermentation. Transcriptome analysis found the yeast producing cordycepin was experiencing severe inhibition in methanol assimilation and peroxisome biogenesis, responsible for delayed growth and decreased carbon flux to pentose phosphate pathway (PPP) which led to lack of precursor supply. Amino acid interconversion and disruption in RNA metabolism were also due to accumulation of cordycepin. The study provided a unique platform for the manufacture of cordycepin based on the emerging non-conventional yeast and gave practical strategies for further optimization of the microbial cell factory.
Collapse
|
3
|
Bittner E, Stehlik T, Freitag J. Sharing the wealth: The versatility of proteins targeted to peroxisomes and other organelles. Front Cell Dev Biol 2022; 10:934331. [PMID: 36225313 PMCID: PMC9549241 DOI: 10.3389/fcell.2022.934331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Peroxisomes are eukaryotic organelles with critical functions in cellular energy and lipid metabolism. Depending on the organism, cell type, and developmental stage, they are involved in numerous other metabolic and regulatory pathways. Many peroxisomal functions require factors also relevant to other cellular compartments. Here, we review proteins shared by peroxisomes and at least one different site within the cell. We discuss the mechanisms to achieve dual targeting, their regulation, and functional consequences. Characterization of dual targeting is fundamental to understand how peroxisomes are integrated into the metabolic and regulatory circuits of eukaryotic cells.
Collapse
|
4
|
Vasilev J, Mix AK, Heimerl T, Maier UG, Moog D. Inferred Subcellular Localization of Peroxisomal Matrix Proteins of Guillardia theta Suggests an Important Role of Peroxisomes in Cryptophytes. FRONTIERS IN PLANT SCIENCE 2022; 13:889662. [PMID: 35783940 PMCID: PMC9244630 DOI: 10.3389/fpls.2022.889662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Peroxisomes participate in several important metabolic processes in eukaryotic cells, such as the detoxification of reactive oxygen species (ROS) or the degradation of fatty acids by β-oxidation. Recently, the presence of peroxisomes in the cryptophyte Guillardia theta and other "chromalveolates" was revealed by identifying proteins for peroxisomal biogenesis. Here, we investigated the subcellular localization of candidate proteins of G. theta in the diatom Phaeodactylum tricornutum, either possessing a putative peroxisomal targeting signal type 1 (PTS1) sequence or factors lacking a peroxisomal targeting signal but known to be involved in β-oxidation. Our results indicate important contributions of the peroxisomes of G. theta to the carbohydrate, ether phospholipid, nucleotide, vitamin K, ROS, amino acid, and amine metabolisms. Moreover, our results suggest that in contrast to many other organisms, the peroxisomes of G. theta are not involved in the β-oxidation of fatty acids, which exclusively seems to occur in the cryptophyte's mitochondria.
Collapse
Affiliation(s)
- Jana Vasilev
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Ann-Kathrin Mix
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Uwe G. Maier
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Daniel Moog
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| |
Collapse
|
5
|
Záhonová K, Treitli SC, Le T, Škodová-Sveráková I, Hanousková P, Čepička I, Tachezy J, Hampl V. Anaerobic derivates of mitochondria and peroxisomes in the free-living amoeba Pelomyxa schiedti revealed by single-cell genomics. BMC Biol 2022; 20:56. [PMID: 35227266 PMCID: PMC8887013 DOI: 10.1186/s12915-022-01247-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/03/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Mitochondria and peroxisomes are the two organelles that are most affected during adaptation to microoxic or anoxic environments. Mitochondria are known to transform into anaerobic mitochondria, hydrogenosomes, mitosomes, and various transition stages in between, collectively called mitochondrion-related organelles (MROs), which vary in enzymatic capacity. Anaerobic peroxisomes were identified only recently, and their putatively most conserved function seems to be the metabolism of inositol. The group Archamoebae includes anaerobes bearing both anaerobic peroxisomes and MROs, specifically hydrogenosomes in free-living Mastigamoeba balamuthi and mitosomes in the human pathogen Entamoeba histolytica, while the organelles within the third lineage represented by Pelomyxa remain uncharacterized. RESULTS We generated high-quality genome and transcriptome drafts from Pelomyxa schiedti using single-cell omics. These data provided clear evidence for anaerobic derivates of mitochondria and peroxisomes in this species, and corresponding vesicles were tentatively identified in electron micrographs. In silico reconstructed MRO metabolism harbors respiratory complex II, electron-transferring flavoprotein, a partial TCA cycle running presumably in the reductive direction, pyruvate:ferredoxin oxidoreductase, [FeFe]-hydrogenases, a glycine cleavage system, a sulfate activation pathway, and an expanded set of NIF enzymes for iron-sulfur cluster assembly. When expressed in the heterologous system of yeast, some of these candidates localized into mitochondria, supporting their involvement in the MRO metabolism. The putative functions of P. schiedti peroxisomes could be pyridoxal 5'-phosphate biosynthesis, amino acid and carbohydrate metabolism, and hydrolase activities. Unexpectedly, out of 67 predicted peroxisomal enzymes, only four were also reported in M. balamuthi, namely peroxisomal processing peptidase, nudix hydrolase, inositol 2-dehydrogenase, and D-lactate dehydrogenase. Localizations in yeast corroborated peroxisomal functions of the latter two. CONCLUSIONS This study revealed the presence and partially annotated the function of anaerobic derivates of mitochondria and peroxisomes in P. schiedti using single-cell genomics, localizations in yeast heterologous systems, and transmission electron microscopy. The MRO metabolism resembles that of M. balamuthi and most likely reflects the state in the common ancestor of Archamoebae. The peroxisomal metabolism is strikingly richer in P. schiedti. The presence of myo-inositol 2-dehydrogenase in the predicted peroxisomal proteome corroborates the situation in other Archamoebae, but future experimental evidence is needed to verify additional functions of this organelle.
Collapse
Affiliation(s)
- Kristína Záhonová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic.
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.
| | | | - Tien Le
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ingrid Škodová-Sveráková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Pavla Hanousková
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic.
| |
Collapse
|
6
|
Verner Z, Žárský V, Le T, Narayanasamy RK, Rada P, Rozbeský D, Makki A, Belišová D, Hrdý I, Vancová M, Lender C, König C, Bruchhaus I, Tachezy J. Anaerobic peroxisomes in Entamoeba histolytica metabolize myo-inositol. PLoS Pathog 2021; 17:e1010041. [PMID: 34780573 PMCID: PMC8629394 DOI: 10.1371/journal.ppat.1010041] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 11/29/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022] Open
Abstract
Entamoeba histolytica is believed to be devoid of peroxisomes, like most anaerobic protists. In this work, we provided the first evidence that peroxisomes are present in E. histolytica, although only seven proteins responsible for peroxisome biogenesis (peroxins) were identified (Pex1, Pex6, Pex5, Pex11, Pex14, Pex16, and Pex19). Targeting matrix proteins to peroxisomes is reduced to the PTS1-dependent pathway mediated via the soluble Pex5 receptor, while the PTS2 receptor Pex7 is absent. Immunofluorescence microscopy showed that peroxisomal markers (Pex5, Pex14, Pex16, Pex19) are present in vesicles distinct from mitosomes, the endoplasmic reticulum, and the endosome/phagosome system, except Pex11, which has dual localization in peroxisomes and mitosomes. Immunoelectron microscopy revealed that Pex14 localized to vesicles of approximately 90-100 nm in diameter. Proteomic analyses of affinity-purified peroxisomes and in silico PTS1 predictions provided datasets of 655 and 56 peroxisomal candidates, respectively; however, only six proteins were shared by both datasets, including myo-inositol dehydrogenase (myo-IDH). Peroxisomal NAD-dependent myo-IDH appeared to be a dimeric enzyme with high affinity to myo-inositol (Km 0.044 mM) and can utilize also scyllo-inositol, D-glucose and D-xylose as substrates. Phylogenetic analyses revealed that orthologs of myo-IDH with PTS1 are present in E. dispar, E. nutalli and E. moshkovskii but not in E. invadens, and form a monophyletic clade of mostly peroxisomal orthologs with free-living Mastigamoeba balamuthi and Pelomyxa schiedti. The presence of peroxisomes in E. histolytica and other archamoebae breaks the paradigm of peroxisome absence in anaerobes and provides a new potential target for the development of antiparasitic drugs.
Collapse
Affiliation(s)
- Zdeněk Verner
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vojtěch Žárský
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Tien Le
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ravi Kumar Narayanasamy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Petr Rada
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Daniel Rozbeský
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Abhijith Makki
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Darja Belišová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Marie Vancová
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, Ceske Budejovice, Czech Republic
| | - Corinna Lender
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Constantin König
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Iris Bruchhaus
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| |
Collapse
|
7
|
Skern-Mauritzen R, Malde K, Eichner C, Dondrup M, Furmanek T, Besnier F, Komisarczuk AZ, Nuhn M, Dalvin S, Edvardsen RB, Klages S, Huettel B, Stueber K, Grotmol S, Karlsbakk E, Kersey P, Leong JS, Glover KA, Reinhardt R, Lien S, Jonassen I, Koop BF, Nilsen F. The salmon louse genome: Copepod features and parasitic adaptations. Genomics 2021; 113:3666-3680. [PMID: 34403763 DOI: 10.1016/j.ygeno.2021.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/06/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022]
Abstract
Copepods encompass numerous ecological roles including parasites, detrivores and phytoplankton grazers. Nonetheless, copepod genome assemblies remain scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod found on salmonid fish. We present the 695.4 Mbp L. salmonis genome assembly containing ≈60% repetitive regions and 13,081 annotated protein-coding genes. The genome comprises 14 autosomes and a ZZ-ZW sex chromosome system. Assembly assessment identified 92.4% of the expected arthropod genes. Transcriptomics supported annotation and indicated a marked shift in gene expression after host attachment, including apparent downregulation of genes related to circadian rhythm coinciding with abandoning diurnal migration. The genome shows evolutionary signatures including loss of genes needed for peroxisome biogenesis, presence of numerous FNII domains, and an incomplete heme homeostasis pathway suggesting heme proteins to be obtained from the host. Despite repeated development of resistance against chemical treatments L. salmonis exhibits low numbers of many genes involved in detoxification.
Collapse
Affiliation(s)
| | - Ketil Malde
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway; Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Christiane Eichner
- Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Michael Dondrup
- Computational Biology Unit, Department of Informatics, University of Bergen, Thormøhlens Gate 55, 5008 Bergen, Norway
| | - Tomasz Furmanek
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Francois Besnier
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Anna Zofia Komisarczuk
- Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Michael Nuhn
- EMBL-The European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Sussie Dalvin
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Rolf B Edvardsen
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Sven Klages
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Carl von Linné Weg 10, D-50829 Köln, Germany
| | - Kurt Stueber
- Max Planck Genome Centre Cologne, Carl von Linné Weg 10, D-50829 Köln, Germany
| | - Sindre Grotmol
- Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Egil Karlsbakk
- Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Paul Kersey
- EMBL-The European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK; Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Jong S Leong
- Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Kevin A Glover
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway; Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Richard Reinhardt
- Max Planck Genome Centre Cologne, Carl von Linné Weg 10, D-50829 Köln, Germany
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Oluf Thesens vei 6, 1433 Ås, Norway
| | - Inge Jonassen
- Computational Biology Unit, Department of Informatics, University of Bergen, Thormøhlens Gate 55, 5008 Bergen, Norway
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Frank Nilsen
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway; Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway.
| |
Collapse
|
8
|
Abstract
The origin of eukaryotes has been defined as the major evolutionary transition since the origin of life itself. Most hallmark traits of eukaryotes, such as their intricate intracellular organization, can be traced back to a putative common ancestor that predated the broad diversity of extant eukaryotes. However, little is known about the nature and relative order of events that occurred in the path from preexisting prokaryotes to this already sophisticated ancestor. The origin of mitochondria from the endosymbiosis of an alphaproteobacterium is one of the few robustly established events to which most hypotheses on the origin of eukaryotes are anchored, but the debate is still open regarding the time of this acquisition, the nature of the host, and the ecological and metabolic interactions between the symbiotic partners. After the acquisition of mitochondria, eukaryotes underwent a fast radiation into several major clades whose phylogenetic relationships have been largely elusive. Recent progress in the comparative analyses of a growing number of genomes is shedding light on the early events of eukaryotic evolution as well as on the root and branching patterns of the tree of eukaryotes. Here I discuss current knowledge and debates on the origin and early evolution of eukaryotes. I focus particularly on how phylogenomic analyses have challenged some of the early assumptions about eukaryotic evolution, including the widespread idea that mitochondrial symbiosis in an archaeal host was the earliest event in eukaryogenesis. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Toni Gabaldón
- Barcelona Supercomputing Centre (BCS-CNS), 08034 Barcelona, Spain; .,Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| |
Collapse
|
9
|
Jansen RLM, Santana-Molina C, van den Noort M, Devos DP, van der Klei IJ. Comparative Genomics of Peroxisome Biogenesis Proteins: Making Sense of the PEX Proteins. Front Cell Dev Biol 2021; 9:654163. [PMID: 34095119 PMCID: PMC8172628 DOI: 10.3389/fcell.2021.654163] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/21/2021] [Indexed: 11/29/2022] Open
Abstract
PEX genes encode proteins involved in peroxisome biogenesis and proliferation. Using a comparative genomics approach, we clarify the evolutionary relationships between the 37 known PEX proteins in a representative set of eukaryotes, including all common model organisms, pathogenic unicellular eukaryotes and human. A large number of previously unknown PEX orthologs were identified. We analyzed all PEX proteins, their conservation and domain architecture and defined the core set of PEX proteins that is required to make a peroxisome. The molecular processes in peroxisome biogenesis in different organisms were put into context, showing that peroxisomes are not static organelles in eukaryotic evolution. Organisms that lack peroxisomes still contain a few PEX proteins, which probably play a role in alternative processes. Finally, the relationships between PEX proteins of two large families, the Pex11 and Pex23 families, were analyzed, thereby contributing to the understanding of their complicated and sometimes incorrect nomenclature. We provide an exhaustive overview of this important eukaryotic organelle.
Collapse
Affiliation(s)
- Renate L M Jansen
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Carlos Santana-Molina
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Seville, Spain
| | - Marco van den Noort
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Seville, Spain
| | - Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| |
Collapse
|
10
|
Kechasov D, de Grahl I, Endries P, Reumann S. Evolutionary Maintenance of the PTS2 Protein Import Pathway in the Stramenopile Alga Nannochloropsis. Front Cell Dev Biol 2020; 8:593922. [PMID: 33330478 PMCID: PMC7710942 DOI: 10.3389/fcell.2020.593922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/13/2020] [Indexed: 12/18/2022] Open
Abstract
The stramenopile alga Nannochloropsis evolved by secondary endosymbiosis of a red alga by a heterotrophic host cell and emerged as a promising organism for biotechnological applications, such as the production of polyunsaturated fatty acids and biodiesel. Peroxisomes play major roles in fatty acid metabolism but experimental analyses of peroxisome biogenesis and metabolism in Nannochloropsis are not reported yet. In fungi, animals, and land plants, soluble proteins of peroxisomes are targeted to the matrix by one of two peroxisome targeting signals (type 1, PTS1, or type 2, PTS2), which are generally conserved across kingdoms and allow the prediction of peroxisomal matrix proteins from nuclear genome sequences. Because diatoms lost the PTS2 pathway secondarily, we investigated its presence in the stramenopile sister group of diatoms, the Eustigmatophyceae, represented by Nannochloropsis. We detected a full-length gene of a putative PEX7 ortholog coding for the cytosolic receptor of PTS2 proteins and demonstrated its expression in Nannochloropsis gaditana. The search for predicted PTS2 cargo proteins in N. gaditana yielded several candidates. In vivo subcellular targeting analyses of representative fusion proteins in different plant expression systems demonstrated that two predicted PTS2 domains were indeed functional and sufficient to direct a reporter protein to peroxisomes. Peroxisome targeting of the predicted PTS2 cargo proteins was further confirmed in Nannochloropsis oceanica by confocal and transmission electron microscopy. Taken together, the results demonstrate for the first time that one group of stramenopile algae maintained the import pathway for PTS2 cargo proteins. To comprehensively map and model the metabolic capabilities of Nannochloropsis peroxisomes, in silico predictions needs to encompass both the PTS1 and the PTS2 matrix proteome.
Collapse
Affiliation(s)
- Dmitry Kechasov
- Centre for Organelle Research, University of Stavanger, Stavanger, Norway
| | - Imke de Grahl
- Plant Biochemistry and Infection Biology, Institute for Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Pierre Endries
- Plant Biochemistry and Infection Biology, Institute for Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Sigrun Reumann
- Centre for Organelle Research, University of Stavanger, Stavanger, Norway
- Plant Biochemistry and Infection Biology, Institute for Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| |
Collapse
|
11
|
Mast FD, Rachubinski RA, Aitchison JD. Peroxisome prognostications: Exploring the birth, life, and death of an organelle. J Cell Biol 2020; 219:133827. [PMID: 32211898 PMCID: PMC7054992 DOI: 10.1083/jcb.201912100] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 02/07/2023] Open
Abstract
Peroxisomes play a central role in human health and have biochemical properties that promote their use in many biotechnology settings. With a primary role in lipid metabolism, peroxisomes share a niche with lipid droplets within the endomembrane-secretory system. Notably, factors in the ER required for the biogenesis of peroxisomes also impact the formation of lipid droplets. The dynamic interface between peroxisomes and lipid droplets, and also between these organelles and the ER and mitochondria, controls their metabolic flux and their dynamics. Here, we review our understanding of peroxisome biogenesis to propose and reframe models for understanding how peroxisomes are formed in cells. To more fully understand the roles of peroxisomes and to take advantage of their many properties that may prove useful in novel therapeutics or biotechnology applications, we recast mechanisms controlling peroxisome biogenesis in a framework that integrates inference from these models with experimental data.
Collapse
Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA
| | | | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA.,Department of Pediatrics, University of Washington, Seattle, WA
| |
Collapse
|
12
|
González-Robles A, González-Lázaro M, Lagunes-Guillén AE, Omaña-Molina M, Lares-Jiménez LF, Lares-Villa F, Martínez-Palomo A. Ultrastructural, Cytochemical, and Comparative Genomic Evidence of Peroxisomes in Three Genera of Pathogenic Free-Living Amoebae, Including the First Morphological Data for the Presence of This Organelle in Heteroloboseans. Genome Biol Evol 2020; 12:1734-1750. [PMID: 32602891 PMCID: PMC7549135 DOI: 10.1093/gbe/evaa129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2020] [Indexed: 12/13/2022] Open
Abstract
Peroxisomes perform various metabolic processes that are primarily related to the elimination of reactive oxygen species and oxidative lipid metabolism. These organelles are present in all major eukaryotic lineages, nevertheless, information regarding the presence of peroxisomes in opportunistic parasitic protozoa is scarce and in many cases it is still unknown whether these organisms have peroxisomes at all. Here, we performed ultrastructural, cytochemical, and bioinformatic studies to investigate the presence of peroxisomes in three genera of free-living amoebae from two different taxonomic groups that are known to cause fatal infections in humans. By transmission electron microscopy, round structures with a granular content limited by a single membrane were observed in Acanthamoeba castellanii, Acanthamoeba griffini, Acanthamoeba polyphaga, Acanthamoeba royreba, Balamuthia mandrillaris (Amoebozoa), and Naegleria fowleri (Heterolobosea). Further confirmation for the presence of peroxisomes was obtained by treating trophozoites in situ with diaminobenzidine and hydrogen peroxide, which showed positive reaction products for the presence of catalase. We then performed comparative genomic analyses to identify predicted peroxin homologues in these organisms. Our results demonstrate that a complete set of peroxins-which are essential for peroxisome biogenesis, proliferation, and protein import-are present in all of these amoebae. Likewise, our in silico analyses allowed us to identify a complete set of peroxins in Naegleria lovaniensis and three novel peroxin homologues in Naegleria gruberi. Thus, our results indicate that peroxisomes are present in these three genera of free-living amoebae and that they have a similar peroxin complement despite belonging to different evolutionary lineages.
Collapse
Affiliation(s)
- Arturo González-Robles
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Mónica González-Lázaro
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Anel Edith Lagunes-Guillén
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Maritza Omaña-Molina
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlanepantla, Estado de México, Mexico
| | - Luis Fernando Lares-Jiménez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, Mexico
| | - Fernando Lares-Villa
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, Mexico
| | - Adolfo Martínez-Palomo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| |
Collapse
|
13
|
Jo DS, Park NY, Cho DH. Peroxisome quality control and dysregulated lipid metabolism in neurodegenerative diseases. Exp Mol Med 2020; 52:1486-1495. [PMID: 32917959 PMCID: PMC8080768 DOI: 10.1038/s12276-020-00503-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/11/2020] [Accepted: 07/14/2020] [Indexed: 12/15/2022] Open
Abstract
In recent decades, the role of the peroxisome in physiology and disease conditions has become increasingly important. Together with the mitochondria and other cellular organelles, peroxisomes support key metabolic platforms for the oxidation of various fatty acids and regulate redox conditions. In addition, peroxisomes contribute to the biosynthesis of essential lipid molecules, such as bile acid, cholesterol, docosahexaenoic acid, and plasmalogen. Therefore, the quality control mechanisms that regulate peroxisome biogenesis and degradation are important for cellular homeostasis. Current evidence indicates that peroxisomal function is often reduced or dysregulated in various human disease conditions, such as neurodegenerative diseases. Here, we review the recent progress that has been made toward understanding the quality control systems that regulate peroxisomes and their pathological implications. Systematic studies of cellular organelles called peroxisomes are needed to determine their influence on the progression of neurodegenerative diseases. Peroxisomes play vital roles in biological processes including the metabolism of lipids and reactive oxygen species, and the synthesis of key molecules, including bile acid and cholesterol. Disruption to peroxisome activity has been linked to metabolic disorders, cancers and neurodegenerative conditions. Dong-Hyung Cho at Kyungpook National University in Daegu, South Korea, and coworkers reviewed current understanding of peroxisome regulation, with a particular focus on brain disorders. The quantity and activity of peroxisomes alter according to environmental and stress cues. The brain is lipid-rich, and even small changes in fatty acid composition may influence neuronal function. Changes in fatty acid metabolism are found in early stage Alzheimer’s and Parkinson’s diseases, but whether peroxisome disruption is responsible requires clarification.
Collapse
Affiliation(s)
- Doo Sin Jo
- Brain Science and Engineering Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Na Yeon Park
- School of Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Dong-Hyung Cho
- Brain Science and Engineering Institute, Kyungpook National University, Daegu, 41566, Republic of Korea. .,School of Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
| |
Collapse
|
14
|
Ferdigg A, Dimmer KS, Rapaport D, Vitali DG. Hydrogenosomal tail-anchored proteins are targeted to both mitochondria and ER upon their expression in yeast cells. PLoS One 2020; 15:e0237982. [PMID: 32817700 PMCID: PMC7446849 DOI: 10.1371/journal.pone.0237982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/06/2020] [Indexed: 11/18/2022] Open
Abstract
Some organisms, like Trichomonas vaginalis, contain mitochondria-related hydrogen-producing organelles, called hydrogenosomes. The protein targeting into these organelles is proposed to be similar to the well-studied mitochondria import. Indeed, S. cerevisiae mitochondria and T. vaginalis hydrogenosomes share some components of protein import complexes. However, it is still unknown whether targeting signals directing substrate proteins to hydrogenosomes can support in other eukaryotes specific mitochondrial localization. To address this issue, we investigated the intracellular localization of three hydrogenosomal tail-anchored proteins expressed in yeast cells. We observed that these proteins were targeted to both mitochondria and ER with a variable dependency on the mitochondrial MIM complex. Our results suggest that the targeting signal of TA proteins are only partially conserved between hydrogenosomes and yeast mitochondria.
Collapse
Affiliation(s)
- Andrè Ferdigg
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Kai S. Dimmer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
- * E-mail: (DR); (DGV)
| | - Daniela G. Vitali
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
- * E-mail: (DR); (DGV)
| |
Collapse
|
15
|
Coppa A, Guha S, Fourcade S, Parameswaran J, Ruiz M, Moser AB, Schlüter A, Murphy MP, Lizcano JM, Miranda-Vizuete A, Dalfó E, Pujol A. The peroxisomal fatty acid transporter ABCD1/PMP-4 is required in the C. elegans hypodermis for axonal maintenance: A worm model for adrenoleukodystrophy. Free Radic Biol Med 2020; 152:797-809. [PMID: 32017990 PMCID: PMC7611262 DOI: 10.1016/j.freeradbiomed.2020.01.177] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/20/2020] [Accepted: 01/20/2020] [Indexed: 02/07/2023]
Abstract
Adrenoleukodystrophy is a neurometabolic disorder caused by a defective peroxisomal ABCD1 transporter of very long-chain fatty acids (VLCFAs). Its pathogenesis is incompletely understood. Here we characterize a nematode model of X-ALD with loss of the pmp-4 gene, the worm orthologue of ABCD1. These mutants recapitulate the hallmarks of X-ALD: i) VLCFAs accumulation and impaired mitochondrial redox homeostasis and ii) axonal damage coupled to locomotor dysfunction. Furthermore, we identify a novel role for PMP-4 in modulating lipid droplet dynamics. Importantly, we show that the mitochondria targeted antioxidant MitoQ normalizes lipid droplets size, and prevents axonal degeneration and locomotor disability, highlighting its therapeutic potential. Moreover, PMP-4 acting solely in the hypodermis rescues axonal and locomotion abnormalities, suggesting a myelin-like role for the hypodermis in providing essential peroxisomal functions for the nematode nervous system.
Collapse
Affiliation(s)
- Andrea Coppa
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, L'Hospitalet de Llobregat, Spain
| | - Sanjib Guha
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, L'Hospitalet de Llobregat, Spain
| | - Stéphane Fourcade
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, L'Hospitalet de Llobregat, Spain; CIBERER U759, Center for Biomedical Research on Rare Diseases, Spain
| | - Janani Parameswaran
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, L'Hospitalet de Llobregat, Spain; CIBERER U759, Center for Biomedical Research on Rare Diseases, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, L'Hospitalet de Llobregat, Spain; CIBERER U759, Center for Biomedical Research on Rare Diseases, Spain
| | - Ann B Moser
- Peroxisomal Diseases Laboratory, Kennedy Krieger Institute, 707 N. Broadway, Baltimore, MD, 21205, USA
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, L'Hospitalet de Llobregat, Spain; CIBERER U759, Center for Biomedical Research on Rare Diseases, Spain
| | | | - Jose Miguel Lizcano
- Departament de Bioquímica i Biologia Molecular, Institut de Neurociències, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra (Barcelona), Spain
| | - Antonio Miranda-Vizuete
- Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío /CSIC/ Universidad de Sevilla, E-41013, Sevilla, Spain
| | - Esther Dalfó
- Departament de Bioquímica i Biologia Molecular, Institut de Neurociències, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra (Barcelona), Spain; Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), 08500, Vic, Spain.
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, L'Hospitalet de Llobregat, Spain; CIBERER U759, Center for Biomedical Research on Rare Diseases, Spain; ICREA (Institució Catalana de Recerca i Estudis Avançats), Barcelona, Spain.
| |
Collapse
|
16
|
Slyusarev GS, Starunov VV, Bondarenko AS, Zorina NA, Bondarenko NI. Extreme Genome and Nervous System Streamlining in the Invertebrate Parasite Intoshia variabili. Curr Biol 2020; 30:1292-1298.e3. [PMID: 32084405 DOI: 10.1016/j.cub.2020.01.061] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/21/2019] [Accepted: 01/17/2020] [Indexed: 11/19/2022]
Abstract
Orthonectida is a small, rare, and in many aspects enigmatic group of organisms with a unique life cycle and a highly simplified adult free-living stage parasitizing various marine invertebrates [1, 2]. Phylogenetic relationships of Orthonectida have remained controversial for a long time. According to recent data, they are close to Annelida, specifically to Clitellata [3-5]. Several studies have shown that parasitism can not only lead to a dramatic reduction of the body plan and morphological structures but also affect organisms at the genomic level [6, 7]. Comparative studies of parasites and closely related non-parasitic species could clarify the genome reduction degree and evolution of parasitism. Here, we report on the morphology, genome structure, and content of the smallest known Orthonectida species Intoshia variabili, inhabiting the flatworm Graffiellus croceus. This orthonectid with an extremely simplified nervous system demonstrates the smallest known genome (15.3 Mbp) and one of the lowest reported so far gene numbers (5,120 protein-coding genes) among metazoans. The genome is extremely compact, due to a significant reduction of gene number, intergenic regions, intron length, and repetitive elements. The small genome size is probably a result of extreme genome reduction due to their parasitic lifestyle, as well as of simplification and miniaturization of the free-living stages. Our data could provide further insights into the evolution of parasitism and could help to define a minimal bilaterian gene set.
Collapse
Affiliation(s)
- George S Slyusarev
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Viktor V Starunov
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia; Zoological Institute RAS, Universitetskaya nab. 1, 199034 St. Petersburg, Russia
| | - Anton S Bondarenko
- Faculty of Physics, Saint-Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Natalia A Zorina
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Natalya I Bondarenko
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia.
| |
Collapse
|
17
|
Le T, Žárský V, Nývltová E, Rada P, Harant K, Vancová M, Verner Z, Hrdý I, Tachezy J. Anaerobic peroxisomes in Mastigamoeba balamuthi. Proc Natl Acad Sci U S A 2020; 117:2065-2075. [PMID: 31932444 PMCID: PMC6994998 DOI: 10.1073/pnas.1909755117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The adaptation of eukaryotic cells to anaerobic conditions is reflected by substantial changes to mitochondrial metabolism and functional reduction. Hydrogenosomes belong among the most modified mitochondrial derivative and generate molecular hydrogen concomitant with ATP synthesis. The reduction of mitochondria is frequently associated with loss of peroxisomes, which compartmentalize pathways that generate reactive oxygen species (ROS) and thus protect against cellular damage. The biogenesis and function of peroxisomes are tightly coupled with mitochondria. These organelles share fission machinery components, oxidative metabolism pathways, ROS scavenging activities, and some metabolites. The loss of peroxisomes in eukaryotes with reduced mitochondria is thus not unexpected. Surprisingly, we identified peroxisomes in the anaerobic, hydrogenosome-bearing protist Mastigamoeba balamuthi We found a conserved set of peroxin (Pex) proteins that are required for protein import, peroxisomal growth, and division. Key membrane-associated Pexs (MbPex3, MbPex11, and MbPex14) were visualized in numerous vesicles distinct from hydrogenosomes, the endoplasmic reticulum (ER), and Golgi complex. Proteomic analysis of cellular fractions and prediction of peroxisomal targeting signals (PTS1/PTS2) identified 51 putative peroxisomal matrix proteins. Expression of selected proteins in Saccharomyces cerevisiae revealed specific targeting to peroxisomes. The matrix proteins identified included components of acyl-CoA and carbohydrate metabolism and pyrimidine and CoA biosynthesis, whereas no components related to either β-oxidation or catalase were present. In conclusion, we identified a subclass of peroxisomes, named "anaerobic" peroxisomes that shift the current paradigm and turn attention to the reductive evolution of peroxisomes in anaerobic organisms.
Collapse
Affiliation(s)
- Tien Le
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, 25242 Vestec, Czech Republic
| | - Vojtěch Žárský
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, 25242 Vestec, Czech Republic
| | - Eva Nývltová
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, 25242 Vestec, Czech Republic
| | - Petr Rada
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, 25242 Vestec, Czech Republic
| | - Karel Harant
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, 25242 Vestec, Czech Republic
| | - Marie Vancová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Zdeněk Verner
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, 25242 Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, 25242 Vestec, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, 25242 Vestec, Czech Republic;
| |
Collapse
|
18
|
Jiao T, Yang TT, Wang D, Gao ZQ, Wang JL, Tang BP, Liu QN, Zhang DZ, Dai LS. Characterization and expression analysis of immune-related genes in the red swamp crayfish, Procambarus clarkii in response to lipopolysaccharide challenge. FISH & SHELLFISH IMMUNOLOGY 2019; 95:140-150. [PMID: 31629063 DOI: 10.1016/j.fsi.2019.09.072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
To learn more about red swamp crayfish related genes in response to bacterial infections, we investigated immune-related genes induced by lipopolysaccharide (LPS) in the hepatopancreas using high-throughput sequencing method. In present the study, a total of 55,107 unigenes were identified, with an average length of 678 bp. A total of 2215 differentially expressed genes (DEGs) were found, including 669 up-regulated genes and 1546 down-regulated genes. The result of Gene ontology (GO) analysis revealed that 3017 DEGs were enriched in 19 biological process subcategories, 17 cellular component subcategories and 15 molecular function subcategories. The top 20 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that "ribosome" was the most abundant group, which had 34 DEGs. KEGG enrichment analysis identified several immune response pathways. Real-time quantitative reverse transcription-PCR (qRT-PCR) results exhibited that several immune responsive genes were greatly up-regulated following LPS stimulation as observed in the results of high-throughput sequencing. Overall, this study provides new insight into the immune defense mechanisms of P. clarkii against LPS infection.
Collapse
Affiliation(s)
- Ting Jiao
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China; School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, PR China
| | - Ting-Ting Yang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China; Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, PR China; College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, 210009, PR China
| | - Dong Wang
- Instrumental Analysis Center, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Zhen-Qiu Gao
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China; School of Pharmacy, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Jia-Lian Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China; Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, PR China.
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China.
| | - Li-Shang Dai
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, PR China.
| |
Collapse
|
19
|
A Mechanistic Perspective on PEX1 and PEX6, Two AAA+ Proteins of the Peroxisomal Protein Import Machinery. Int J Mol Sci 2019; 20:ijms20215246. [PMID: 31652724 PMCID: PMC6862443 DOI: 10.3390/ijms20215246] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022] Open
Abstract
In contrast to many protein translocases that use ATP or GTP hydrolysis as the driving force to transport proteins across biological membranes, the peroxisomal matrix protein import machinery relies on a regulated self-assembly mechanism for this purpose and uses ATP hydrolysis only to reset its components. The ATP-dependent protein complex in charge of resetting this machinery—the Receptor Export Module (REM)—comprises two members of the “ATPases Associated with diverse cellular Activities” (AAA+) family, PEX1 and PEX6, and a membrane protein that anchors the ATPases to the organelle membrane. In recent years, a large amount of data on the structure/function of the REM complex has become available. Here, we discuss the main findings and their mechanistic implications.
Collapse
|
20
|
Ferrández-Roldán A, Martí-Solans J, Cañestro C, Albalat R. Oikopleura dioica: An Emergent Chordate Model to Study the Impact of Gene Loss on the Evolution of the Mechanisms of Development. Results Probl Cell Differ 2019; 68:63-105. [PMID: 31598853 DOI: 10.1007/978-3-030-23459-1_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The urochordate Oikopleura dioica is emerging as a nonclassical animal model in the field of evolutionary developmental biology (a.k.a. evo-devo) especially attractive for investigating the impact of gene loss on the evolution of mechanisms of development. This is because this organism fulfills the requirements of an animal model (i.e., has a simple and accessible morphology, a short generation time and life span, and affordable culture in the laboratory and amenable experimental manipulation), but also because O. dioica occupies a key phylogenetic position to understand the diversification and origin of our own phylum, the chordates. During its evolution, O. dioica genome has suffered a drastic process of compaction, becoming the smallest known chordate genome, a process that has been accompanied by exacerbating amount of gene losses. Interestingly, however, despite the extensive gene losses, including entire regulatory pathways essential for the embryonic development of other chordates, O. dioica retains the typical chordate body plan. This unexpected situation led to the formulation of the so-called inverse paradox of evo-devo, that is, when a genetic diversity is able to maintain a phenotypic unity. This chapter reviews the biological features of O. dioica as a model animal, along with the current data on the evolution of its genes and genome. We pay special attention to the numerous examples of gene losses that have taken place during the evolution of this unique animal model, which is helping us to understand to which the limits of evo-devo can be pushed off.
Collapse
Affiliation(s)
- Alfonso Ferrández-Roldán
- Facultat de Biologia, Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Josep Martí-Solans
- Facultat de Biologia, Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Cristian Cañestro
- Facultat de Biologia, Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Ricard Albalat
- Facultat de Biologia, Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain.
| |
Collapse
|
21
|
Paight C, Slamovits CH, Saffo MB, Lane CE. Nephromyces Encodes a Urate Metabolism Pathway and Predicted Peroxisomes, Demonstrating That These Are Not Ancient Losses of Apicomplexans. Genome Biol Evol 2019; 11:41-53. [PMID: 30500900 PMCID: PMC6320678 DOI: 10.1093/gbe/evy251] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2018] [Indexed: 12/21/2022] Open
Abstract
The phylum Apicomplexa is a quintessentially parasitic lineage, whose members infect a broad range of animals. One exception to this may be the apicomplexan genus Nephromyces, which has been described as having a mutualistic relationship with its host. Here we analyze transcriptome data from Nephromyces and its parasitic sister taxon, Cardiosporidium, revealing an ancestral purine degradation pathway thought to have been lost early in apicomplexan evolution. The predicted localization of many of the purine degradation enzymes to peroxisomes, and the in silico identification of a full set of peroxisome proteins, indicates that loss of both features in other apicomplexans occurred multiple times. The degradation of purines is thought to play a key role in the unusual relationship between Nephromyces and its host. Transcriptome data confirm previous biochemical results of a functional pathway for the utilization of uric acid as a primary nitrogen source for this unusual apicomplexan.
Collapse
Affiliation(s)
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Mary Beth Saffo
- Department of Biological Sciences, University of Rhode Island
- Smithsonian National Museum of Natural History, Washington, District of Columbia
| | | |
Collapse
|
22
|
Barros-Barbosa A, Rodrigues TA, Ferreira MJ, Pedrosa AG, Teixeira NR, Francisco T, Azevedo JE. The intrinsically disordered nature of the peroxisomal protein translocation machinery. FEBS J 2018; 286:24-38. [PMID: 30443986 DOI: 10.1111/febs.14704] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/14/2018] [Indexed: 12/18/2022]
Abstract
Despite having a membrane that is impermeable to all but the smallest of metabolites, peroxisomes acquire their newly synthesized (cytosolic) matrix proteins in an already folded conformation. In some cases, even oligomeric proteins have been reported to translocate the organelle membrane. The protein sorting machinery that accomplishes this feat must be rather flexible and, unsurprisingly, several of its key components have large intrinsically disordered domains. Here, we provide an overview on these domains and their interactions trying to infer their functional roles in this protein sorting pathway.
Collapse
Affiliation(s)
- Aurora Barros-Barbosa
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Tony A Rodrigues
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Maria J Ferreira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Ana G Pedrosa
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Nélson R Teixeira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Tânia Francisco
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Jorge E Azevedo
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| |
Collapse
|
23
|
Gabaldón T. Relative timing of mitochondrial endosymbiosis and the "pre-mitochondrial symbioses" hypothesis. IUBMB Life 2018; 70:1188-1196. [PMID: 30358047 PMCID: PMC6282991 DOI: 10.1002/iub.1950] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/07/2018] [Accepted: 08/24/2018] [Indexed: 12/16/2022]
Abstract
The origin of eukaryotes stands as a major open question in biology. Central to this question is the nature and timing of the origin of the mitochondrion, an ubiquitous eukaryotic organelle originated by the endosymbiosis of an alphaproteobacterial ancestor. Different hypotheses disagree, among other aspects, on whether mitochondria were acquired early or late during eukaryogenesis. Similarly, the nature and complexity of the receiving host is debated, with models ranging from a simple prokaryotic host to an already complex proto-eukaryote. Here, I will discuss recent findings from phylogenomics analyses of extant genomes that are shedding light into the evolutionary origins of the eukaryotic ancestor, and which suggest a later acquisition of alpha-proteobacterial derived proteins as compared to those with different bacterial ancestries. I argue that simple eukaryogenesis models that assume a binary symbiosis between an archaeon host and an alpha-proteobacterial proto-mitochondrion cannot explain the complex chimeric nature that is inferred for the eukaryotic ancestor. To reconcile existing hypotheses with the new data, I propose the "pre-mitochondrial symbioses" hypothesis that provides a framework for eukaryogenesis scenarios involving alternative symbiotic interactions that predate the acquisition of mitochondria. © 2018 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(12):1188-1196, 2018.
Collapse
Affiliation(s)
- Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Department of experimental and health sciences, Universitat Pompeu Fabra (UPF)BarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
| |
Collapse
|
24
|
Lutfullahoğlu-Bal G, Seferoğlu AB, Keskin A, Akdoğan E, Dunn CD. A bacteria-derived tail anchor localizes to peroxisomes in yeast and mammalian cells. Sci Rep 2018; 8:16374. [PMID: 30401812 PMCID: PMC6219538 DOI: 10.1038/s41598-018-34646-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/18/2018] [Indexed: 11/18/2022] Open
Abstract
Prokaryotes can provide new genetic information to eukaryotes by horizontal gene transfer (HGT), and such transfers are likely to have been particularly consequential in the era of eukaryogenesis. Since eukaryotes are highly compartmentalized, it is worthwhile to consider the mechanisms by which newly transferred proteins might reach diverse organellar destinations. Toward this goal, we have focused our attention upon the behavior of bacteria-derived tail anchors (TAs) expressed in the eukaryote Saccharomyces cerevisiae. In this study, we report that a predicted membrane-associated domain of the Escherichia coli YgiM protein is specifically trafficked to peroxisomes in budding yeast, can be found at a pre-peroxisomal compartment (PPC) upon disruption of peroxisomal biogenesis, and can functionally replace an endogenous, peroxisome-directed TA. Furthermore, the YgiM(TA) can localize to peroxisomes in mammalian cells. Since the YgiM(TA) plays no endogenous role in peroxisomal function or assembly, this domain is likely to serve as an excellent tool allowing further illumination of the mechanisms by which TAs can travel to peroxisomes. Moreover, our findings emphasize the ease with which bacteria-derived sequences might target to organelles in eukaryotic cells following HGT, and we discuss the importance of flexible recognition of organelle targeting information during and after eukaryogenesis.
Collapse
Affiliation(s)
- Güleycan Lutfullahoğlu-Bal
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014, Helsinki, Finland
- Department of Molecular Biology and Genetics, Koç University, 34450, Sarıyer, İstanbul, Turkey
| | - Ayşe Bengisu Seferoğlu
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014, Helsinki, Finland
| | - Abdurrahman Keskin
- Department of Molecular Biology and Genetics, Koç University, 34450, Sarıyer, İstanbul, Turkey
- Department of Biological Sciences, Columbia University, New York, NY, 10027, United States of America
| | - Emel Akdoğan
- Department of Molecular Biology and Genetics, Koç University, 34450, Sarıyer, İstanbul, Turkey
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616, United States of America
| | - Cory D Dunn
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014, Helsinki, Finland.
- Department of Molecular Biology and Genetics, Koç University, 34450, Sarıyer, İstanbul, Turkey.
| |
Collapse
|
25
|
Ludewig-Klingner AK, Michael V, Jarek M, Brinkmann H, Petersen J. Distribution and Evolution of Peroxisomes in Alveolates (Apicomplexa, Dinoflagellates, Ciliates). Genome Biol Evol 2018; 10:1-13. [PMID: 29202176 PMCID: PMC5755239 DOI: 10.1093/gbe/evx250] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2017] [Indexed: 12/13/2022] Open
Abstract
The peroxisome was the last organelle to be discovered and five decades later it is still the Cinderella of eukaryotic compartments. Peroxisomes have a crucial role in the detoxification of reactive oxygen species, the beta-oxidation of fatty acids, and the biosynthesis of etherphospholipids, and they are assumed to be present in virtually all aerobic eukaryotes. Apicomplexan parasites including the malaria and toxoplasmosis agents were described as the first group of mitochondriate protists devoid of peroxisomes. This study was initiated to reassess the distribution and evolution of peroxisomes in the superensemble Alveolata (apicomplexans, dinoflagellates, ciliates). We established transcriptome data from two chromerid algae (Chromera velia, Vitrella brassicaformis), and two dinoflagellates (Prorocentrum minimum, Perkinsus olseni) and identified the complete set of essential peroxins in all four reference species. Our comparative genome analysis provides unequivocal evidence for the presence of peroxisomes in Toxoplasma gondii and related genera. Our working hypothesis of a common peroxisomal origin of all alveolates is supported by phylogenetic analyses of essential markers such as the import receptor Pex5. Vitrella harbors the most comprehensive set of peroxisomal proteins including the catalase and the glyoxylate cycle and it is thus a promising model organism to investigate the functional role of this organelle in Apicomplexa.
Collapse
Affiliation(s)
- Ann-Kathrin Ludewig-Klingner
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Protists and Cyanobacteria (PuC), Braunschweig, Germany
| | - Victoria Michael
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Protists and Cyanobacteria (PuC), Braunschweig, Germany
| | - Michael Jarek
- Helmholtz-Centre for Infection Research (HZI), Group of Genome Analytics, Braunschweig, Germany
| | - Henner Brinkmann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Protists and Cyanobacteria (PuC), Braunschweig, Germany
| | - Jörn Petersen
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Protists and Cyanobacteria (PuC), Braunschweig, Germany
| |
Collapse
|
26
|
Mix AK, Cenci U, Heimerl T, Marter P, Wirkner ML, Moog D. Identification and Localization of Peroxisomal Biogenesis Proteins Indicates the Presence of Peroxisomes in the Cryptophyte Guillardia theta and Other "Chromalveolates". Genome Biol Evol 2018; 10:2834-2852. [PMID: 30247558 PMCID: PMC6203080 DOI: 10.1093/gbe/evy214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2018] [Indexed: 12/11/2022] Open
Abstract
Peroxisomes are single-membrane-bound organelles with a huge metabolic versatility, including the degradation of fatty acids (β-oxidation) and the detoxification of reactive oxygen species as most conserved functions. Although peroxisomes seem to be present in the majority of investigated eukaryotes, where they are responsible for many eclectic and important spatially separated metabolic reactions, knowledge about their existence in the plethora of protists (eukaryotic microorganisms) is scarce. Here, we investigated genomic data of organisms containing complex plastids with red algal ancestry (so-called “chromalveolates”) for the presence of genes encoding peroxins—factors specific for the biogenesis, maintenance, and division of peroxisomes in eukaryotic cells. Our focus was on the cryptophyte Guillardia theta, a marine microalga, which possesses two phylogenetically different nuclei of host and endosymbiont origin, respectively, thus being of enormous evolutionary significance. Besides the identification of a complete set of peroxins in G. theta, we heterologously localized selected factors as GFP fusion proteins via confocal and electron microscopy in the model diatom Phaeodactylum tricornutum. Furthermore, we show that peroxins, and thus most likely peroxisomes, are present in haptophytes as well as eustigmatophytes, brown algae, and alveolates including dinoflagellates, chromerids, and noncoccidian apicomplexans. Our results indicate that diatoms are not the only “chromalveolate” group devoid of the PTS2 receptor Pex7, and thus a PTS2-dependent peroxisomal import pathway, which seems to be absent in haptophytes (Emiliania huxleyi) as well. Moreover, important aspects of peroxisomal biosynthesis and protein import in “chromalveolates”are highlighted.
Collapse
Affiliation(s)
- Ann-Kathrin Mix
- Laboratory for Cell Biology, Philipps University Marburg, Germany
| | - Ugo Cenci
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS-USTL, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq Cedex, France
| | - Thomas Heimerl
- LOEWE Center for Synthetic Microbiology (Synmikro), Philipps University Marburg, Germany
| | - Pia Marter
- Laboratory for Cell Biology, Philipps University Marburg, Germany
| | | | - Daniel Moog
- Laboratory for Cell Biology, Philipps University Marburg, Germany
| |
Collapse
|
27
|
Joshi AS, Nebenfuehr B, Choudhary V, Satpute-Krishnan P, Levine TP, Golden A, Prinz WA. Lipid droplet and peroxisome biogenesis occur at the same ER subdomains. Nat Commun 2018; 9:2940. [PMID: 30054481 PMCID: PMC6063926 DOI: 10.1038/s41467-018-05277-3] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 06/18/2018] [Indexed: 12/19/2022] Open
Abstract
Nascent lipid droplet (LD) formation occurs in the endoplasmic reticulum (ER) membrane but it is not known how sites of biogenesis are determined. We previously identified ER domains in S. cerevisiae containing the reticulon homology domain (RHD) protein Pex30 that are regions where preperoxisomal vesicles (PPVs) form. Here, we show that Pex30 domains are also sites where most nascent LDs form. Mature LDs usually remain associated with Pex30 subdomains, and the same Pex30 subdomain can simultaneously associate with a LD and a PPV or peroxisome. We find that in higher eukaryotes multiple C2 domain containing transmembrane protein (MCTP2) is similar to Pex30: it contains an RHD and resides in ER domains where most nascent LD biogenesis occurs and that often associate with peroxisomes. Together, these findings indicate that most LDs and PPVs form and remain associated with conserved ER subdomains, and suggest a link between LD and peroxisome biogenesis.
Collapse
Affiliation(s)
- Amit S Joshi
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA.
| | - Benjamin Nebenfuehr
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Vineet Choudhary
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | | | - Tim P Levine
- University College London, Institute of Ophthalmology, London, EC1V 9EL, UK
| | - Andy Golden
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - William A Prinz
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
28
|
Intracellular organelles in health and kidney disease. Nephrol Ther 2018; 15:9-21. [PMID: 29887266 DOI: 10.1016/j.nephro.2018.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 02/01/2023]
Abstract
Subcellular organelles consist of smaller substructures called supramolecular assemblies and these in turn consist of macromolecules. Various subcellular organelles have critical functions that consist of genetic disorders of organelle biogenesis and several metabolic disturbances that occur during non-genetic diseases e.g. infection, intoxication and drug treatments. Mitochondrial damage can cause renal dysfunction as ischemic acute renal injury, chronic kidney disease progression. Moreover, mitochondrial dysfunction is an early event in aldosterone-induced podocyte injury and cardiovascular disease due to oxidative stress in chronic kidney disease. Elevated production of reactive oxygen species could be able to activate NLRP3 inflammasome representing new deregulated biological machinery and a novel therapeutic target in hemodialysis patients. Peroxisomes are actively involved in apoptosis and inflammation, innate immunity, aging and in the pathogenesis of age related diseases, such as diabetes mellitus and cancer. Peroxisomal catalase causes alterations of mitochondrial membrane proteins and stimulates generation of mitochondrial reactive oxygen species. High concentrations of hydrogen peroxide exacerbate organelles and cellular aging. The importance of proper peroxisomal function for the biosynthesis of bile acids has been firmly established. Endoplasmic reticulum stress-induced pathological diseases in kidney cause glomerular injury and tubulointerstitial injury. Furthermore, there is a link between oxidative stress and inflammations in pathological states are associated with endoplasmic reticulum stress. Proteinuria and hyperglycemia in diabetic nephropathy may induce endoplasmic reticulum stress in tubular cells of the kidney. Due to the accumulation in the proximal tubule lysosomes, impaired function of these organelles may be an important mechanism leading to proximal tubular toxicity.
Collapse
|
29
|
Moog D, Przyborski JM, Maier UG. Genomic and Proteomic Evidence for the Presence of a Peroxisome in the Apicomplexan Parasite Toxoplasma gondii and Other Coccidia. Genome Biol Evol 2018; 9:3108-3121. [PMID: 29126146 PMCID: PMC5737649 DOI: 10.1093/gbe/evx231] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2017] [Indexed: 02/06/2023] Open
Abstract
Apicomplexans are successful parasites responsible for severe human diseases including malaria, toxoplasmosis, and cryptosporidiosis. For many years, it has been discussed whether these parasites are in possession of peroxisomes, highly variable eukaryotic organelles usually involved in fatty acid degradation and cellular detoxification. Conflicting experimental data has been published. With the age of genomics, ever more high quality apicomplexan genomes have become available, that now allow a new assessment of the dispute. Here, we provide bioinformatic evidence for the presence of peroxisomes in Toxoplasma gondii and other coccidians. For these organisms, we have identified a complete set of peroxins, probably responsible for peroxisome biogenesis, division, and protein import. Moreover, via a global screening for peroxisomal targeting signals, we were able to show that a complete set of fatty acid β-oxidation enzymes is equipped with either PTS1 or PTS2 sequences, most likely mediating transport of these factors to putative peroxisomes in all investigated Coccidia. Our results further imply a life cycle stage-specific presence of peroxisomes in T. gondii and suggest several independent losses of peroxisomes during the evolution of apicomplexan parasites.
Collapse
Affiliation(s)
- Daniel Moog
- Laboratory for Cell Biology, Philipps University Marburg, Germany
| | - Jude M Przyborski
- Laboratory for Parasitology, Philipps University Marburg, Germany.,Centre for Infectious Diseases, Parasitology, Heidelberg University Medical School, INF324, Heidelberg, Germany
| | - Uwe G Maier
- Laboratory for Cell Biology, Philipps University Marburg, Germany.,LOEWE Center for Synthetic Microbiology (Synmikro), Philipps University, Marburg, Germany
| |
Collapse
|
30
|
Cho DH, Kim YS, Jo DS, Choe SK, Jo EK. Pexophagy: Molecular Mechanisms and Implications for Health and Diseases. Mol Cells 2018; 41:55-64. [PMID: 29370694 PMCID: PMC5792714 DOI: 10.14348/molcells.2018.2245] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/28/2017] [Accepted: 12/29/2017] [Indexed: 02/06/2023] Open
Abstract
Autophagy is an intracellular degradation pathway for large protein aggregates and damaged organelles. Recent studies have indicated that autophagy targets cargoes through a selective degradation pathway called selective autophagy. Peroxisomes are dynamic organelles that are crucial for health and development. Pexophagy is selective autophagy that targets peroxisomes and is essential for the maintenance of homeostasis of peroxisomes, which is necessary in the prevention of various peroxisome-related disorders. However, the mechanisms by which pexophagy is regulated and the key players that induce and modulate pexophagy are largely unknown. In this review, we focus on our current understanding of how pexophagy is induced and regulated, and the selective adaptors involved in mediating pexophagy. Furthermore, we discuss current findings on the roles of pexophagy in physiological and pathological responses, which provide insight into the clinical relevance of pexophagy regulation. Understanding how pexophagy interacts with various biological functions will provide fundamental insights into the function of pexophagy and facilitate the development of novel therapeutics against peroxisomal dysfunction-related diseases.
Collapse
Affiliation(s)
- Dong-Hyung Cho
- Graduate School of East-West Medical Science, Kyung Hee University, Yongin 17104,
Korea
| | - Yi Sak Kim
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon 35015,
Korea
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon 35015,
Korea
- Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon 35015,
Korea
| | - Doo Sin Jo
- Graduate School of East-West Medical Science, Kyung Hee University, Yongin 17104,
Korea
| | - Seong-Kyu Choe
- Department of Microbiology and Center for Metabolic Function Regulation, Wonkwang University School of Medicine, Iksan 54538,
Korea
| | - Eun-Kyeong Jo
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon 35015,
Korea
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon 35015,
Korea
- Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon 35015,
Korea
| |
Collapse
|
31
|
Abstract
Peroxisomes are single-membrane bound intracellular organelles that can be found in organisms across the tree of eukaryotes, and thus are likely to derive from an ancestral peroxisome in the last eukaryotic common ancestor (LECA). Yet, peroxisomes in different lineages can present a large diversity in terms of their metabolic capabilities, which reflects a highly variable proteomic content. Theories on the evolutionary origin of peroxisomes have shifted in the last decades from scenarios involving an endosymbiotic origin, similar to those of mitochondria and plastids, towards hypotheses purporting an endogenous origin from within the endomembrane system. The peroxisomal proteome is highly dynamic in evolutionary terms, and can evolve via differential loss and gain of proteins, as well as via relocalization of proteins from and to other sub-cellular compartments. Here, I review current knowledge and discussions on the diversity, origin, and evolution of the peroxisomal proteome.
Collapse
|
32
|
Tauroursodeoxycholic bile acid arrests axonal degeneration by inhibiting the unfolded protein response in X-linked adrenoleukodystrophy. Acta Neuropathol 2017; 133:283-301. [PMID: 28004277 PMCID: PMC5250669 DOI: 10.1007/s00401-016-1655-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 12/09/2016] [Accepted: 12/09/2016] [Indexed: 12/11/2022]
Abstract
The activation of the highly conserved unfolded protein response (UPR) is prominent in the pathogenesis of the most prevalent neurodegenerative disorders, such as Alzheimer’s disease (AD), Parkinson’s disease (PD) and amyotrophic lateral sclerosis (ALS), which are classically characterized by an accumulation of aggregated or misfolded proteins. This activation is orchestrated by three endoplasmic reticulum (ER) stress sensors: PERK, ATF6 and IRE1. These sensors transduce signals that induce the expression of the UPR gene programme. Here, we first identified an early activator of the UPR and investigated the role of a chronically activated UPR in the pathogenesis of X-linked adrenoleukodystrophy (X-ALD), a neurometabolic disorder that is caused by ABCD1 malfunction; ABCD1 transports very long-chain fatty acids (VLCFA) into peroxisomes. The disease manifests as inflammatory demyelination in the brain or and/or degeneration of corticospinal tracts, thereby resulting in spastic paraplegia, with the accumulation of intracellular VLCFA instead of protein aggregates. Using X-ALD mouse model (Abcd1− and Abcd1−/Abcd2−/− mice) and X-ALD patient’s fibroblasts and brain samples, we discovered an early engagement of the UPR. The response was characterized by the activation of the PERK and ATF6 pathways, but not the IRE1 pathway, showing a difference from the models of AD, PD or ALS. Inhibition of PERK leads to the disruption of homeostasis and increased apoptosis during ER stress induced in X-ALD fibroblasts. Redox imbalance appears to be the mechanism that initiates ER stress in X-ALD. Most importantly, we demonstrated that the bile acid tauroursodeoxycholate (TUDCA) abolishes UPR activation, which results in improvement of axonal degeneration and its associated locomotor impairment in Abcd1−/Abcd2−/− mice. Altogether, our preclinical data provide evidence for establishing the UPR as a key drug target in the pathogenesis cascade. Our study also highlights the potential role of TUDCA as a treatment for X-ALD and other axonopathies in which similar molecular mediators are implicated.
Collapse
|
33
|
Kienle N, Kloepper TH, Fasshauer D. Shedding light on the expansion and diversification of the Cdc48 protein family during the rise of the eukaryotic cell. BMC Evol Biol 2016; 16:215. [PMID: 27756227 PMCID: PMC5070193 DOI: 10.1186/s12862-016-0790-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 10/04/2016] [Indexed: 11/22/2022] Open
Abstract
Background A defining feature of eukaryotic cells is the presence of various distinct membrane-bound compartments with different metabolic roles. Material exchange between most compartments occurs via a sophisticated vesicle trafficking system. This intricate cellular architecture of eukaryotes appears to have emerged suddenly, about 2 billion years ago, from much less complex ancestors. How the eukaryotic cell acquired its internal complexity is poorly understood, partly because no prokaryotic precursors have been found for many key factors involved in compartmentalization. One exception is the Cdc48 protein family, which consists of several distinct classical ATPases associated with various cellular activities (AAA+) proteins with two consecutive AAA domains. Results Here, we have classified the Cdc48 family through iterative use of hidden Markov models and tree building. We found only one type, Cdc48, in prokaryotes, although a set of eight diverged members that function at distinct subcellular compartments were retrieved from eukaryotes and were probably present in the last eukaryotic common ancestor (LECA). Pronounced changes in sequence and domain structure during the radiation into the LECA set are delineated. Moreover, our analysis brings to light lineage-specific losses and duplications that often reflect important biological changes. Remarkably, we also found evidence for internal duplications within the LECA set that probably occurred during the rise of the eukaryotic cell. Conclusions Our analysis corroborates the idea that the diversification of the Cdc48 family is closely intertwined with the development of the compartments of the eukaryotic cell. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0790-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Nickias Kienle
- Département des neurosciences fondamentales, Université de Lausanne, Rue du Bugnon 9, CH-1005, Lausanne, Switzerland
| | - Tobias H Kloepper
- Sir William Dunn School of Pathology, Research Group Cell Biology of Intercellular Signaling, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Dirk Fasshauer
- Département des neurosciences fondamentales, Université de Lausanne, Rue du Bugnon 9, CH-1005, Lausanne, Switzerland.
| |
Collapse
|
34
|
Abstract
SIGNIFICANCE Peroxisomes are organelles present in most eukaryotic cells. The organs with the highest density of peroxisomes are the liver and kidneys. Peroxisomes possess more than fifty enzymes and fulfill a multitude of biological tasks. They actively participate in apoptosis, innate immunity, and inflammation. In recent years, a considerable amount of evidence has been collected to support the involvement of peroxisomes in the pathogenesis of kidney injury. RECENT ADVANCES The nature of the two most important peroxisomal tasks, beta-oxidation of fatty acids and hydrogen peroxide turnover, functionally relates peroxisomes to mitochondria. Further support for their communication and cooperation is furnished by the evidence that both organelles share the components of their division machinery. Until recently, the majority of studies on the molecular mechanisms of kidney injury focused primarily on mitochondria and neglected peroxisomes. CRITICAL ISSUES The aim of this concise review is to introduce the reader to the field of peroxisome biology and to provide an overview of the evidence about the contribution of peroxisomes to the development and progression of kidney injury. The topics of renal ischemia-reperfusion injury, endotoxin-induced kidney injury, diabetic nephropathy, and tubulointerstitial fibrosis, as well as the potential therapeutic implications of peroxisome activation, are addressed in this review. FUTURE DIRECTIONS Despite recent progress, further studies are needed to elucidate the molecular mechanisms induced by dysfunctional peroxisomes and the role of the dysregulated mitochondria-peroxisome axis in the pathogenesis of renal injury. Antioxid. Redox Signal. 25, 217-231.
Collapse
Affiliation(s)
- Radovan Vasko
- Department of Nephrology and Rheumatology, University Medical Center Göttingen , Göttingen, Germany
| |
Collapse
|
35
|
Hahn C, Fromm B, Bachmann L. Comparative genomics of flatworms (platyhelminthes) reveals shared genomic features of ecto- and endoparastic neodermata. Genome Biol Evol 2016; 6:1105-17. [PMID: 24732282 PMCID: PMC4040987 DOI: 10.1093/gbe/evu078] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The ectoparasitic Monogenea comprise a major part of the obligate parasitic flatworm diversity. Although genomic adaptations to parasitism have been studied in the endoparasitic tapeworms (Cestoda) and flukes (Trematoda), no representative of the Monogenea has been investigated yet. We present the high-quality draft genome of Gyrodactylus salaris, an economically important monogenean ectoparasite of wild Atlantic salmon (Salmo salar). A total of 15,488 gene models were identified, of which 7,102 were functionally annotated. The controversial phylogenetic relationships within the obligate parasitic Neodermata were resolved in a phylogenomic analysis using 1,719 gene models (alignment length of >500,000 amino acids) for a set of 16 metazoan taxa. The Monogenea were found basal to the Cestoda and Trematoda, which implies ectoparasitism being plesiomorphic within the Neodermata and strongly supports a common origin of complex life cycles. Comparative analysis of seven parasitic flatworm genomes identified shared genomic features for the ecto- and endoparasitic lineages, such as a substantial reduction of the core bilaterian gene complement, including the homeodomain-containing genes, and a loss of the piwi and vasa genes, which are considered essential for animal development. Furthermore, the shared loss of functional fatty acid biosynthesis pathways and the absence of peroxisomes, the latter organelles presumed ubiquitous in eukaryotes except for parasitic protozoans, were inferred. The draft genome of G. salaris opens for future in-depth analyses of pathogenicity and host specificity of poorly characterized G. salaris strains, and will enhance studies addressing the genomics of host–parasite interactions and speciation in the highly diverse monogenean flatworms.
Collapse
Affiliation(s)
- Christoph Hahn
- Department for Research and Collections, Natural History Museum, University of Oslo, Oslo, Norway
| | | | | |
Collapse
|
36
|
Reumann S, Chowdhary G, Lingner T. Characterization, prediction and evolution of plant peroxisomal targeting signals type 1 (PTS1s). BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1863:790-803. [PMID: 26772785 DOI: 10.1016/j.bbamcr.2016.01.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 01/01/2016] [Accepted: 01/04/2016] [Indexed: 12/22/2022]
Abstract
Our knowledge of the proteome of plant peroxisomes and their functional plasticity is far from being complete, primarily due to major technical challenges in experimental proteome research of the fragile cell organelle. Several unexpected novel plant peroxisome functions, for instance in biotin and phylloquinone biosynthesis, have been uncovered recently. Nevertheless, very few regulatory and membrane proteins of plant peroxisomes have been identified and functionally described up to now. To define the matrix proteome of plant peroxisomes, computational methods have emerged as important powerful tools. Novel prediction approaches of high sensitivity and specificity have been developed for peroxisome targeting signals type 1 (PTS1) and have been validated by in vivo subcellular targeting analyses and thermodynamic binding studies with the cytosolic receptor, PEX5. Accordingly, the algorithms allow the correct prediction of many novel peroxisome-targeted proteins from plant genome sequences and the discovery of additional organelle functions. In this review, we provide an overview of methodologies, capabilities and accuracies of available prediction algorithms for PTS1 carrying proteins. We also summarize and discuss recent quantitative, structural and mechanistic information of the interaction of PEX5 with PTS1 carrying proteins in relation to in vivo import efficiency. With this knowledge, we develop a model of how proteins likely evolved peroxisomal targeting signals in the past and still nowadays, in which order the two import pathways might have evolved in the ancient eukaryotic cell, and how the secondary loss of the PTS2 pathway probably happened in specific organismal groups.
Collapse
Affiliation(s)
- S Reumann
- Department of Plant Biochemistry and Infection Biology, Biocentre Klein Flottbek, University of Hamburg, D-22609 Hamburg, Germany; Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway.
| | - G Chowdhary
- Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway; KIIT School of Biotechnology, Campus XI, KIIT University, I-751024 Bhubaneswar, India.
| | - T Lingner
- Department of Bioinformatics, Institute for Microbiology and Genetics, D-37077 Goettingen, Germany.
| |
Collapse
|
37
|
Cross LL, Ebeed HT, Baker A. Peroxisome biogenesis, protein targeting mechanisms and PEX gene functions in plants. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:850-62. [DOI: 10.1016/j.bbamcr.2015.09.027] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/15/2015] [Accepted: 09/21/2015] [Indexed: 12/16/2022]
|
38
|
Sibirny AA. Yeast peroxisomes: structure, functions and biotechnological opportunities. FEMS Yeast Res 2016; 16:fow038. [DOI: 10.1093/femsyr/fow038] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2016] [Indexed: 01/02/2023] Open
|
39
|
Gabaldón T, Ginger ML, Michels PAM. Peroxisomes in parasitic protists. Mol Biochem Parasitol 2016; 209:35-45. [PMID: 26896770 DOI: 10.1016/j.molbiopara.2016.02.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/12/2016] [Accepted: 02/13/2016] [Indexed: 01/24/2023]
Abstract
Representatives of all major lineages of eukaryotes contain peroxisomes with similar morphology and mode of biogenesis, indicating a monophyletic origin of the organelles within the common ancestor of all eukaryotes. Peroxisomes originated from the endoplasmic reticulum, but despite a common origin and shared morphological features, peroxisomes from different organisms show a remarkable diversity of enzyme content and the metabolic processes present can vary dependent on nutritional or developmental conditions. A common characteristic and probable evolutionary driver for the origin of the organelle is an involvement in lipid metabolism, notably H2O2-dependent fatty-acid oxidation. Subsequent evolution of the organelle in different lineages involved multiple acquisitions of metabolic processes-often involving retargeting enzymes from other cell compartments-and losses. Information about peroxisomes in protists is still scarce, but available evidence, including new bioinformatics data reported here, indicate striking diversity amongst free-living and parasitic protists from different phylogenetic supergroups. Peroxisomes in only some protists show major involvement in H2O2-dependent metabolism, as in peroxisomes of mammalian, plant and fungal cells. Compartmentalization of glycolytic and gluconeogenic enzymes inside peroxisomes is characteristic of kinetoplastids and diplonemids, where the organelles are hence called glycosomes, whereas several other excavate parasites (Giardia, Trichomonas) have lost peroxisomes. Amongst alveolates and amoebozoans patterns of peroxisome loss are more complicated. Often, a link is apparent between the niches occupied by the parasitic protists, nutrient availability, and the absence of the organelles or their presence with a specific enzymatic content. In trypanosomatids, essentiality of peroxisomes may be considered for use in anti-parasite drug discovery.
Collapse
Affiliation(s)
- Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Michael L Ginger
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, UK; Department of Biological Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK.
| | - Paul A M Michels
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, UK; Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, UK; Laboratorio de Enzimología de Parásitos, Departamento de Biología, Universidad de Los Andes, Mérida, Venezuela.
| |
Collapse
|
40
|
Žárský V, Tachezy J. Evolutionary loss of peroxisomes--not limited to parasites. Biol Direct 2015; 10:74. [PMID: 26700421 PMCID: PMC4690255 DOI: 10.1186/s13062-015-0101-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/14/2015] [Indexed: 11/26/2022] Open
Abstract
Background Peroxisomes are ubiquitous eukaryotic organelles that compartmentalize a variety of metabolic pathways that are primarily related to the oxidative metabolism of lipids and the detoxification of reactive oxygen species. The importance of peroxisomes is underscored by serious human diseases, which are caused by disorders in peroxisomal functions. Some eukaryotic lineages, however, lost peroxisomes. These organisms are mainly anaerobic protists and some parasitic lineages including Plasmodium and parasitic platyhelminths. Here we performed a systematic in-silico analysis of peroxisomal markers among metazoans to assess presence of peroxisomes and peroxisomal enzymes. Results Our analyses reveal an obvious loss of peroxisomes in all tested flukes, tapeworms, and parasitic roundworms of the order Trichocephalida. Intriguingly, peroxisomal markers are absent from the genome of the free-living tunicate Oikopleura dioica, which inhabits oxygen-containing niches of sea waters. We further map the presence and predicted subcellular localization of putative peroxisomal enzymes, showing that in organisms without the peroxisomal markers the set of these enzymes is highly reduced and none of them contains a predicted peroxisomal targeting signal. Conclusions We have shown that several lineages of metazoans independently lost peroxisomes and that the loss of peroxisomes was not exclusively associated with adaptation to anaerobic habitats and a parasitic lifestyle. Although the reason for the loss of peroxisomes from O. dioica is unclear, organisms lacking peroxisomes, including the free-living O. dioica, share certain typical r-selected traits: high fecundity, limited ontogenesis and relatively low complexity of the gene content. We hypothesize that peroxisomes are generally the first compartment to be lost during evolutionary reductions of the eukaryotic cell. Reviewers This article was reviewed by Michael Gray and Nick Lane. Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0101-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Vojtěch Žárský
- Department of Parasitology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44, Prague, Czech Republic.
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44, Prague, Czech Republic.
| |
Collapse
|
41
|
Fourcade S, Ferrer I, Pujol A. Oxidative stress, mitochondrial and proteostasis malfunction in adrenoleukodystrophy: A paradigm for axonal degeneration. Free Radic Biol Med 2015; 88:18-29. [PMID: 26073123 DOI: 10.1016/j.freeradbiomed.2015.05.041] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/07/2015] [Accepted: 05/26/2015] [Indexed: 12/15/2022]
Abstract
Peroxisomal and mitochondrial malfunction, which are highly intertwined through redox regulation, in combination with defective proteostasis, are hallmarks of the most prevalent multifactorial neurodegenerative diseases-including Alzheimer's (AD) and Parkinson's disease (PD)-and of the aging process, and are also found in inherited conditions. Here we review the interplay between oxidative stress and axonal degeneration, taking as groundwork recent findings on pathomechanisms of the peroxisomal neurometabolic disease adrenoleukodystrophy (X-ALD). We explore the impact of chronic redox imbalance caused by the excess of very long-chain fatty acids (VLCFA) on mitochondrial respiration and biogenesis, and discuss how this impairs protein quality control mechanisms essential for neural cell survival, such as the proteasome and autophagy systems. As consequence, prime molecular targets in the pathogenetic cascade emerge, such as the SIRT1/PGC-1α axis of mitochondrial biogenesis, and the inhibitor of autophagy mTOR. Thus, we propose that mitochondria-targeted antioxidants; mitochondrial biogenesis boosters such as the antidiabetic pioglitazone and the SIRT1 ligand resveratrol; and the autophagy activator temsirolimus, a derivative of the mTOR inhibitor rapamycin, hold promise as disease-modifying therapies for X-ALD.
Collapse
Affiliation(s)
- Stéphane Fourcade
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospitalet de Llobregat, 08908 Barcelona, Spain; Institut of Neuropathology, Pathologic Anatomy Service, Bellvitge Biomedical Research Institute, IDIBELL-Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, 08908 Barcelona, Spain; Center for Biomedical Research on Rare Diseases (CIBERER), U759, ISCIII, Spain.
| | - Isidre Ferrer
- Institut of Neuropathology, Pathologic Anatomy Service, Bellvitge Biomedical Research Institute, IDIBELL-Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, 08908 Barcelona, Spain; Center for Biomedical Research on Neurodegenerative Diseases (CIBERNED), Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospitalet de Llobregat, 08908 Barcelona, Spain; Institut of Neuropathology, Pathologic Anatomy Service, Bellvitge Biomedical Research Institute, IDIBELL-Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, 08908 Barcelona, Spain; Center for Biomedical Research on Rare Diseases (CIBERER), U759, ISCIII, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona 08010, Catalonia, Spain.
| |
Collapse
|
42
|
The Design and Structure of Outer Membrane Receptors from Peroxisomes, Mitochondria, and Chloroplasts. Structure 2015; 23:1783-1800. [DOI: 10.1016/j.str.2015.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/20/2015] [Accepted: 08/10/2015] [Indexed: 01/03/2023]
|
43
|
The first minutes in the life of a peroxisomal matrix protein. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:814-20. [PMID: 26408939 DOI: 10.1016/j.bbamcr.2015.09.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 01/30/2023]
Abstract
In the field of intracellular protein sorting, peroxisomes are most famous by their capacity to import oligomeric proteins. The data supporting this remarkable property are abundant and, understandably, have inspired a variety of hypothetical models on how newly synthesized (cytosolic) proteins reach the peroxisome matrix. However, there is also accumulating evidence suggesting that many peroxisomal oligomeric proteins actually arrive at the peroxisome still as monomers. In support of this idea, recent data suggest that PEX5, the shuttling receptor for peroxisomal matrix proteins, is also a chaperone/holdase, binding newly synthesized peroxisomal proteins in the cytosol and blocking their oligomerization. Here we review the data behind these two different perspectives and discuss their mechanistic implications on this protein sorting pathway.
Collapse
|
44
|
Goto-Yamada S, Mano S, Yamada K, Oikawa K, Hosokawa Y, Hara-Nishimura I, Nishimura M. Dynamics of the Light-Dependent Transition of Plant Peroxisomes. PLANT & CELL PHYSIOLOGY 2015; 56:1264-71. [PMID: 26063394 DOI: 10.1093/pcp/pcv081] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 05/29/2015] [Indexed: 05/21/2023]
Abstract
Peroxisomes are present in almost all plant cells. These organelles are involved in various metabolic processes, such as lipid catabolism and photorespiration. A notable feature of plant peroxisomes is their flexible adaptive responses to environmental conditions such as light. When plants shift from heterotrophic to autotrophic growth during the post-germinative stage, peroxisomes undergo a dynamic response, i.e. enzymes involved in lipid catabolism are replaced with photorespiratory enzymes. Although the detailed molecular mechanisms underlying the functional transition of peroxisomes have previously been unclear, recent analyses at the cellular level have enabled this detailed machinery to be characterized. During the functional transition, obsolete enzymes are degraded inside peroxisomes by Lon protease, while newly synthesized enzymes are transported into peroxisomes. In parallel, mature and oxidized peroxisomes are eliminated via autophagy; this functional transition occurs in an efficient manner. Moreover, it has become clear that quality control mechanisms are important for the peroxisomal response to environmental stimuli. In this review, we highlight recent advances in elucidating the molecular mechanisms required for the regulation of peroxisomal roles in response to changes in environmental conditions.
Collapse
Affiliation(s)
| | - Shoji Mano
- Laboratory of Biological Diversity, Department of Evolutionary Biology and Biodiversity, National Institute for Basic Biology, Okazaki, 444-8585 Japan Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, 444-8585 Japan
| | - Kenji Yamada
- Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
| | - Kazusato Oikawa
- Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Niigata, 950-2181 Japan
| | - Yoichiroh Hosokawa
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
| | | | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, 444-8585 Japan Present address: Research Enhancement Strategy Office, National Institute for Basic Biology, Okazaki, 444-8585 Japan.
| |
Collapse
|
45
|
Abstract
Many protists with high ecological and medical relevance harbor plastids surrounded by four membranes. Thus, nucleus-encoded proteins of these complex plastids have to traverse these barriers. Here we report on the identification of the protein translocators located in two of the plastid surrounding membranes and present recent findings on the mechanisms of protein import into the plastids of diatoms.
Collapse
|
46
|
Mast FD, Rachubinski RA, Aitchison JD. Signaling dynamics and peroxisomes. Curr Opin Cell Biol 2015; 35:131-6. [PMID: 26042681 DOI: 10.1016/j.ceb.2015.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 05/09/2015] [Indexed: 02/08/2023]
Abstract
Peroxisomes are remarkably responsive organelles. Their composition, abundance and even their mechanism of biogenesis are influenced strongly by cell type and the environment. This plasticity underlies peroxisomal functions in metabolism and the detoxification of dangerous reactive oxygen species. However, peroxisomes are integrated into the cellular system as a whole such that they communicate intimately with other organelles, control signaling dynamics as in the case of innate immune responses to infectious disease, and contribute to processes as fundamental as longevity. The increasing evidence for peroxisomes having roles in various cellular and organismal functions, combined with their malleability, suggests complex mechanisms operate to control cellular dynamics and the specificity of cellular responses and functions extending well beyond the peroxisome itself. A deeper understanding of the functions of peroxisomes and the mechanisms that control their plasticity could offer opportunities for exploiting changes in peroxisome abundance to control cellular function.
Collapse
Affiliation(s)
- Fred D Mast
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, USA; Institute for Systems Biology, Seattle, USA
| | | | - John D Aitchison
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, USA; Institute for Systems Biology, Seattle, USA.
| |
Collapse
|
47
|
Gabaldón T, Pittis AA. Origin and evolution of metabolic sub-cellular compartmentalization in eukaryotes. Biochimie 2015; 119:262-8. [PMID: 25869000 PMCID: PMC4678951 DOI: 10.1016/j.biochi.2015.03.021] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 03/25/2015] [Indexed: 12/19/2022]
Abstract
A high level of subcellular compartmentalization is a hallmark of eukaryotic cells. This intricate internal organization was present already in the common ancestor of all extant eukaryotes, and the determination of the origins and early evolution of the different organelles remains largely elusive. Organellar proteomes are determined through regulated pathways that target proteins produced in the cytosol to their final subcellular destinations. This internal sorting of proteins can vary across different physiological conditions, cell types and lineages. Evolutionary retargeting - the alteration of a subcellular localization of a protein in the course of evolution - has been rampant in eukaryotes and involves any possible combination of organelles. This fact adds another layer of difficulty to the reconstruction of the origins and evolution of organelles. In this review we discuss current themes in relation to the origin and evolution of organellar proteomes. Throughout the text, a special focus is set on the evolution of mitochondrial and peroxisomal proteomes, which are two organelles for which extensive proteomic and evolutionary studies have been performed.
Collapse
Affiliation(s)
- Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Alexandros A Pittis
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| |
Collapse
|
48
|
Gardner BM, Chowdhury S, Lander GC, Martin A. The Pex1/Pex6 complex is a heterohexameric AAA+ motor with alternating and highly coordinated subunits. J Mol Biol 2015; 427:1375-1388. [PMID: 25659908 DOI: 10.1016/j.jmb.2015.01.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 01/23/2015] [Accepted: 01/24/2015] [Indexed: 12/13/2022]
Abstract
Pex1 and Pex6 are Type-2 AAA+ ATPases required for the de novo biogenesis of peroxisomes. Mutations in Pex1 and Pex6 account for the majority of the most severe forms of peroxisome biogenesis disorders in humans. Here, we show that the ATP-dependent complex of Pex1 and Pex6 from Saccharomyces cerevisiae is a heterohexamer with alternating subunits. Within the Pex1/Pex6 complex, only the D2 ATPase ring hydrolyzes ATP, while nucleotide binding in the D1 ring promotes complex assembly. ATP hydrolysis by Pex1 is highly coordinated with that of Pex6. Furthermore, Pex15, the membrane anchor required for Pex1/Pex6 recruitment to peroxisomes, inhibits the ATP-hydrolysis activity of Pex1/Pex6.
Collapse
Affiliation(s)
- Brooke M Gardner
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA; Miller Institute for Basic Research in Science, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Saikat Chowdhury
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Andreas Martin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720-3220, USA.
| |
Collapse
|
49
|
Chang J, Klute MJ, Tower RJ, Mast FD, Dacks JB, Rachubinski RA. An ancestral role in peroxisome assembly is retained by the divisional peroxin Pex11 in the yeast Yarrowia lipolytica. J Cell Sci 2015; 128:1327-40. [PMID: 25663700 DOI: 10.1242/jcs.157743] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The peroxin Pex11 has a recognized role in peroxisome division. Pex11p remodels and elongates peroxisomal membranes prior to the recruitment of dynamin-related GTPases that act in membrane scission to divide peroxisomes. We performed a comprehensive comparative genomics survey to understand the significance of the evolution of the Pex11 protein family in yeast and other eukaryotes. Pex11p is highly conserved and ancestral, and has undergone numerous lineage-specific duplications, whereas other Pex11 protein family members are fungal-specific innovations. Functional characterization of the in-silico-predicted Pex11 protein family members of the yeast Yarrowia lipolytica, i.e. Pex11p, Pex11Cp and Pex11/25p, demonstrated that Pex11Cp and Pex11/25p have a role in the regulation of peroxisome size and number characteristic of Pex11 protein family members. Unexpectedly, deletion of PEX11 in Y. lipolytica produces cells that lack morphologically identifiable peroxisomes, mislocalize peroxisomal matrix proteins and preferentially degrade peroxisomal membrane proteins, i.e. they exhibit the classical pex mutant phenotype, which has not been observed previously in cells deleted for the PEX11 gene. Our results are consistent with an unprecedented role for Pex11p in de novo peroxisome assembly.
Collapse
Affiliation(s)
- Jinlan Chang
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Mary J Klute
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Robert J Tower
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Fred D Mast
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Joel B Dacks
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | | |
Collapse
|
50
|
Shellman ER, Chen Y, Lin X, Burant CF, Schnell S. Metabolic network motifs can provide novel insights into evolution: The evolutionary origin of Eukaryotic organelles as a case study. Comput Biol Chem 2014; 53PB:242-250. [PMID: 25462333 PMCID: PMC4254655 DOI: 10.1016/j.compbiolchem.2014.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 09/15/2014] [Accepted: 09/15/2014] [Indexed: 01/28/2023]
Abstract
Phylogenetic trees are typically constructed using genetic and genomic data, and provide robust evolutionary relationships of species from the genomic point of view. We present an application of network motif mining and analysis of metabolic pathways that when used in combination with phylogenetic trees can provide a more complete picture of evolution. By using distributions of three-node motifs as a proxy for metabolic similarity, we analyze the ancestral origin of Eukaryotic organelles from the metabolic point of view to illustrate the application of our motif mining and analysis network approach. Our analysis suggests that the hypothesis of an early proto-Eukaryote could be valid. It also suggests that a δ- or ϵ-Proteobacteria may have been the endosymbiotic partner that gave rise to modern mitochondria. Our evolutionary analysis needs to be extended by building metabolic network reconstructions of species from the phylum Crenarchaeota, which is considered to be a possible archaeal ancestor of the eukaryotic cell. In this paper, we also propose a methodology for constructing phylogenetic trees that incorporates metabolic network signatures to identify regions of genomically-estimated phylogenies that may be spurious. We find that results generated from our approach are consistent with a parallel phylogenetic analysis using the method of feature frequency profiles.
Collapse
Affiliation(s)
- Erin R Shellman
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yu Chen
- Department of Chemical Engineering, University of Michigan School of Engineering, Ann Arbor, MI, USA
| | - Xiaoxia Lin
- Department of Chemical Engineering, University of Michigan School of Engineering, Ann Arbor, MI, USA
| | - Charles F Burant
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Santiago Schnell
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA.
| |
Collapse
|