Publications by year
In Press
Van Der Giezen M (In Press). Disease prevention and treatment.
2019
Huang J, Nguyen VH, Hamblin KA, Maytum R, van der Giezen M, Fraser ME (2019). ATP-specificity of succinyl-CoA synthetase from Blastocystis hominis.
Acta Crystallogr D Struct Biol,
75(Pt 7), 647-659.
Abstract:
ATP-specificity of succinyl-CoA synthetase from Blastocystis hominis.
Succinyl-CoA synthetase (SCS) catalyzes the only step of the tricarboxylic acid cycle that leads to substrate-level phosphorylation. Some forms of SCS are specific for ADP/ATP or for GDP/GTP, while others can bind all of these nucleotides, generally with different affinities. The theory of `gatekeeper' residues has been proposed to explain the nucleotide-specificity. Gatekeeper residues lie outside the binding site and create specific electrostatic interactions with incoming nucleotides to determine whether the nucleotides can enter the binding site. To test this theory, the crystal structure of the nucleotide-binding domain in complex with Mg2+-ADP was determined, as well as the structures of four proteins with single mutations, K46βE, K114βD, V113βL and L227βF, and one with two mutations, K46βE/K114βD. The crystal structures show that the enzyme is specific for ADP/ATP because of interactions between the nucleotide and the binding site. Nucleotide-specificity is provided by hydrogen-bonding interactions between the adenine base and Gln20β, Gly111β and Val113β. The O atom of the side chain of Gln20β interacts with N6 of ADP, while the side-chain N atom interacts with the carbonyl O atom of Gly111β. It is the different conformations of the backbone at Gln20β, of the side chain of Gln20β and of the linker that make the enzyme ATP-specific. This linker connects the two subdomains of the ATP-grasp fold and interacts differently with adenine and guanine bases. The mutant proteins have similar conformations, although the L227βF mutant shows structural changes that disrupt the binding site for the magnesium ion. Although the K46βE/K114βD double mutant of Blastocystis hominis SCS binds GTP better than ATP according to kinetic assays, only the complex with Mg2+-ADP was obtained.
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Minardi D, Studholme DJ, Oidtmann B, Pretto T, van der Giezen M (2019). Improved method for genotyping the causative agent of crayfish plague (Aphanomyces astaci) based on mitochondrial DNA.
Parasitology,
146(8), 1022-1029.
Abstract:
Improved method for genotyping the causative agent of crayfish plague (Aphanomyces astaci) based on mitochondrial DNA.
Aphanomyces astaci causes crayfish plague, which is a devastating disease of European freshwater crayfish. The likely first introduction of A. astaci into Europe was in the mid-19th century in Italy, presumably with the introduction of North American crayfish. These crayfish can carry A. astaci in their cuticle as a benign infection. Aphanomyces astaci rapidly spread across Europe causing the decline of the highly susceptible indigenous crayfish species. Random amplified polymorphic DNA-PCR analysis of A. astaci pure cultures characterized five genotype groups (A, B, C, D and E). Current A. astaci genotyping techniques (microsatellites and genotype-specific regions, both targeting nuclear DNA) can be applied directly to DNA extracted from infected cuticles but require high infection levels. Therefore, they are not suitable for genotyping benign infections in North American crayfish (carriers). In the present study, we combine bioinformatics and molecular biology techniques to develop A. astaci genotyping molecular markers that target the mitochondrial DNA, increasing the sensitivity of the genotyping tools. The assays were validated on DNA extracts of A. astaci pure cultures, crayfish tissue extractions from crayfish plague outbreaks and tissue extractions from North American carriers. We demonstrate the presence of A. astaci genotype groups a and B in UK waters.
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Lear R, O'Leary M, O'Brien Andersen L, Holt CC, Stensvold CR, van der Giezen M, Bowtell JL (2019). Tart Cherry Concentrate Does Not Alter the Gut Microbiome, Glycaemic Control or Systemic Inflammation in a Middle-Aged Population.
Nutrients,
11(5).
Abstract:
Tart Cherry Concentrate Does Not Alter the Gut Microbiome, Glycaemic Control or Systemic Inflammation in a Middle-Aged Population.
Limited evidence suggests that the consumption of polyphenols may improve glycaemic control and insulin sensitivity. The gut microbiome produces phenolic metabolites and increases their bioavailability. A handful of studies have suggested that polyphenol consumption alters gut microbiome composition. There are no data available investigating such effects in polyphenol-rich Montmorency cherry (MC) supplementation. A total of 28 participants (aged 40-60 years) were randomized to receive daily MC or glucose and energy-matched placebo supplementation for 4 wk. Faecal and blood samples were obtained at baseline and at 4 wk. There was no clear effect of supplementation on glucose handling (Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) and Gutt indices), although the Matsuda index decreased significantly in the MC group post-supplementation, reflecting an increase in serum insulin concentration. Contrastingly, placebo, but not MC supplementation induced a 6% increase in the Oral Glucose Insulin Sensitivity (OGIS) estimate of glucose clearance. Serum IL-6 and C reactive protein were unaltered by either supplement. The faecal bacterial microbiome was sequenced; species richness and diversity were unchanged by MC or placebo and no significant correlation existed between changes in Bacteroides and Faecalibacterium abundance and any index of insulin sensitivity. Therefore, 4 weeks of MC supplementation did not alter the gut microbiome, glycaemic control or systemic concentrations of IL-6 and CRP in a middle-aged population.
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Holt CC, Stone M, Bass D, Bateman KS, van Aerle R, Daniels CL, van der Giezen M, Ross SH, Hooper C, Stentiford GD, et al (2019). The first clawed lobster virus Homarus gammarus nudivirus (HgNV n. sp.) expands the diversity of the Nudiviridae.
Sci Rep,
9(1).
Abstract:
The first clawed lobster virus Homarus gammarus nudivirus (HgNV n. sp.) expands the diversity of the Nudiviridae.
Viral diseases of crustaceans are increasingly recognised as challenges to shellfish farms and fisheries. Here we describe the first naturally-occurring virus reported in any clawed lobster species. Hypertrophied nuclei with emarginated chromatin, characteristic histopathological lesions of DNA virus infection, were observed within the hepatopancreatic epithelial cells of juvenile European lobsters (Homarus gammarus). Transmission electron microscopy revealed infection with a bacilliform virus containing a rod shaped nucleocapsid enveloped in an elliptical membrane. Assembly of PCR-free shotgun metagenomic sequencing produced a circular genome of 107,063 bp containing 97 open reading frames, the majority of which share sequence similarity with a virus infecting the black tiger shrimp: Penaeus monodon nudivirus (PmNV). Multiple phylogenetic analyses confirm the new virus to be a novel member of the Nudiviridae: Homarus gammarus nudivirus (HgNV). Evidence of occlusion body formation, characteristic of PmNV and its closest relatives, was not observed, questioning the horizontal transmission strategy of HgNV outside of the host. We discuss the potential impacts of HgNV on juvenile lobster growth and mortality and present HgNV-specific primers to serve as a diagnostic tool for monitoring the virus in wild and farmed lobster stocks.
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2018
Stensvold CR, van der Giezen M (2018). Associations between Gut Microbiota and Common Luminal Intestinal Parasites.
Trends in Parasitology,
34(5), 369-377.
Abstract:
Associations between Gut Microbiota and Common Luminal Intestinal Parasites
The development and integration of DNA-based methods in research and clinical microbiology laboratories have enabled standardised and comprehensive detection and differentiation of the microbes colonising our guts. For instance, the single-celled parasites Blastocystis and Dientamoeba appear to be much more common than previously thought, especially so in healthy individuals. While increasing evidence appears to suggest limited pathogenicity of these parasites, next-generation-sequencing-based studies have helped us to appreciate links between parasite colonisation and certain host phenotypical characteristics and gut microbial profiles. The fundamental question remains as to whether such parasites are merely indicators or active manipulators of gut microbiota structure and function. In this article, we collate existing evidence that these parasites are, at minimum, indicators of intestinal microbiota structure.
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Holt C, Foster R, Daniels CL, van der Giezen M, Feist SW, Stentiford GD, Bass D (2018). Halioticida noduliformans infection in eggs of lobster (Homarus gammarus) reveals its generalist parasitic strategy in marine invertebrates.
Journal of Invertebrate Pathology,
154, 109-116.
Abstract:
Halioticida noduliformans infection in eggs of lobster (Homarus gammarus) reveals its generalist parasitic strategy in marine invertebrates
A parasite exhibiting Oomycete-like morphology and pathogenesis was isolated from discoloured eggs of the European lobster (Homarus gammarus) and later found in gill tissues of adults. Group-specific Oomycete primers were designed to amplify the 18S ribosomal small subunit (SSU), which initially identified the organism as the same as the ‘Haliphthoros’ sp. NJM 0034 strain (AB178865.1) previously isolated from abalone (imported from South Australia to Japan). However, in accordance with other published SSU-based phylogenies, the NJM 0034 isolate did not group with other known Haliphthoros species in our Maximum Likelihood and Bayesian phylogenies. Instead, the strain formed an orphan lineage, diverging before the separation of the Saprolegniales and Pythiales. Based upon 28S large subunit (LSU) phylogeny, our own isolate and the previously unidentified 0034 strain are both identical to the abalone pathogen Halioticida noduliformans. The genus shares morphological similarities with Haliphthoros and Halocrusticida and forms a clade with these in LSU phylogenies. Here, we confirm the first recorded occurrence of H. noduliformans in European lobsters and associate its presence with pathology of the egg mass, likely leading to reduced fecundity.
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Río Bártulos C, Rogers MB, Williams TA, Gentekaki E, Brinkmann H, Cerff R, Liaud M-F, Hehl AB, Yarlett NR, Gruber A, et al (2018). Mitochondrial Glycolysis in a Major Lineage of Eukaryotes.
Genome Biol Evol,
10(9), 2310-2325.
Abstract:
Mitochondrial Glycolysis in a Major Lineage of Eukaryotes.
The establishment of the mitochondrion is seen as a transformational step in the origin of eukaryotes. With the mitochondrion came bioenergetic freedom to explore novel evolutionary space leading to the eukaryotic radiation known today. The tight integration of the bacterial endosymbiont with its archaeal host was accompanied by a massive endosymbiotic gene transfer resulting in a small mitochondrial genome which is just a ghost of the original incoming bacterial genome. This endosymbiotic gene transfer resulted in the loss of many genes, both from the bacterial symbiont as well the archaeal host. Loss of genes encoding redundant functions resulted in a replacement of the bulk of the host's metabolism for those originating from the endosymbiont. Glycolysis is one such metabolic pathway in which the original archaeal enzymes have been replaced by bacterial enzymes from the endosymbiont. Glycolysis is a major catabolic pathway that provides cellular energy from the breakdown of glucose. The glycolytic pathway of eukaryotes appears to be bacterial in origin, and in well-studied model eukaryotes it takes place in the cytosol. In contrast, here we demonstrate that the latter stages of glycolysis take place in the mitochondria of stramenopiles, a diverse and ecologically important lineage of eukaryotes. Although our work is based on a limited sample of stramenopiles, it leaves open the possibility that the mitochondrial targeting of glycolytic enzymes in stramenopiles might represent the ancestral state for eukaryotes.
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Minardi D, Studholme DJ, van der Giezen M, Pretto T, Oidtmann B (2018). New genotyping method for the causative agent of crayfish plague (Aphanomyces astaci) based on whole genome data.
Journal of Invertebrate Pathology,
156, 6-13.
Abstract:
New genotyping method for the causative agent of crayfish plague (Aphanomyces astaci) based on whole genome data
The oomycete Aphanomyces astaci causes crayfish plague, the most important disease of European freshwater crayfish species. Presumably introduced into Europe 150 years ago with the import of North American crayfish, A. astaci is highly pathogenic to European crayfish species. Five genotypes (A, B, C, D, and E) have been defined based on random amplified polymorphic DNA analysis (RAPD-PCR) from A. astaci pure cultures. The distinction of genotypes is an essential tool to conduct molecular epidemiological studies on crayfish plague and it has been used to clarify and better understand the history and spread of this disease in Europe. Whereas RAPD-PCR requires DNA from pure culture isolates, the development of genotyping tools that can be applied to DNA extracted from clinical samples allows a much wider application of genotyping studies, including revisiting historic samples. In this study, we present a new approach that adds to currently available methods for genotyping A. astaci strains directly from clinical crayfish samples. Whole-genome sequencing of A. astaci strains representing all currently known genotypes was employed, genomic regions unique to the respective genotype identified, and a PCR-based genotyping assay designed, which focuses on the presence/absence of PCR product after amplification with the genotype-specific primers. Our diagnostic methodology was tested using DNA extracts from pure A. astaci cultures, other Aphanomyces species and additional oomycetes, samples from a recent Italian crayfish plague outbreak and additional historical samples available in the Centre for Environment, Fisheries and Aquaculture Science laboratory. The new markers were reliable for pure culture and clinical samples from a recent outbreak and successfully discriminated genotype A, B, D, and E. The marker for genotype C required an additional sequencing step of the generated PCR product to confirm genotype.
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Vanhatalo A, Blackwell JR, L'Heureux JE, Williams DW, Smith A, van der Giezen M, Winyard PG, Kelly J, Jones AM (2018). Nitrate-responsive oral microbiome modulates nitric oxide homeostasis and blood pressure in humans.
Free Radic Biol Med,
124, 21-30.
Abstract:
Nitrate-responsive oral microbiome modulates nitric oxide homeostasis and blood pressure in humans.
Imbalances in the oral microbial community have been associated with reduced cardiovascular and metabolic health. A possible mechanism linking the oral microbiota to health is the nitrate (NO3-)-nitrite (NO2-)-nitric oxide (NO) pathway, which relies on oral bacteria to reduce NO3- to NO2-. NO (generated from both NO2- and L-arginine) regulates vascular endothelial function and therefore blood pressure (BP). By sequencing bacterial 16S rRNA genes we examined the relationships between the oral microbiome and physiological indices of NO bioavailability and possible changes in these variables following 10 days of NO3- (12 mmol/d) and placebo supplementation in young (18-22 yrs) and old (70-79 yrs) normotensive humans (n = 18). NO3- supplementation altered the salivary microbiome compared to placebo by increasing the relative abundance of Proteobacteria (+225%) and decreasing the relative abundance of Bacteroidetes (-46%; P
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Tsaousis AD, Hamblin KA, Elliott CR, Young L, Rosen-Hidalgo A, Gourlay CW, Moore AL, van der Giezen M (2018). The Human Gut Colonizer Blastocystis Respires Using Complex II and Alternative Oxidase to Buffer Transient Oxygen Fluctuations in the Gut.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY,
8 Author URL.
2017
Vashisht K, Verma S, Gupta S, Lynn AM, Dixit R, Mishra N, Valecha N, Hamblin KA, Maytum R, Pandey KC, et al (2017). Engineering Nucleotide Specificity of Succinyl-CoA Synthetase in <i>Blastocystis</i>: the Emerging Role of Gatekeeper Residues. Biochemistry, 56(3), 534-542.
Gentekaki E, Curtis BA, Stairs CW, Klimeš V, Eliáš M, Salas-Leiva DE, Herman EK, Eme L, Arias MC, Henrissat B, et al (2017). Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis.
PLoS Biol,
15(9).
Abstract:
Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis.
Blastocystis is the most prevalent eukaryotic microbe colonizing the human gut, infecting approximately 1 billion individuals worldwide. Although Blastocystis has been linked to intestinal disorders, its pathogenicity remains controversial because most carriers are asymptomatic. Here, the genome sequence of Blastocystis subtype (ST) 1 is presented and compared to previously published sequences for ST4 and ST7. Despite a conserved core of genes, there is unexpected diversity between these STs in terms of their genome sizes, guanine-cytosine (GC) content, intron numbers, and gene content. ST1 has 6,544 protein-coding genes, which is several hundred more than reported for ST4 and ST7. The percentage of proteins unique to each ST ranges from 6.2% to 20.5%, greatly exceeding the differences observed within parasite genera. Orthologous proteins also display extreme divergence in amino acid sequence identity between STs (i.e. 59%-61% median identity), on par with observations of the most distantly related species pairs of parasite genera. The STs also display substantial variation in gene family distributions and sizes, especially for protein kinase and protease gene families, which could reflect differences in virulence. It remains to be seen to what extent these inter-ST differences persist at the intra-ST level. A full 26% of genes in ST1 have stop codons that are created on the mRNA level by a novel polyadenylation mechanism found only in Blastocystis. Reconstructions of pathways and organellar systems revealed that ST1 has a relatively complete membrane-trafficking system and a near-complete meiotic toolkit, possibly indicating a sexual cycle. Unlike some intestinal protistan parasites, Blastocystis ST1 has near-complete de novo pyrimidine, purine, and thiamine biosynthesis pathways and is unique amongst studied stramenopiles in being able to metabolize α-glucans rather than β-glucans. It lacks all genes encoding heme-containing cytochrome P450 proteins. Predictions of the mitochondrion-related organelle (MRO) proteome reveal an expanded repertoire of functions, including lipid, cofactor, and vitamin biosynthesis, as well as proteins that may be involved in regulating mitochondrial morphology and MRO/endoplasmic reticulum (ER) interactions. In sharp contrast, genes for peroxisome-associated functions are absent, suggesting Blastocystis STs lack this organelle. Overall, this study provides an important window into the biology of Blastocystis, showcasing significant differences between STs that can guide future experimental investigations into differences in their virulence and clarifying the roles of these organisms in gut health and disease.
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Herman E, Siegesmund MA, Bottery MJ, van Aerle R, Shather MM, Caler E, Dacks JB, van der Giezen M (2017). Membrane Trafficking Modulation during Entamoeba Encystation.
SCIENTIFIC REPORTS,
7 Author URL.
van Aerle R, van der Giezen M (2017). Next-Generation Sequencing, Bioinformatics, and Infectious Diseases. In (Ed)
Genetics and Evolution of Infectious Diseases: Second Edition, 405-420.
Abstract:
Next-Generation Sequencing, Bioinformatics, and Infectious Diseases
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2016
van der Giezen M (2016). Evolution: Organelles Caught in the Act.
Current Biology,
26(20), R913-R915.
Abstract:
Evolution: Organelles Caught in the Act
Mitochondria in the protist Brevimastigomonas motovehiculus are in the process of dismantling their mitochondrial electron transport chain complexes as they adapt to anaerobic environments. Novel protein interactions suggest a highly complicated process rather than the simple removal of unnecessary genes.
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2015
van der Giezen M (2015). Nature's Magic Algebra; or, How One Plus One Still Equaled One. BioScience, 65(8), 832-833.
2014
Stairs CW, Eme L, Brown MW, Mutsaers C, Susko E, Dellaire G, Soanes DM, Van Der Giezen M, Roger AJ (2014). A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia.
Current Biology,
24(11), 1176-1186.
Abstract:
A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia
Background Many microbial eukaryotes have evolved anaerobic alternatives to mitochondria known as mitochondrion-related organelles (MROs). Yet, only a few of these have been experimentally investigated. Here we report an RNA-seq-based reconstruction of the MRO proteome of Pygsuia biforma, an anaerobic representative of an unexplored deep-branching eukaryotic lineage. Results Pygsuia's MRO has a completely novel suite of functions, defying existing "function-based" organelle classifications. Most notable is the replacement of the mitochondrial iron-sulfur cluster machinery by an archaeal sulfur mobilization (SUF) system acquired via lateral gene transfer (LGT). Using immunolocalization in Pygsuia and heterologous expression in yeast, we show that the SUF system does indeed localize to the MRO. The Pygsuia MRO also possesses a unique assemblage of features, including: cardiolipin, phosphonolipid, amino acid, and fatty acid metabolism; a partial Kreb's cycle; a reduced respiratory chain; and a laterally acquired rhodoquinone (RQ) biosynthesis enzyme. The latter observation suggests that RQ is an electron carrier of a fumarate reductase-type complex II in this MRO. Conclusions the unique functional profile of this MRO underscores the tremendous plasticity of mitochondrial function within eukaryotes and showcases the role of LGT in forging metabolic mosaics of ancestral and newly acquired organellar pathways. © 2014 Elsevier Ltd.
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Bertolini C, van Aerle R, Lampis S, Moore KA, Paszkiewicz K, Butler CS, Vallini G, van der Giezen M (2014). Draft Genome Sequence of Stenotrophomonas maltophilia SeITE02, a Gammaproteobacterium Isolated from Selenite-Contaminated Mining Soil.
Genome Announc,
2(3).
Abstract:
Draft Genome Sequence of Stenotrophomonas maltophilia SeITE02, a Gammaproteobacterium Isolated from Selenite-Contaminated Mining Soil.
Stenotrophomonas maltophilia strain SeITE02 was isolated from the rhizosphere of the selenium-hyperaccumulating legume Astragalus bisculcatus. In this report, we provide the 4.56-Mb draft genome sequence of S. maltophilia SeITE02, a gammaproteobacterium that can withstand high concentrations of selenite and reduce these to elemental selenium.
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2013
van der Giezen M (2013). Evolution: one thread to unite them all.
Curr Biol,
23(16), R679-R681.
Abstract:
Evolution: one thread to unite them all.
Mitochondria play import roles in the overall metabolism of eukaryotes. Traditionally, they have played a secondary role to the nucleus in the origin of eukaryotes. However, their relative positions in this crucial event for eukaryotic evolution might be reversed.
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Koumandou VL, Wickstead B, Ginger ML, van der Giezen M, Dacks JB, Field MC (2013). Molecular paleontology and complexity in the last eukaryotic common ancestor.
Crit Rev Biochem Mol Biol,
48(4), 373-396.
Abstract:
Molecular paleontology and complexity in the last eukaryotic common ancestor.
Eukaryogenesis, the origin of the eukaryotic cell, represents one of the fundamental evolutionary transitions in the history of life on earth. This event, which is estimated to have occurred over one billion years ago, remains rather poorly understood. While some well-validated examples of fossil microbial eukaryotes for this time frame have been described, these can provide only basic morphology and the molecular machinery present in these organisms has remained unknown. Complete and partial genomic information has begun to fill this gap, and is being used to trace proteins and cellular traits to their roots and to provide unprecedented levels of resolution of structures, metabolic pathways and capabilities of organisms at these earliest points within the eukaryotic lineage. This is essentially allowing a molecular paleontology. What has emerged from these studies is spectacular cellular complexity prior to expansion of the eukaryotic lineages. Multiple reconstructed cellular systems indicate a very sophisticated biology, which by implication arose following the initial eukaryogenesis event but prior to eukaryotic radiation and provides a challenge in terms of explaining how these early eukaryotes arose and in understanding how they lived. Here, we provide brief overviews of several cellular systems and the major emerging conclusions, together with predictions for subsequent directions in evolution leading to extant taxa. We also consider what these reconstructions suggest about the life styles and capabilities of these earliest eukaryotes and the period of evolution between the radiation of eukaryotes and the eukaryogenesis event itself.
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Read BA, Kegel J, Klute MJ, Kuo A, Lefebvre SC, Maumus F, Mayer C, Miller J, Monier A, Salamov A, et al (2013). Pan genome of the phytoplankton Emiliania underpins its global distribution.
Nature,
499(7457), 209-213.
Abstract:
Pan genome of the phytoplankton Emiliania underpins its global distribution.
Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.
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Clark CG, van der Giezen M, Alfellani MA, Stensvold CR (2013). Recent developments in Blastocystis research.
Adv Parasitol,
82, 1-32.
Abstract:
Recent developments in Blastocystis research.
Blastocystis is a common parasite of the human large intestine but has an uncertain role in disease. In this review, we appraise the published evidence addressing this and its weaknesses. Genetic diversity studies have led to the identification of numerous subtypes (STs) within the genus Blastocystis and, recently, methods for studying variation within STs have been developed, with implications for our understanding of host specificity. The geographic distribution of STs is summarised and the impact this may have on investigations into the role of the organism in disease is discussed. Finally, we describe the organelle and nuclear genome characteristics and look to future developments in the field.
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Terali K, Beavil RL, Pickersgill RW, van der Giezen M (2013). The effect of the adaptor protein Isd11 on the quaternary structure of the eukaryotic cysteine desulphurase Nfs1.
Biochem Biophys Res Commun,
440(2), 235-240.
Abstract:
The effect of the adaptor protein Isd11 on the quaternary structure of the eukaryotic cysteine desulphurase Nfs1.
Small inorganic assemblies of alternating ferrous/ferric iron and sulphide ions, so-called iron-sulphur (Fe-S) clusters, are possibly nature's most ancient prosthetic groups. One of the early actors in Fe-S cluster biosynthesis is a protein complex composed of a cysteine desulphurase, Nfs1, and its functional binding partner, Isd11. Although the essential function of Nfs1·Isd11 in the liberation of elemental sulphur from free cysteine is well established, little is known about its structure. Here, we provide evidence that shows Isd11 has a profound effect on the oligomeric state of Nfs1.
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2012
Müller M, Mentel M, van Hellemond JJ, Henze K, Woehle C, Gould SB, Yu R-Y, van der Giezen M, Tielens AGM, Martin WF, et al (2012). Biochemistry and evolution of anaerobic energy metabolism in eukaryotes.
Microbiol Mol Biol Rev,
76(2), 444-495.
Abstract:
Biochemistry and evolution of anaerobic energy metabolism in eukaryotes.
Major insights into the phylogenetic distribution, biochemistry, and evolutionary significance of organelles involved in ATP synthesis (energy metabolism) in eukaryotes that thrive in anaerobic environments for all or part of their life cycles have accrued in recent years. All known eukaryotic groups possess an organelle of mitochondrial origin, mapping the origin of mitochondria to the eukaryotic common ancestor, and genome sequence data are rapidly accumulating for eukaryotes that possess anaerobic mitochondria, hydrogenosomes, or mitosomes. Here we review the available biochemical data on the enzymes and pathways that eukaryotes use in anaerobic energy metabolism and summarize the metabolic end products that they generate in their anaerobic habitats, focusing on the biochemical roles that their mitochondria play in anaerobic ATP synthesis. We present metabolic maps of compartmentalized energy metabolism for 16 well-studied species. There are currently no enzymes of core anaerobic energy metabolism that are specific to any of the six eukaryotic supergroup lineages; genes present in one supergroup are also found in at least one other supergroup. The gene distribution across lineages thus reflects the presence of anaerobic energy metabolism in the eukaryote common ancestor and differential loss during the specialization of some lineages to oxic niches, just as oxphos capabilities have been differentially lost in specialization to anoxic niches and the parasitic life-style. Some facultative anaerobes have retained both aerobic and anaerobic pathways. Diversified eukaryotic lineages have retained the same enzymes of anaerobic ATP synthesis, in line with geochemical data indicating low environmental oxygen levels while eukaryotes arose and diversified.
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de Paula WBM, Allen JF, van der Giezen M (2012). Mitochondria, Hydrogenosomes and Mitosomes in Relation to the CoRR Hypothesis for Genome Function and Evolution. In Bullerwell CE (Ed) Organelle Genetics, 105-122.
Standley DM, van der Giezen M (2012). Modeling the alternative oxidase from the human pathogen Blastocystis using automated hybrid structural template assembly.
Research and Reports in Biochemistry,
2, 1-8.
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Modeling the alternative oxidase from the human pathogen Blastocystis using automated hybrid structural template assembly
Alternative oxidases (AOX) of human parasites represent attractive drug targets due to their absence in humans. However, the lack of a structure has prevented structure-based drug design. Moreover, a large helical insertion proves difficult for automated structural modeling efforts. We have used a novel hybrid structural modeling approach to generate a model that is globally consistent with a previous model but based on a phylogenetically closer template and systematic sampling of known fragments in the helical insertion. Our model, in agreement with site-directed mutagenesis studies, clearly assigns E200 as the iron-ligating residue as opposed to the previously suggested E201. Crystallization of AOX from another species has recently been reported suggesting that our blind prediction can be independently validated in the near future.
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van der Giezen M, Lenton TM (2012). The rise of oxygen and complex life. Journal of Eukaryotic Microbiology, 59(2), 111-113.
2011
van der Giezen M (2011). Mitochondria and the Rise of Eukaryotes.
BIOSCIENCE,
61(8), 594-601.
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Siegesmund MA, Hehl AB, van der Giezen M (2011). Mitosomes in trophozoites and cysts of the reptilian parasite Entamoeba invadens.
Eukaryot Cell,
10(11), 1582-1585.
Abstract:
Mitosomes in trophozoites and cysts of the reptilian parasite Entamoeba invadens.
Heat shock protein genes led to the discovery of mitosomes in Entamoeba histolytica, but mitosomes have not been described for any other Entamoeba species, nor have they been identified in the cyst stage. Here, we show that the distantly related reptilian pathogen Entamoeba invadens contains mitosomes, in both trophozoites and cysts, suggesting all Entamoeba species contain these organelles.
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Herman EK, Walker G, van der Giezen M, Dacks JB (2011). Multivesicular bodies in the enigmatic amoeboflagellate Breviata anathema and the evolution of ESCRT 0.
Journal of Cell Science,
124, 613-621.
Abstract:
Multivesicular bodies in the enigmatic amoeboflagellate Breviata anathema and the evolution of ESCRT 0
Endosomal sorting complexes required for transport (ESCRTs) are heteromeric protein complexes required for multivesicular body (MVB) morphogenesis. ESCRTs I, II, III and III-associated are ubiquitous in eukaryotes and presumably ancient in origin. ESCRT 0 recruits cargo to the MVB and appears to be opisthokont-specific, bringing into question aspects of the current model of ESCRT mechanism. One caveat to the restricted distribution of ESCRT 0 was the previous limited availability of amoebozoan genomes, the supergroup closest to opisthokonts. Here, we significantly expand the sampling of ESCRTs in Amoebozoa. Our electron micrographic and bioinformatics evidence confirm the presence of MVBs in the amoeboflagellate Breviata anathema. Searches of genomic databases of amoebozoans confirm the ubiquitous nature of ESCRTs I-III-associated and the restriction of ESCRT 0 to opisthokonts. Recently, an alternate ESCRT 0 complex, centering on Tom1 proteins, has been proposed. We determine the distribution of Tom1 family proteins across eukaryotes and show that the Tom1, Tom1L1 and Tom1L2 proteins are a vertebrate-specific expansion of the single Tom1 family ancestor, which has indeed been identified in at least one member of each of the major eukaryotic supergroups. This implies a more widely conserved and ancient role for the Tom1 family in endocytosis than previously suspected.
Abstract.
2010
Griffith GW, Baker S, Fliegerova K, Liggenstoffer A, van der Giezen M, Voigt K, Beakes G (2010). Anaerobic fungi: Neocallimastigomycota.
IAM Fungus,
1, 181-185.
Author URL.
Maralikova B, Ali V, Nakada-Tsukui K, Nozaki T, van der Giezen M, Henze K, Tovar J (2010). Bacterial-type oxygen detoxification and iron-sulfur cluster assembly in amoebal relict mitochondria.
Cell Microbiol,
12(3), 331-342.
Abstract:
Bacterial-type oxygen detoxification and iron-sulfur cluster assembly in amoebal relict mitochondria.
The assembly of vital reactive iron-sulfur (Fe-S) cofactors in eukaryotes is mediated by proteins inherited from the original mitochondrial endosymbiont. Uniquely among eukaryotes, however, Entamoeba and Mastigamoeba lack such mitochondrial-type Fe-S cluster assembly proteins and possess instead an analogous bacterial-type system acquired by lateral gene transfer. Here we demonstrate, using immunomicroscopy and biochemical methods, that beyond their predicted cytosolic distribution the bacterial-type Fe-S cluster assembly proteins NifS and NifU have been recruited to function within the relict mitochondrial organelles (mitosomes) of Entamoeba histolytica. Both Nif proteins are 10-fold more concentrated within mitosomes compared with their cytosolic distribution suggesting that active Fe-S protein maturation occurs in these organelles. Quantitative immunoelectron microscopy showed that amoebal mitosomes are minute but highly abundant cellular structures that occupy up to 2% of the total cell volume. In addition, protein colocalization studies allowed identification of the amoebal hydroperoxide detoxification enzyme rubrerythrin as a mitosomal protein. This protein contains functional Fe-S centres and exhibits peroxidase activity in vitro. Our findings demonstrate the role of analogous protein replacement in mitochondrial organelle evolution and suggest that the relict mitochondrial organelles of Entamoeba are important sites of metabolic activity that function in Fe-S protein-mediated oxygen detoxification.
Abstract.
Author URL.
Paszkiewicz KH, van der Giezen M (2010). Omics, bioinformatics and infectious disease research. In Tibayrenc M (Ed)
Genetics and Evolution of Infectious Disease, Elsevier, 523-539.
Abstract:
Omics, bioinformatics and infectious disease research.
Abstract.
2009
van DGM (2009). Eukaryotic life without mitochondria?. Annual Meeting of the Society-for-Experimental-Biology. 28th Jun - 1st Jul 2009.
van der Giezen, M (2009). Hydrogenosomes and Mitosomes: Conservation and Evolution of Functions.
J EUKARYOT MICROBIOL,
56(3), 221-231.
Abstract:
Hydrogenosomes and Mitosomes: Conservation and Evolution of Functions
The field studying unusual mitochondria in microbial eukaryotes has come full circle. Some 10-15 years ago it had the evangelical task of informing the wider scientific community that not all eukaryotes had mitochondria. Advances in the field indicated that although some protists might not have mitochondria, the presence of genes of mitochondrial ancestry suggested their lineage once had. The subsequent discovery of mitochondrial compartments in all supposedly amitochondriate protists studied so far indicates that all eukaryotes do have mitochondria indeed. This assertion has fuelled novel eukaryotic origin theories and weakened others. But what do we know about these unusual mitochondria from anaerobic protists? Have they all converged onto similar roles? Iron-sulphur cluster assembly is often hailed as the unifying feature of these organelles. However, the iron-sulphur protein that is so important that a complete organelle is being maintained has not been identified. Is it to be expected that all unusual mitochondria perform the same physiological role? These organelles have been found in numerous protists occupying different ecological niches. Different selection pressures operate on different organisms so there is no reason to suspect that their mitochondria should all be the same.
Abstract.
Tsaousis AD, Stechmann A, Hamblin KA, van der Giezen M, Pérez-Brocal V, Clark CG (2009). The Blastocystis mitochondrion-like organelles. In Clark CG, Johnson PJ, Adam RD (Eds.) Anaerobic parasitic protozoa: Genomics and molecular biology, Norwich: Caister Academic Press Ltd, 207-221.
2008
van Grinsven KWA, Rosnowsky S, van Weelden SWH, Puetz S, van der Giezen M, Martin W, van Hellemond JJ, Tielens AGM, Henze K (2008). Acetate : succinate CoA-transferase in the hydrogenosomes of Trichomonas vaginalis - Identification and characterization.
JOURNAL OF BIOLOGICAL CHEMISTRY,
283(3), 1411-1418.
Author URL.
Hamblin K, Standley DM, Rogers MB, Stechmann A, Roger AJ, Maytum R, van der Giezen M (2008). Localisation and nucleotide specificity of Blastocystis succinyl-CoA synthetase. Molecular Microbiology, 68, 1395-1405.
Stechmann A, Hamblin K, Pérez-Brocal V, Gaston D, Richmond GS, van der Giezen M, Clark CG, Roger AJ (2008). Organelles in Blastocystis that blur the distinction between mitochondria and hydrogenosomes.
Curr Biol,
18(8), 580-585.
Abstract:
Organelles in Blastocystis that blur the distinction between mitochondria and hydrogenosomes.
Blastocystis is a unicellular stramenopile of controversial pathogenicity in humans. Although it is a strict anaerobe, Blastocystis has mitochondrion-like organelles with cristae, a transmembrane potential and DNA. An apparent lack of several typical mitochondrial pathways has led some to suggest that these organelles might be hydrogenosomes, anaerobic organelles related to mitochondria. We generated 12,767 expressed sequence tags (ESTs) from Blastocystis and identified 115 clusters that encode putative mitochondrial and hydrogenosomal proteins. Among these is the canonical hydrogenosomal protein iron-only [FeFe] hydrogenase that we show localizes to the organelles. The organelles also have mitochondrial characteristics, including pathways for amino acid metabolism, iron-sulfur cluster biogenesis, and an incomplete tricarboxylic acid cycle as well as a mitochondrial genome. Although complexes I and II of the electron transport chain (ETC) are present, we found no evidence for complexes III and IV or F1Fo ATPases. The Blastocystis organelles have metabolic properties of aerobic and anaerobic mitochondria and of hydrogenosomes. They are convergently similar to organelles recently described in the unrelated ciliate Nyctotherus ovalis. These findings blur the boundaries between mitochondria, hydrogenosomes, and mitosomes, as currently defined, underscoring the disparate selective forces that shape these organelles in eukaryotes.
Abstract.
Author URL.
Standley DM, Kinjo AR, Lis M, van der Giezen M, Nakamura H (2008). Structure-based functional annotation of protein sequences guided by comparative models. the Second International Symposium on Optimization and Systems Biology (OSB’08). 1st Oct 1931 - 1st Nov 2003.
Puthiyaveetil S, Kavanagh TA, Cain P, Sullivan JA, Newall CA, Gray JC, Robinson C, van der Giezen M, Rogers MB, Allen JF, et al (2008). The ancestral symbiont sensor kinase CSK links photosynthesis with gene expression in chloroplasts. Proceedings of the National Academy of Sciences USA, 105, 10061-10066.
2007
Tovar J, Cox SSE, van der Giezen M (2007). A mitosome purification protocol based on percoll density gradients and its use in validating the mitosomal nature of Entamoeba histolytica mitochondrial Hsp70.
Methods Mol Biol,
390, 167-177.
Abstract:
A mitosome purification protocol based on percoll density gradients and its use in validating the mitosomal nature of Entamoeba histolytica mitochondrial Hsp70.
Mitochondria are indispensable for aerobic respiration, but many microbial eukaryotes have lost this function through reductive evolution. Their modified mitochondria are known as hydrogenosomes or mitosomes depending on whether or not they produce molecular hydrogen. The intestinal parasite Entamoeba histolytica contains mitosomes whose role in cellular metabolism is unclear. Only three proteins have been shown thus far to reside in these organelles: the molecular chaperones Hsp10 and Hsp60 and an unusual ADP/ATP carrier. Here we describe the isolation of E. histolytica mitosomes by cellular fractionation and density gradient centrifugation and show that the mitochondrial-type chaperone Hsp70 is also housed in Entamoeba mitosomes.
Abstract.
Author URL.
Van Der Giezen M (2007). Methods in Molecular Biology: Preface. Methods in Molecular Biology, 390
Allen CA, van der Giezen M, Allen JF (2007). Origin, function, and transmission of mitochondria. In Martin W, Müller M (Eds.) Origin of mitochondria and hydrogenosomes, 39-56.
van der Giezen, M. (2007). Protein targeting protocols., Humana Press Inc.
2006
Cox SSE, van der Giezen M, Tarr SJ, Crompton MR, Tovar J (2006). Evidence from bioinformatics, expression and inhibition studies of phosphoinositide-3 kinase signalling in Giardia intestinalis.
BMC Microbiol,
6Abstract:
Evidence from bioinformatics, expression and inhibition studies of phosphoinositide-3 kinase signalling in Giardia intestinalis.
BACKGROUND: Giardia intestinalis is a parasitic protozoan and major cause of diarrhoeal disease. Disease transmission is dependent on the ability of the parasite to differentiate back and forth between an intestine-colonising trophozoite and an environmentally-resistant infective cyst. Our current understanding of the intracellular signalling mechanisms that regulate parasite replication and differentiation is limited, yet such information could suggest new methods of disease control. Phosphoinositide-3 kinase (PI3K) signalling pathways have a central involvement in many vital eukaryotic processes, such as regulation of cell growth, intracellular membrane trafficking and cell motility. Here we present evidence for the existence of functional PI3K intracellular signalling pathways in G. intestinalis. RESULTS: We have identified and characterised two genes, Gipi3k1 and Gipi3k2, which encode putative PI3Ks. Both genes are expressed in trophozoites and encysting cells, suggesting a possible role of GiPI3K1 and GiPI3K2 in regulating giardial growth and differentiation. Extensive nucleotide and amino acid sequence characterisation predicts that both encoded PI3Ks are functional as indicated by the presence of highly conserved structural domains and essential catalytic residues. The inhibitory effect of the PI3K inhibitor LY294002 on trophozoite proliferation also supports their functionality. Phylogenetic analysis supports the identity of GiPI3K1 as a Class I isoform and GiPI3K2 as a Class III isoform. In addition, giardial genes encoding putative homologues of phosphoinositide-metabolising enzymes such as PTEN, MTM, PIPkin and PI 5-phosphatase as well as downstream effectors with phosphoinositide-binding domains have been identified, placing GiPI3K1 and GiPI3K2 in a broader signalling context. Compared with twenty-six PI3Ks from other organisms, GiPI3K1 and GiPI3K2 are unique in that they contain large insertions within their highly conserved kinase domains. The function of these insertions is unknown; however we show here that they are not intron-derived and would probably not hinder substrate binding. These insertions may represent a plausible drug target. CONCLUSION: G. intestinalis encodes and expresses two putative PI3Ks, at least one of which appears to be required during normal parasite proliferation. The identification of Class I and Class III but not Class II isoforms suggests that both extracellularly-initiated signalling (Class I-regulated) and intracellular vesicle trafficking (Class III-regulated) might be controlled by PI3Ks in G. intestinalis. The presence of genes encoding putative homologues of phosphoinositide-metabolising enzymes and downstream effectors in the G. intestinalis genome further suggests that the overall architecture of PI3K signalling may be comparable with pathways present in other better-studied organisms.
Abstract.
Author URL.
Richards TA, van der Giezen M (2006). Evolution of the Isd11-IscS complex reveals a single alpha-proteobacterial endosymbiosis for all eukaryotes.
MOLECULAR BIOLOGY AND EVOLUTION,
23(7), 1341-1344.
Author URL.
Dacks JB, Dyal PL, Embley TM, van der Giezen M (2006). Hydrogenosomal succinyl-CoA synthetase from the rumen-dwelling fungus Neocallimastix patriciarum; an energy-producing enzyme of mitochondrial origin.
GENE,
373, 75-82.
Author URL.
van der Giezen, M. (2006). Mitochondrial amazement. EMBO Reports, 7(478).
van der Giezen M (2006). Mitochondrial amazement. EMBO reports, 7(5), 478-478.
2005
Chan KW, Slotboom DJ, Cox S, Embley TM, Fabre O, van der Giezen M, Harding M, Horner DS, Kunji ERS, Leon-Avila G, et al (2005). A novel ADP/ATP transporter in the mitosome of the microaerophilic human parasite Entamoeba histolytica.
CURRENT BIOLOGY,
15(8), 737-742.
Author URL.
Brinkmann H, van der Giezen M, Zhou Y, Poncelin de Raucourt G, Philippe H (2005). An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics.
Syst Biol,
54(5), 743-757.
Abstract:
An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics.
In the context of exponential growing molecular databases, it becomes increasingly easy to assemble large multigene data sets for phylogenomic studies. The expected increase of resolution due to the reduction of the sampling (stochastic) error is becoming a reality. However, the impact of systematic biases will also become more apparent or even dominant. We have chosen to study the case of the long-branch attraction artefact (LBA) using real instead of simulated sequences. Two fast-evolving eukaryotic lineages, whose evolutionary positions are well established, microsporidia and the nucleomorph of cryptophytes, were chosen as model species. A large data set was assembled (44 species, 133 genes, and 24,294 amino acid positions) and the resulting rooted eukaryotic phylogeny (using a distant archaeal outgroup) is positively misled by an LBA artefact despite the use of a maximum likelihood-based tree reconstruction method with a complex model of sequence evolution. When the fastest evolving proteins from the fast lineages are progressively removed (up to 90%), the bootstrap support for the apparently artefactual basal placement decreases to virtually 0%, and conversely only the expected placement, among all the possible locations of the fast-evolving species, receives increasing support that eventually converges to 100%. The percentage of removal of the fastest evolving proteins constitutes a reliable estimate of the sensitivity of phylogenetic inference to LBA. This protocol confirms that both a rich species sampling (especially the presence of a species that is closely related to the fast-evolving lineage) and a probabilistic method with a complex model are important to overcome the LBA artefact. Finally, we observed that phylogenetic inference methods perform strikingly better with simulated as opposed to real data, and suggest that testing the reliability of phylogenetic inference methods with simulated data leads to overconfidence in their performance. Although phylogenomic studies can be affected by systematic biases, the possibility of discarding a large amount of data containing most of the nonphylogenetic signal allows recovering a phylogeny that is less affected by systematic biases, while maintaining a high statistical support.
Abstract.
Author URL.
van der Giezen M, Leon-Avila G, Tovar J (2005). Characterization of chaperonin 10 (Cpn10) from the intestinal human pathogen Entamoeba histolytica.
MICROBIOLOGY-SGM,
151, 3107-3115.
Author URL.
van der Giezen M, Tovar J (2005). Degenerate mitochondria.
EMBO REPORTS,
6(6), 525-530.
Author URL.
van der Giezen M (2005). Endosymbiosis: past and present.
HEREDITY,
95(5), 335-336.
Author URL.
Van Der Giezen M (2005). Evolutionary biology. Endosymbiosis: Past and present. Heredity, 95(5), 335-336.
van der Giezen M, Tovar J, Clark CG (2005). Mitochondrion-derived organelles in protists and fungi.
Int Rev Cytol,
244, 175-225.
Abstract:
Mitochondrion-derived organelles in protists and fungi.
The mitochondrion is generally considered to be a defining feature of eukaryotic cells, yet most anaerobic eukaryotes lack this organelle. Many of these were previously thought to derive from eukaryotes that diverged prior to acquisition of the organelle through endosymbiosis. It is now known that all extant eukaryotes are descended from an ancestor that had a mitochondrion and that in anaerobic eukaryotes the organelle has been modified into either hydrogenosomes, which continue to generate energy for the host cell, or mitosomes, which do not. These organelles have each arisen independently several times. Recent evidence suggests a shared derived characteristic that may be responsible for the retention of the organelles in the absence of the better-known mitochondrial functions--iron-sulfur cluster assembly. This review explores the events leading to this new understanding of mitochondrion-derived organelles in amitochondriate eukaryotes, the current state of our knowledge, and future areas for investigation.
Abstract.
Author URL.
Regoes A, Zourmpanou D, León-Avila G, van der Giezen M, Tovar J, Hehl AB (2005). Protein import, replication, and inheritance of a vestigial mitochondrion.
J Biol Chem,
280(34), 30557-30563.
Abstract:
Protein import, replication, and inheritance of a vestigial mitochondrion.
Mitochondrial remnant organelles (mitosomes) that exist in a range of "amitochondrial" eukaryotic organisms represent ideal models for the study of mitochondrial evolution and for the establishment of the minimal set of proteins required for the biogenesis of an endosymbiosis-derived organelle. Giardia intestinalis, often described as the earliest branching eukaryote, contains double membrane-bounded structures involved in iron-sulfur cluster biosynthesis, an essential function of mitochondria. Here we present evidence that Giardia mitosomes also harbor Cpn60, mtHsp70, and ferredoxin and that despite their advanced state of reductive evolution they have retained vestiges of presequence-dependent and -independent protein import pathways akin to those that operate in mammalian mitochondria. Although import of IscU and ferredoxin is still reliant on their amino-terminal presequences, targeting of Giardia Cpn60, IscS, or mtHsp70 into mitosomes no longer requires cleavable presequences, a derived feature from their mitochondrial homologues. In addition, we found that division and segregation of a single centrally positioned mitosome tightly associated with the microtubular cytoskeleton is coordinated with the cell cycle, whereas peripherally located mitosomes are inherited into daughter cells stochastically.
Abstract.
Author URL.
2004
van der Giezen M, Tovar J (2004). Hydrogenosomes, mitosomes and mitochondria; variations on a theme?. In Horner DS, Hirt RP (Eds.) Organelles, genomes and eukaryote phylogeny: an evolutionary synthesis in the age of genomics, Organelles, genomes and eukaryote phylogeny: an evolutionary synthesis in the age of genomics. (Horner, D.S. and R.P. Hirt, Eds.): CRC Press Ltd, 283-302.
van der Giezen M, Cox S, Tovar J (2004). The iron-sulfur cluster assembly genes iscS and iscU of Entamoeba histolytica were acquired by horizontal gene transfer.
BMC EVOLUTIONARY BIOLOGY,
4 Author URL.
2003
van der Giezen M, Birdsey GM, Horner DS, Lucocq J, Dyal PL, Benchimol M, Danpure CJ, Embley TM (2003). Fungal hydrogenosomes contain mitochondrial heat-shock proteins.
MOLECULAR BIOLOGY AND EVOLUTION,
20(7), 1051-1061.
Author URL.
Embley TM, van der Giezen M, Horner DS, Dyal PL, Bell S, Foster PG (2003). Hydrogenosomes, mitochondria and early eukaryotic evolution.
IUBMB LIFE,
55(7), 387-395.
Author URL.
Cammack R, Horner DS, van der Giezen M, Kulda J, Lloyd D (2003). Iron-sulfur proteins in anaerobic eukaryotes. In: Biochemistry and physiology of anaerobic bacteria. In Ljungdahl L, Adams MWW, Barton LL, Ferry JG, Johnson MK (Eds.) Biochemistry and physiology of anaerobic bacteria, Biochemistry and physiology of anaerobic bacteria.: Springer, 113-127.
Embley TM, van der Giezen M, Horner DS, Dyal PL, Foster P (2003). Mitochondria and hydrogenosomes are two forms of the same fundamental organelle.
Philos Trans R Soc Lond B Biol Sci,
358(1429), 191-201.
Abstract:
Mitochondria and hydrogenosomes are two forms of the same fundamental organelle.
Published data suggest that hydrogenosomes, organelles found in diverse anaerobic eukaryotes that make energy and hydrogen, were once mitochondria. As hydrogenosomes generally lack a genome, the conversion is probably one way. The sources of the key hydrogenosomal enzymes, pyruvate : ferredoxin oxidoreductase (PFO) and hydrogenase, are not resolved by current phylogenetic analyses, but it is likely that both were present at an early stage of eukaryotic evolution. Once thought to be restricted to a few unusual anaerobic eukaryotes, the proteins are intimately integrated into the fabric of diverse eukaryotic cells, where they are targeted to different cell compartments, and not just hydrogenosomes. There is no evidence supporting the view that PFO and hydrogenase originated from the mitochondrial endosymbiont, as posited by the hydrogen hypothesis for eukaryogenesis. Other organelles derived from mitochondria have now been described in anaerobic and parasitic microbial eukaryotes, including species that were once thought to have diverged before the mitochondrial symbiosis. It thus seems possible that all eukaryotes may eventually be shown to contain an organelle of mitochondrial ancestry, to which different types of biochemistry can be targeted. It remains to be seen if, despite their obvious differences, this family of organelles shares a common function of importance for the eukaryotic cell, other than energy production, that might provide the underlying selection pressure for organelle retention.
Abstract.
Author URL.
Tovar J, León-Avila G, Sánchez LB, Sutak R, Tachezy J, van der Giezen M, Hernández M, Müller M, Lucocq JM (2003). Mitochondrial remnant organelles of Giardia function in iron-sulphur protein maturation.
Nature,
426(6963), 172-176.
Abstract:
Mitochondrial remnant organelles of Giardia function in iron-sulphur protein maturation.
Giardia intestinalis (syn. lamblia) is one of the most widespread intestinal protozoan pathogens worldwide, causing hundreds of thousands of cases of diarrhoea each year. Giardia is a member of the diplomonads, often described as an ancient protist group whose primitive nature is suggested by the lack of typical eukaryotic organelles (for example, mitochondria, peroxisomes), the presence of a poorly developed endomembrane system and by their early branching in a number of gene phylogenies. The discovery of nuclear genes of putative mitochondrial ancestry in Giardia and the recent identification of mitochondrial remnant organelles in amitochondrial protists such as Entamoeba histolytica and Trachipleistophora hominis suggest that the eukaryotic amitochondrial state is not a primitive condition but is rather the result of reductive evolution. Using an in vitro protein reconstitution assay and specific antibodies against IscS and IscU--two mitochondrial marker proteins involved in iron-sulphur cluster biosynthesis--here we demonstrate that Giardia contains mitochondrial remnant organelles (mitosomes) bounded by double membranes that function in iron-sulphur protein maturation. Our results indicate that Giardia is not primitively amitochondrial and that it has retained a functional organelle derived from the original mitochondrial endosymbiont.
Abstract.
Author URL.
2002
Davidson EA, van der Giezen M, Horner DS, Embley TM, Howe CJ (2002). An [Fe] hydrogenase from the anaerobic hydrogenosome-containing fungus Neocallimastix frontalis L2.
Gene,
296(1-2), 45-52.
Abstract:
An [Fe] hydrogenase from the anaerobic hydrogenosome-containing fungus Neocallimastix frontalis L2.
Hydrogenases, oxygen-sensitive enzymes that can make hydrogen gas, are key to the function of hydrogen-producing organelles (hydrogenosomes), which occur in anaerobic eukaryotes scattered throughout the eukaryotic tree. All of the eukaryotic enzymes characterized so far are iron-only [Fe] hydrogenases. In contrast, it has previously been suggested that hydrogenosomes of the best-studied anaerobic fungus Neocallimastix frontalis L2 contain an unrelated iron-nickel-selenium [NiFeSe] hydrogenase. We have isolated a gene from strain L2 that encodes a putative protein containing all of the characteristic features of an iron-only [Fe] hydrogenase, including the cysteine residues required for the co-ordination of the unique 'hydrogen cluster'. As is the case for experimentally verified hydrogenosomal matrix enzymes from N. frontalis, the [Fe] hydrogenase encodes a plausible amino terminal extension that resembles mitochondrial targeting signals. Phylogenetic analyses of an expanded [Fe] hydrogenase dataset reveal a complicated picture that is difficult to interpret in the light of current ideas of species relationships. Nevertheless, our analyses cannot reject the hypothesis that the novel [Fe] hydrogenase gene of Neocallimastix is specifically related to other eukaryote [Fe] hydrogenases, and thus ultimately might be traced to the same ancestral source.
Abstract.
Author URL.
van der Giezen M, Slotboom DJ, Horner DS, Dyal PL, Harding M, Xue GP, Embley TM, Kunji ERS (2002). Conserved properties of hydrogenosomal and mitochondrial ADP/ATP carriers: a common origin for both organelles.
EMBO JOURNAL,
21(4), 572-579.
Author URL.
Van der Giezen M (2002). Strange fungi with even stranger insides. Mycologist, 16(3), 129-131.
2000
Gasc A, Giammarinaro P, Ton-Hoang B, Geslin P, van der Giezen M, Sicard M (2000). Structural organization of the Streptococcus pneumoniae chromosome and relatedness of penicillin-sensitive and -resistant strains in type 9V. In Tomasz A (Ed) Streptococcus pneumoniae, molecular biology and mechanisms of disease, Mary Ann Liebert, 25-32.
1998
van der Giezen M, Kiel JA, Sjollema KA, Prins RA (1998). The hydrogenosomal malic enzyme from the anaerobic fungus neocallimastix frontalis is targeted to mitochondria of the methylotrophic yeast hansenula polymorpha.
Curr Genet,
33(2), 131-135.
Abstract:
The hydrogenosomal malic enzyme from the anaerobic fungus neocallimastix frontalis is targeted to mitochondria of the methylotrophic yeast hansenula polymorpha.
Hydrogenosomal proteins always contain an amino-terminal extension which is believed to be a hydrogenosomal targeting signal. In the anaerobic fungus Neocallimastix frontalis these putative targeting signals are 27 amino acids long, are enriched in Ala, Leu, Ser and Arg, and have an Arg at position -2 relative to amino-acid 1 of the mature protein. These features are typically observed in mitochondrial targeting signals. Here we show that the 27 amino-acid leader sequence of the hydrogenosomal malic enzyme of N. frontalis was capable of targeting the enzyme to mitochondria of the methylotrophic ascomycete yeast Hansenula polymorpha. The same protein without this leader sequence remained cytosolic. These data suggest a close relationship between the protein import machineries of mitochondria and hydrogenosomes in fungi and provide further support for the notion that these two organelles share a common evolutionary origin.
Abstract.
Author URL.
1997
Van der Giezen M, Prins RA (1997). A common evolutionary origin for mitochondria and hydrogenosomes. Reproduction Nutrition Development, 37(SUPPL.).
van der Giezen M, Rechinger KB, Svendsen I, Durand R, Hirt RP, Fèvre M, Embley TM, Prins RA (1997). A mitochondrial-like targeting signal on the hydrogenosomal malic enzyme from the anaerobic fungus Neocallimastix frontalis: support for the hypothesis that hydrogenosomes are modified mitochondria.
Mol Microbiol,
23(1), 11-21.
Abstract:
A mitochondrial-like targeting signal on the hydrogenosomal malic enzyme from the anaerobic fungus Neocallimastix frontalis: support for the hypothesis that hydrogenosomes are modified mitochondria.
The hydrogenosomal malic enzyme (ME) was purified from the anaerobic fungus Neocallimastix frontalis. Using reverse genetics, the corresponding cDNA was isolated and characterized. The deduced amino acid sequence of the ME showed high similarity to ME from metazoa, plants and protists. Putative functional domains for malate and NAD+/NADP+ binding were identified. Phylogenetic analysis of the deduced amino acid sequence of the new ME suggests that it is homologous to reference bacterial and eukaryotic ME. Most interestingly, the cDNA codes for a protein which contains a 27-amino-acid N-terminus which is not present on the purified mature protein. This presequence shares features with known mitochondrial targeting signals, including an enrichment in Ala, Leu, Ser, and Arg, and the presence of an Arg at position-2 relative to amino acid 1 of the mature protein. This is the first report of a mitochondrial-like targeting signal on a hydrogenosomal enzyme from an anaerobic fungus and provides support for the hypothesis that hydrogenosomes in Neocallimastix frontalis might be modified mitochondria.
Abstract.
Author URL.
Biagini GA, Van Der Giezen M, Hill B, Winters C, Lloyd D (1997). Ca<sup>2+</sup> accumulation in the hydrogenosomes of Neocallimastix frontalis L2: a mitochondrial-like physiological role.
FEMS Microbiology Letters,
149(2), 227-232.
Abstract:
Ca2+ accumulation in the hydrogenosomes of Neocallimastix frontalis L2: a mitochondrial-like physiological role
The anaerobic fungus Neocallimastix frontalis L2 does not carry out oxidative phosphorylation but instead obtains energy from a fermentative metabolism. It does not have mitochondria, but does contain specialised redox organelles, the hydrogenosomes. With the aid of confocal laser scanning microscopy, we were able to follow the compartmentalisation of the ΔpH probe BCECF-AM (bis-(3-propyl-5-oxoisoxazol-4-yl)pentamethine(oxonolVi),2',7'-bis-(2 -carboxyethyl)-5-carboxyfluorescein acetomethyl ester) into hydrogenosomes in situ. Association of the Ca2+-specific dye Fluo-3AM (1-[2-amino-5-(2,7-dichloro 6-hydroxy-3-oxy-9-xanthenyl)-phenoxyl]-2-[2-amino-5-methylphenoxy]ethane -N,N,N',N'-tetraacetic acid acetomethyl ester) within the lumen of the hydrogenosomes was also observed. In addition, transmission electron microscopy revealed that the hydrogenosomes contained electron-dense inclusions. X-ray microanalysis of these granules indicated the presence of calcium and phosphate. Our results indicate that hydrogenosomes from N. frontalis L2 maintain an internal alkaline pH and are involved in the calcium regulation of the cell. These physiological features resemble those of mitochondria from aerobic fungi.
Abstract.
van der Giezen M, Sjollema KA, Artz RR, Alkema W, Prins RA (1997). Hydrogenosomes in the anaerobic fungus Neocallimastix frontalis have a double membrane but lack an associated organelle genome.
FEBS Lett,
408(2), 147-150.
Abstract:
Hydrogenosomes in the anaerobic fungus Neocallimastix frontalis have a double membrane but lack an associated organelle genome.
The presence of hydrogenosomes in phylogenetically distinct anaerobic eukaryotes implies that they have been acquired independently, and previously reported differences in ultrastructure among taxa have suggested that some hydrogenosomes have different origins. of particular interest are reports that Neocallimastix frontalis hydrogenosomes resemble microbodies in possessing a single membrane, in contrast to those in ciliates and trichomonads which have two and thus resemble mitochondria. In this investigation we have clearly demonstrated that N. frontalis hydrogenosomes possess two, rather than one, closely apposed membranes and in some preparations cristae-like structures were observed. These observations have led us to reject the microbody hypothesis and provide some indirect support for a possible mitochondrion origin as proposed for other hydrogenosomes. N. frontalis hydrogenosomes were shown to lack an associated genome as previously demonstrated for trichomonad hydrogenosomes. This might be explained by assuming that a mitochondrial genome encoding proteins for aerobic function is no longer necessary for either organelle.
Abstract.
Author URL.
Gasc AM, Giammarinaro P, Ton-Hoang B, Geslin P, van der Giezen M, Sicard M (1997). Structural organization of the Streptococcus pneumoniae chromosome and relatedness of penicillin-sensitive and -resistant strains in type 9V.
Microb Drug Resist,
3(1), 65-72.
Abstract:
Structural organization of the Streptococcus pneumoniae chromosome and relatedness of penicillin-sensitive and -resistant strains in type 9V.
Fragmentation of Streptococcus pneumoniae genomic DNA with low-frequency-cleavage restriction endonucleases and separation of the fragments by field-inversion gel electrophoresis (FIGE) provides a DNA-fingerprint of a strain. This method enables us to construct a physical and genetic map of the R6 laboratory strain what will be presented. The origin of replication containing several DNA boxes was located in the dnaA region. It was of interest to compare the profiles of subclones. Two clones of strain R36A (R6 and C13) were cultivated separately for more than 15,000 generations in two laboratories. FIGE profiles differed by only one band. Another R36A descendant, isolated in 1958 by Ravin, strain Rx was of interest since it was deficient in Dpn restriction enzymes and methylases and in the hex B function. Its origin was questionable; its profile is identical to others R6 descendants, demonstrating that Rx is derived from R36A. FIGE analysis was carried out on several penicillin-resistant strains of type 9V because penicillin-resistance in this type increased recently. The profiles of a collection of a number of these resistant isolates were very similar, showing that they result from a clone. The profiles of penicillin sensitive isolates of the same type are very similar to the resistant isolates. This suggests that the 9V type has spread recently from a clone, and the resistance genes have mutated and were selected when penicillin was extensively used.
Abstract.
Author URL.
1996
Brondijk THC, Durand R, van der Giezen M, Gottschal JC, Prins RA, Fèvre M (1996). scsB. MGG Molecular & General Genetics, 253(3), 315-315.
Brondijk TH, Durand R, van der Giezen M, Gottschal JC, Prins RA, Fèvre M (1996). scsB, a cDNA encoding the hydrogenosomal beta subunit of succinyl-CoA synthetase from the anaerobic fungus Neocallimastix frontalis.
Mol Gen Genet,
253(3), 315-323.
Abstract:
scsB, a cDNA encoding the hydrogenosomal beta subunit of succinyl-CoA synthetase from the anaerobic fungus Neocallimastix frontalis.
A clone containing a Neocallimastix frontalis cDNA assumed to encode the beta subunit of succinyl-CoA synthetase (SCSB) was identified by sequence homology with prokaryotic and eukaryotic counter-parts. An open reading frame of 1311 bp was found. The deduced 437 amino acid sequence showed a high degree of identity to the beta-succinyl-CoA synthetase of Escherichia coli (46%), the mitochondrial beta-succinyl-CoA synthetase from pig (48%) and the hydrogenosomal beta-succinyl-CoA synthetase from Trichomonas vaginalis (49%). The G + C content of the succinyl-CoA synthetase coding sequence (43.8%) was considerably higher than that of the 5' (14.8%) and 3' (13.3%) non-translated flanking sequences, as has been observed for other genes from N. frontalis. The codon usage pattern was biased, with only 34 codons used and a strong preference for a pyrimidine (T) in the third positions of the codons. The coding sequence of the beta-succinyl-CoA synthetase cDNA was cloned in an E. coli expression vector encoding a 6(His) tag. The recombinant protein was purified by affinity binding and used to produce polyclonal antibodies. The anti-succinyl-CoA synthetase serum recognized a 45 kDa protein from a N. frontalis fraction enriched for hydrogenosomes and similar polypeptides in two related anaerobic fungi, Piromyces rhizinflata (45 kDa) and Caecomyces communis (47 kDa). Immunocytochemical experiments suggest that succinyl-CoA synthetase is located in the hydrogenosomal matrix. Staining for SCS activity in native electrophoretic gels revealed a band with an apparent molecular weight of approximately 330 kDa. The C-terminus of the succinyl-CoA synthetase sequence was devoid of the typical targeting signals identified so far in microbody proteins, indicating that N. frontalis uses a different signal for sorting SCSB into hydrogenosomes. Based on comparisons with other proteins we propose a putative N-terminal targeting signal for succinyl-CoA synthetase of N. frontalis that shows some of the features of mitochondrial targeting sequences.
Abstract.
Author URL.
1994
Prins RA, Marvin-Sikkema FD, van der Giezen M, Gottschal JC (1994). Hydrogenosomes of the anaerobic fungus Neocallimastix sp L2. In Prins RA, Stewart CS (Eds.) Micro-organisms in ruminant nutrition, Nottingham, UK: NOTTINGHAM UNIVERSITY PRESS, 179-194.
van der Giezen M, Gottschal JC, Prins RA (1994). The evolutionary origin of hydrogenosomes from anaerobic fungi. In Prins RA, Stewart CS (Eds.) Micro-organisms in ruminant nutrition, Nottingham, UK: NOTTINGHAM UNIVERSITY PRESS, 195-208.
