Fred R. Opperdoes

Fred R. Opperdoes
Université Catholique de Louvain - UCLouvain | UCLouvain · Duve Institute

Doctor of Philosophy

About

426
Publications
74,177
Reads
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17,772
Citations
Citations since 2017
32 Research Items
3222 Citations
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20172018201920202021202220230100200300400500600
20172018201920202021202220230100200300400500600
Introduction
Fred Opperdoes is emeritus professor since 2010. He has been working in the field of parasite biochemistry, drug target identification, target validation and drug development. He has been teaching general biochemistry, microbial biochemistry, parasitology, bioinformatics and phylogeny. At present his main interests are in the fields of bioinformatics, genome analysis and the prediction of biochemical pathways in organisms for which the genome sequence has become available.
Additional affiliations
August 1978 - present
Université Catholique de Louvain - UCLouvain
Position
  • Professor (Full)
Description
  • Has lectured in: parasitology, general biochemistry, microbial biochemistry, structure and function of proteins, bioinformatics and phylogenetic analysis using protein sequences
August 1978 - March 2020
Université Catholique de Louvain - UCLouvain
Position
  • Professor Emeritus
March 1972 - present
University of Amsterdam
Position
  • PhD student and Post-doctoral fellow
Description
  • PhD student in the Laboratory of Piet Borst Thesis: Energy-related metabolism in trypanosomes
Education
October 1964 - January 1972
University of Amsterdam
Field of study
  • Chemistry, Biochemistry (major ), Synthetic organic chemistry (minor)

Publications

Publications (426)
Article
Full-text available
Leishmaniasis is a parasitic vector-borne disease caused by the protistan flagellates of the genus Leishmania . Leishmania (Viannia) guyanensis is one of the most common causative agents of the American tegumentary leishmaniasis. It has previously been shown that L . guyanensis strains that carry the endosymbiotic Leishmania RNA virus 1 (LRV1) caus...
Article
Full-text available
ABSTRACT The closest relative of human pathogen Leishmania, the trypanosomatid Novymonas esmeraldas, harbors a bacterial endosymbiont “Candidatus Pandoraea novy- monadis.” Based on genomic data, we performed a detailed characterization of the metabolic interactions of both partners. While in many respects the metabolism of N. esmeraldas resembles t...
Article
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While numerous genomes of Leishmania spp. have been sequenced and analyzed, an understanding of the evolutionary history of these organisms remains limited due to the unavailability of the sequence data for their closest known relatives, Endotrypanum and Porcisia spp., infecting sloths and porcupines. We have sequenced and analyzed genomes of three...
Article
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A recently redescribed two-flagellar trypanosomatid Vickermania ingenoplastis is insensitive to the classical inhibitors of respiration and thrives under anaerobic conditions. Using genomic and transcriptomic data, we analyzed its genes of the core metabolism and documented that subunits of the mitochondrial respiratory complexes III and IV are abl...
Article
Full-text available
Background: The Euglenozoa are a protist group with an especially rich history of evolutionary diversity. They include diplonemids, representing arguably the most species-rich clade of marine planktonic eukaryotes; trypanosomatids, which are notorious parasites of medical and veterinary importance; and free-living euglenids. These different lifest...
Experiment Findings
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Presentation describing the theory and practice of phylogenetic analysis based upon protein sequences
Article
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Background: Trypanosomatids of the genus Leishmania are parasites of mammals or reptiles transmitted by bloodsucking dipterans. Many species of these flagellates cause important human diseases with clinical symptoms ranging from skin sores to life-threatening damage of visceral organs. The genus Leishmania contains four subgenera: Leishmania, Saur...
Presentation
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Demonstration of the analysis of the TriTryp genomes
Article
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Unicellular flagellates of the family Trypanosomatidae are obligatory parasites of invertebrates, vertebrates and plants. Dixenous species are aetiological agents of a number of diseases in humans, domestic animals and plants. Their monoxenous relatives are restricted to insects. Because of the high biological diversity, adaptability to dramaticall...
Data
N. gruberi NEG-M trophozoites recorded immediately after addition of 1 mM KCN + 1.5 mM SHAM
Data
N. gruberi NEG-M trophozoites after 24 hour exposure to 1 mM KCN. All movies were recorded at 20 s per frame, played back at 29 frames per second. The bar in the bottom right represents 200 μm.
Data
Table S2. Identified Protein Sequences and Their Accession Numbers of Enzymes Involved in a Number of Metabolic Pathways of, Respectively, Naegleria gruberi and N. fowleri, Related to Figure 2 Identified protein sequences and their accession numbers of enzymes involved in a number of pathways of respectively Naegleria gruberi and N. fowleri. N. gr...
Data
This archive contains the tables to build arelational annotation database with 13 kinetoplastid species used for the following paper: Opperdoes FR, Butenko A, Flegontov P, Yurchenko V, Lukeš J. Comparative Metabolism of Free-living Bodo saltans and Parasitic Trypanosomatids. J Eukaryot Microbiol. 2016 Sep;63(5):657-78. doi: 10.1111/jeu.12315. Epub...
Method
Full-text available
A method to compare the presence of genes involved in core metabolism in any of 13 kinetoplastid genomes as available in 2015. Description of how the relational database was prepared. File with database tables are available in the file Tables.zip
Article
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Naegleria gruberi is a free-living non-pathogenic amoeboflagellate and relative of Naegleria fowleri, a deadly pathogen causing primary amoebic meningoencephalitis (PAM). A genomic analysis of N. gruberi exists, but physiological evidence for its core energy metabolism or in vivo growth substrates is lacking. Here, we show that N. gruberi trophozoi...
Preprint
Full-text available
De afkomst van de Amsterdamse Opperdoezen is onduidelijk. In de Gouden Eeuw waren de Opperdoezen alom aanwezig en speelden een belangrijke rol in West-Friesland en vooral in de toen nog belangrijke havenstad Hoorn, waar zij gedurende drie generaties burgemeesters leverden. De Opperdoezen uit Medemblik, Hoorn, Barsingerhorn en Purmerend waren tegen...
Preprint
Full-text available
Naegleria gruberi is a free-living non-pathogenic amoeboflagellate and relative of Naegleria fowleri, a deadly pathogen causing primary amoebic meningoencephalitis (PAM). A genomic analysis of N. gruberi exists, but physiological evidence for its core energy metabolism or in vivo growth substrates is lacking. Here we show that N. gruberi trophozoit...
Chapter
Full-text available
In addition to nucleotide sequences, protein sequences are frequently used for the analysis of the evolutionary relationships of taxa and they are often preferred for the construction of phylogenetic trees. In this state of the art chapter published in the Phylogenetic Handbook (Ph. Lemey, M. Salemy and A-M. Vandamme, eds, Cambridge Press, 2009), t...
Presentation
Full-text available
Memorial address (slides and text) by Fred Opperdoes on the occasion of the the first Christian de Duve memorial lecture. Also an obituary is availble: Opperdoes F (2013) A Feeling for the Cell: Christian de Duve (1917–2013). PLoS Biol 11(10): e1001671. doi:10.1371/journal.pbio.1001671
Presentation
Full-text available
Lecture in honour of C. de Duve, by Fred Opperdoes, November 2013
Book
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Organized and sponsored by the Nencki Institute of Experimental Biology in Warsaw, with the assistance of the Committee on Cell Biology, Polish Academy of Sciences (Member of ECBO) and the Protozoological Section of the Polish Zoological Society on behalf of the International Commission of Protozoology.
Article
Full-text available
Background: Leptomonas pyrrhocoris is a parasite of the firebug Pyrrhocoris apterus. This flagellate has been recently proposed as a model species for studying different aspects of the biology of monoxenous trypanosomatids, including host - parasite interactions. During its life cycle L. pyrrhocoris never tightly attaches to the epithelium of the...
Article
Mammalian hibernation is characterized by metabolic rate depression and a strong decrease in core body temperature. Brown adipose tissue (BAT), a thermogenic tissue that uses uncoupled mitochondrial respiration to generate heat instead of ATP, plays a major role in rewarming from deep torpor. In the present study we developed a label-free LC-MS str...
Article
Full-text available
Vilyuisk human encephalitis virus (VHEV) is a picornavirus related to Theiler's murine encephalomyelitis virus (TMEV). VHEV was isolated from human material passaged in mice. Whether this VHEV is of human or mouse origin is therefore unclear. We took advantage of the species-specific activity of the nonstructural L* protein of theiloviruses to trac...
Article
Full-text available
In the present work, we investigated molecular mechanisms governing thermal resistance of a monoxenous trypanosomatid Crithidia luciliae thermophila, which we reclassified as a separate species C. thermophila. We analyzed morphology, growth kinetics, and transcriptomic profiles of flagellates cultivated at low (23°C) and elevated (34°C) temperature...
Data
Genes up- or down-regulated at elevated temperature in Crithidia thermophila. Annotation and orthologs IDs are provided when available. (XLSX)
Article
Full-text available
Many high-quality genomes are available for dixenous (two hosts) trypanosomatid species of the genera Trypanosoma, Leishmania, and Phytomonas, but only fragmentary information is available for monoxenous (single-host) trypanosomatids. In trypanosomatids, monoxeny is ancestral to dixeny, thus it is anticipated that the genome sequences of the key mo...
Article
Full-text available
Comparison of the genomes of free-living Bodo saltans and those of parasitic trypanosomatids reveals that the transition from a free-living to a parasitic life style has resulted in the loss of approximately 50% of protein-coding genes. Despite this dramatic reduction in genome size, B. saltans and trypanosomatids still share a significant number o...
Article
Full-text available
The co-infection cases involving dixenous Leishmania spp. (mostly of the L. donovani complex) and presumably monoxenous trypanosomatids in immunocompromised mammalian hosts including humans are well documented. The main opportunistic parasite has been identified as Leptomonas seymouri of the sub-family Leishmaniinae. The molecular mechanisms allowi...
Presentation
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Invited lecture given at the university of Granada, Spain
Article
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Although protein S (PROS1) and growth arrest-specific protein 6 (GAS6) proteins are homologous with a high degree of structural similarity, they are functionally different. The objectives of this study were to identify the evolutionary origins from which these functional differences arose. Bioinformatics methods were used to estimate the evolutiona...
Article
Full-text available
The metabolic network of a cell represents the catabolic and anabolic reactions that interconvert small molecules (metabolites) through the activity of enzymes, transporters and non-catalyzed chemical reactions. Our understanding of individual metabolic networks is increasing as we learn more about the enzymes that are active in particular cells un...
Presentation
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These teaching materials are meant for students and professional working in the field of molecular biology, genomics, virology and parasitology and interested in familiarizing themselves with some basic knowledge of phylogeny
Article
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Members of the family Trypanosomatidae infect many organisms, including animals, plants and humans. Plant-infecting trypanosomes are grouped under the single genus Phytomonas, failing to reflect the wide biological and pathological diversity of these protists. While some Phytomonas spp. multiply in the latex of plants, or in fruit or seeds without...
Article
Full-text available
Christian de Duve was an internationally renowned cell biologist whose serendipitous observation while investigating the workings of insulin led to groundbreaking insights into the organization of the cell. The observation, which he once described as “essentially irrelevant to the object of our research,” ultimately led him to discover two organell...
Presentation
Full-text available
Overview of the activities of 45 meetings of the series of Microsymposia on Glycosomes and other Biochemical and Molecular Aspects of Trypanosomes.
Article
Antimonial (sodium stibogluconate, SSG) resistance and differentiation have been shown to be closely linked in Leishmania donovani, with SSG-resistant strains showing an increased capacity to generate infectious (metacyclic) forms. This is the first untargeted LC-MS metabolomics study which integrated both phenomena in one experimental design and p...
Article
Les trypanosomatides sont responsables de maladies redoutables, tres repandues dans les pays tropicaux, dont les traitements actuels sont peu efficaces et dangereux. La recherche visant a la mise au point de nouveaux medicaments s'appuie sur une propriete tres particuliere du trypanosome: toute sa fourniture d'energie repose sur la glycolyse, qui a...
Presentation
Full-text available
A presentation about the genome of Phytomonas given at the French genome centre Genoscope in Ivry, Paris 2012
Presentation
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Lecture given on the 8th of June, 2012 by Fred Opperdoes at a scientific event organized to celebrate the retirement of Paul Michels and Fred Opperdoes
Poster
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Kinetoplastid parasites are completely dependent on purine salvage and scavenging of host purines due to the lack of a de novo biosynthetic pathway. Adenylosuccinate lyase (ASL), as the only enzyme of the pathway, has been retained because it is essential in purine salvage as well. Many of the salvaging enzymes, together with other enzymes of nucle...
Article
Full-text available
The completion of the genome project for Naegleria gruberi provides a unique insight into the metabolic capacities of an organism, for which there is an almost complete lack of experimental data. The metabolism of Naegleria seems to be extremely versatile, as can be expected for a free-living amoeboflagellate, but although considered to be fully ae...
Article
Full-text available
An amoeba was isolated from a soil sample collected at the edge of a fumarole of the volcano Ceboruco in the state of Nayarit, Mexico. The trophozoites of this new isolate have eruptive pseudopodes and do not transform into flagellates. The strain forms cysts that have a double wall. This thermophilic amoeba grows at temperatures up to 50 degrees C...
Article
Comparative studies showed that, like Trypanosoma cruzi, Trypanosoma brucei exhibits functional cytosolic and mitochondrial malic enzymes (MEs), which are specifically linked to NADP. Kinetic studies provided evidence that T. cruzi and T. brucei MEs display similarly high affinities towards NADP(+) and are also almost equally efficient in catalyzin...
Chapter
Full-text available
Glycosomes are the microbodies of the Kinetoplastida. They belong to the family of peroxisomes present in almost all eukaryotic cells. Glycosomes share the same machinery for their biosynthesis and several metabolic pathways with the microbodies of other organisms. However, glycosomes contain in addition the enzymes of glycolysis and glycerol metab...
Article
Full-text available
An amoeba strain was isolated from marine sediment taken from the beach near a fumarole in Italy. The trophozoites of this new marine species transforms into flagellates with variable numbers of flagella, from 2 to 10. The strain forms round to oval cysts. This thermophilic amoeboflagellate grows at temperatures up to 54°C. Molecular phylogenetic a...
Article
Full-text available
The purpose of the present work was to determine the identity of the enzymes that synthesize N-acetylaspartylglutamate (NAAG), the most abundant dipeptide present in vertebrate central nervous system (CNS), and β-citrylglutamate, a structural analogue of NAAG present in testis and immature brain. Previous evidence suggests that NAAG is not synthesi...
Presentation
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Technical course presented at the 16th International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiologyon with specific emphasis on the methods of molecular phylogeny using protein sequences
Presentation
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This seminar was presented in preparation of a manuscript that has not been finalized
Presentation
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Accession codes of over 700 protein sequences, all of metabolic enzymes from the L. major genome project, were collected and the corresponding sequences retrieved. These sequences were used to search for the presence of orthologous protein-encoding genes in the L. tarentolae genome (BlastP, best hit, < 1e-50). Except for one sequence (subunit VIII...
Article
Full-text available
Our goal was to identify the reaction catalyzed by NAT8 (N-acetyltransferase 8), a putative N-acetyltransferase homologous to the enzyme (NAT8L) that produces N-acetylaspartate in brain. The almost exclusive expression of NAT8 in kidney and liver and its predicted association with the endoplasmic reticulum suggested that it was cysteinyl-S-conjugat...
Method
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Course (in English) on protein function and structure and how to use protein sequences for phylogenetic reconstruction
Article
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Mammalian GKRP [GK (glucokinase) regulatory protein], a fructose 6-phosphate and fructose 1-phosphate sensitive inhibitor of GK, appears to have resulted from the duplication of a gene similar to bacterial N-acetylmuramate 6-phosphate etherase MurQ. In the present study, we show that several genomes of primitive eukaryotes encode a GKRP-like protei...
Presentation
Full-text available
Presentation given at a meeting of the Belgian Society of Protozoology that took place in Antwerp in 2009
Article
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Two amoeba strains were isolated from marine sediment taken at the same place with 18 months interval from a region of the sea floor heated by extended submarine hot springs and fumaroles. These thermophilic amoebae grow at temperatures up to 50 degrees C. Sequences of the internal transcribed spacer demonstrated that the two strains belong to the...
Article
Full-text available
The presence of complex I, or NADH dehydrogenase, in Trypanosomatidae is debated. Several subunits of complex I have been identified by biochemical studies, but the overall composition of the complex has remained elusive. Here, the authors review the present literature related to this mitochondrial activity and carry out a bioinformatic analysis to...
Article
Full-text available
Three genes encoding putative aspartate aminotransferases (ASATs) were identified in the Trypanosoma cruzi genome. Two of these ASAT genes, presumably corresponding to a cytosolic and mitochondrial isoform, were cloned and expressed as soluble His-tagged proteins in Escherichia coli. The specific activities determined for both T. cruzi isozymes wer...
Article
Label-free semi-quantitative differential three-dimensional liquid chromatography coupled to mass spectrometry (3D-LC-MS/MS) was used to compare the glycosomal and mitochondrial proteomes of the bloodstream- and insect-form of Trypanosoma brucei. The abundance of glycosomal marker proteins identified in the two life-cycle stages corresponded well w...
Presentation
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This presentation describes the striking resemblances between trypanosomatids and yeast with respect to their possibility to survive and thrive while their mitochondrial metabolism has been switched off, either as the result of environmental changes or by mutations or deletions in their mitochondrial DNA.
Chapter
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The development of new anti-Leishmania compounds and the study of the mode of action of existing drugs has long been hampered by the difficulties of obtaining sufficient numbers of intracellular amastigotes or to culture in the laboratory well-defined parasites representative of intracellular amastigote stages. Most of the early studies have been c...
Article
Full-text available
To survive extremely different environments, intracellular parasites require highly adaptable physiological and metabolic systems. Leishmania donovani extracellular promastigotes reside in a glucose-rich, slightly alkaline environment in the sand fly vector alimentary tract. On entry into human macrophage phagolysosomes, promastigotes differentiate...
Article
Full-text available
The development of new anti-Leishmania compounds and the study of the mode of action of existing drugs has long been hampered by the difficulties of obtaining sufficient numbers of intracellular amastigotes or to culture in the laboratory well-defined parasites representative of intracellular amastigote stages. Most of the early studies have been c...
Article
Full-text available
Trypanosomes harbour a large number of structural and biochemical peculiarities. Kinetoplast DNA, mitochondrial RNA editing, the sequestration of glycolysis inside glycosomes and unique oxidative-stress protection mechanisms (to name but a few) are found only in the members of the order Kinetoplastida. Thus, it is not surprising that they have prov...
Presentation
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An overview of African sleeping sickness, South American trypanosomiasis, or Chagas' disease, and Leishmaniasis , the drugs available for treatment and potential drug targets
Article
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Fractionation of an antitrypanosomal lipophilic leaf extract from Strychnos spinosa led to the isolation of eight triterpenoids and sterols in this plant part for the first time. Two of these were found to possess in vitro antitrypanosomal activity, namely, saringosterol (14) and 24-hydroperoxy-24-vinylcholesterol (15), with IC(50) values of 7.8 +/...
Article
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The energy metabolism was compared among four different representatives of the genus Phytomonas isolated from different plants and localities: the sieve tubes of the hartrot-infected coconut palm in French Guyana, the latex fluid of Euphorbia hyssopifolia in French Guyana and the fruits of tomato and cherimoya in Spain. All four isolates produced a...
Article
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We describe the in vitro culture of Phytomonas species isolated from Euphorbia characias. The best choice between tested media was SDM-79, in which promastigotes, after 6 days of culture, reached cell densities as high as 4 × 107 cells/ml. Cells growing in LIT or MTL medium showed longer division times and lower cell densities. We succeeded in obta...