201
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Parker JDK, Bradley BA, Mooers AO, Quarmby LM. Phylogenetic analysis of the Neks reveals early diversification of ciliary-cell cycle kinases. PLoS One 2007; 2:e1076. [PMID: 17957258 PMCID: PMC2031824 DOI: 10.1371/journal.pone.0001076] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2007] [Accepted: 10/04/2007] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND NIMA-related kinases (Neks) have been studied in diverse eukaryotes, including the fungus Aspergillus and the ciliate Tetrahymena. In the former, a single Nek plays an essential role in cell cycle regulation; in the latter, which has more than 30 Neks in its genome, multiple Neks regulate ciliary length. Mammalian genomes encode an intermediate number of Neks, several of which are reported to play roles in cell cycle regulation and/or localize to centrosomes. Previously, we reported that organisms with cilia typically have more Neks than organisms without cilia, but were unable to establish the evolutionary history of the gene family. METHODOLOGY/PRINCIPLE FINDINGS We have performed a large-scale analysis of the Nek family using Bayesian techniques, including tests of alternate topologies. We find that the Nek family had already expanded in the last common ancestor of eukaryotes, a ciliated cell which likely expressed at least five Neks. We suggest that Neks played an important role in the common ancestor in regulating cilia, centrioles, and centrosomes with respect to mitotic entry, and that this role continues today in organisms with cilia. Organisms that lack cilia generally show a reduction in the number of Nek clades represented, sometimes associated with lineage specific expansion of a single clade, as has occurred in the plants. CONCLUSION/SIGNIFICANCE This is the first rigorous phylogenetic analysis of a kinase family across a broad array of phyla. Our findings provide a coherent framework for the study of Neks and their roles in coordinating cilia and cell cycle progression.
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Affiliation(s)
- Jeremy D. K. Parker
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Brian A. Bradley
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Arne O. Mooers
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Lynne M. Quarmby
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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202
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Abstract
The yeast putative RNA helicase Mtr4p is implicated in exosome-mediated RNA quality control in the nucleus, interacts with the exosome, and is found in the ‘TRAMP’ complex with a yeast nuclear poly(A) polymerase (Trf4p/Pap2p or Trf5p) and a putative RNA-binding protein, Air1p or Air2p. Depletion of the Trypanosoma brucei MTR4-like protein TbMTR4 caused growth arrest and defects in 5.8S rRNA processing similar to those seen after depletion of the exosome. TbNPAPL, a nuclear protein which is a putative homolog of Trf4p/Pap2p, was required for normal cell growth. Depletion of MTR4 resulted in the accumulation of polyadenylated rRNA precursors, while depletion of TbNPAPL had little effect. These results suggest that polyadenylation-dependent nuclear rRNA quality control is conserved in eukaryotic evolution. In contrast, there was no evidence for a trypanosome TRAMP complex since no stable interactions between TbMTR4 and the exosome, TbNPAPL or RNA-binding proteins were detected.
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Affiliation(s)
- Marina Cristodero
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
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203
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Opperdoes FR, Michels PAM. Horizontal gene transfer in trypanosomatids. Trends Parasitol 2007; 23:470-6. [PMID: 17826337 DOI: 10.1016/j.pt.2007.08.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Revised: 06/27/2007] [Accepted: 08/23/2007] [Indexed: 11/21/2022]
Abstract
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 provoked much speculation about why and how such oddities have evolved in trypanosomes. However, the true reasons for their existence within the eukaryotic world are still far from clear. Here, Fred Opperdoes and Paul Michels argue that the trypanosome-specific evolution of novel processes and organization could only have been made possible by the acquisition of a large number of foreign genes, which entered a trypanosomatid ancestor through lateral gene transfer. Many different organisms must have served as donors. Some of them were viruses, and others were bacteria, such as cyanobacterial endosymbionts and non-phototrophic bacteria.
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Affiliation(s)
- Fred R Opperdoes
- Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Université catholique de Louvain, Avenue Hippocrate 74-75, B-1200 Brussels, Belgium.
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204
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Svobodová M, Zídková L, Čepička I, Oborník M, Lukeš J, Votýpka J. Sergeia podlipaevi gen. nov., sp. nov. (Trypanosomatidae, Kinetoplastida), a parasite of biting midges (Ceratopogonidae, Diptera). Int J Syst Evol Microbiol 2007; 57:423-432. [PMID: 17267991 DOI: 10.1099/ijs.0.64557-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three strains of a trypanosomatid protozoan were isolated from the midguts of two naturally infected species of biting midges [Culicoides (Oecacta) festivipennis and Culicoides (Oecacta) truncorum] and characterized by light and electron microscopy and by molecular techniques. Morphological characteristics and sequences of the 18S rRNA, 5S rRNA, spliced leader RNA and glycosomal glyceraldehyde-3-phosphate dehydrogenase genes indicate that the studied flagellates represent a novel phylogenetic lineage within the Trypanosomatidae. Based on phylogenetic analyses, the novel endosymbiont-free, monoxenous trypanosomatid was classified as Sergeia podlipaevi gen. nov., sp. nov. Interestingly, it is closely related to another trypanosomatid species that parasitizes the sand fly Lutzomyia evansi, a blood-sucking dipteran from South America. The type strain of S. podlipaevi sp. nov., ICUL/CZ/2000/CER3, was obtained from Malpighian tubes. Of 2518 females of seven species of biting midges trapped in the Czech Republic, more than 1.5 % were infected by trypanosomatid parasites. An unrelated insect species, Culicoides (Monoculicoides) nubeculosus, was experimentally infected with S. podlipaevi, demonstrating that its host range extends to different subgenera of biting midges.
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MESH Headings
- Animals
- Ceratopogonidae/cytology
- Ceratopogonidae/parasitology
- Ceratopogonidae/ultrastructure
- DNA, Kinetoplast/analysis
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Gastrointestinal Tract/parasitology
- Genes, rRNA
- Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating)/genetics
- Microscopy, Electron
- Molecular Sequence Data
- Phylogeny
- RNA, Protozoan/genetics
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 5S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Trypanosomatina/classification
- Trypanosomatina/cytology
- Trypanosomatina/genetics
- Trypanosomatina/isolation & purification
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Affiliation(s)
- Milena Svobodová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lenka Zídková
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Miroslav Oborník
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Faculty of Biology, University of South Bohemia, České Budějovice (Budweis), Czech Republic
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Jan Votýpka
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
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205
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Poinar G. Early Cretaceous trypanosomatids associated with fossil sand fly larvae in Burmese amber. Mem Inst Oswaldo Cruz 2007; 102:635-7. [PMID: 17710310 DOI: 10.1590/s0074-02762007005000070] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Accepted: 06/13/2007] [Indexed: 11/22/2022] Open
Abstract
Early Cretaceous flagellates with characters typical of trypanosomatids were found in the gut of sand fly larvae, as well as in surrounding debris, in Burmese amber. This discovery supports a hypothesis in which free-living trypanosomatids could have been acquired by sand fly larvae in their feeding environment and then carried transtadially into the adult stage. At some point in time, specific genera were introduced into vertebrates, thus establishing a dixenous life cycle.
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Affiliation(s)
- George Poinar
- Department of Zoology, Oregon State University, Corvallis, OR, 97331, USA.
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206
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Annoura T, Sariego I, Nara T, Makiuchi T, Fujimura T, Taka H, Mineki R, Murayama K, Aoki T. Dihydroorotate dehydrogenase arises from novel fused gene product with aspartate carbamoyltransferase in Bodo saliens. Biochem Biophys Res Commun 2007; 358:253-8. [PMID: 17475213 DOI: 10.1016/j.bbrc.2007.04.102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 04/17/2007] [Indexed: 11/22/2022]
Abstract
The ACT-DHOD gene in the kinetoplastid Bodo saliens encodes aspartate carbamoyltransferase and dihydroorotate dehydrogenase, the second and fourth enzymes of pyrimidine biosynthesis. Although the single mRNA species yielded a 70-kDa ACT-DHOD protein, Western blotting with anti-DHOD-peptide antibody showed a major band of 35-kDa and minor bands. In-gel digestion and liquid chromatography-tandem mass (MS/MS) spectrometry showed that the 35-kDa band contained DHOD-specific polypeptides and an ACT-specific polypeptide, suggesting the occurrence of independent DHOD and ACT. Immunoprecipitation and MS/MS analysis identified a 70-kDa ACT-DHOD and a 35-kDa DHOD independently, and the N-terminal amino acid of 35-kDa DHOD was blocked. In vitro processing assay showed that recombinant ACT-DHOD was decreased by the B. saliens lysate, accompanying the appearance of 35-kDa DHOD and 35-kDa ACT. These results indicate that fused ACT-DHOD is the precursor to mature DHOD. Large amount of 35-kDa DHOD in B. saliens is discussed from a viewpoint of its physiological roles.
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Affiliation(s)
- Takeshi Annoura
- Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
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207
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Ferreira RC, Campaner M, Viola LB, Takata CSA, Takeda GF, Teixeira MMG. Morphological and molecular diversity and phylogenetic relationships among anuran trypanosomes from the Amazonia, Atlantic Forest and Pantanal biomes in Brazil. Parasitology 2007; 134:1623-38. [PMID: 17577425 DOI: 10.1017/s0031182007003058] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
SUMMARYWe examined for the presence of trypanosomes in blood samples from 259 anurans (47 species from 8 families), the majority of which were from the Brazilian Amazonia, Atlantic Forest and Pantanal biomes. Trypanosomes were detected by a combination of microhaematocrit and haemoculture methods in 45% of the anurans, and 87 cultures were obtained: 44 from Hylidae, 22 from Leptodactylidae, 15 from Bufonidae, 5 from Leiuperidae and 1 from an unidentified anuran. High morphological diversity (11 morphotypes) was observed among blood trypanosomes from anurans of different species and of the same species as well as among trypanosomes from the same individual. Conversely, morphologically similar trypanosomes were found in anurans from distinct species and biomes. ITS and SSU rDNA polymorphisms revealed high diversity among the 82 isolates examined.† Twenty-nine genotypes could be distinguished, the majority distributed in 11 groups. Phylogenetic relationships based on rDNA sequences indicated that isolates from more phylogenetically related anurans are more closely related. Comparison of anuran trypanosomes from Brazil and other countries revealed several new species among the isolates examined in this study. Phylogenetic relationships suggest that host restriction, host switching and overall ecogeographical structure may have played a role in the evolution of the anuran trypanosomes.
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Affiliation(s)
- R C Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, 05508-900, Brazil
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208
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Lukeš J, Mauricio IL, Schönian G, Dujardin JC, Soteriadou K, Dedet JP, Kuhls K, Tintaya KWQ, Jirků M, Chocholová E, Haralambous C, Pratlong F, Oborník M, Horák A, Ayala FJ, Miles MA. Evolutionary and geographical history of the Leishmania donovani complex with a revision of current taxonomy. Proc Natl Acad Sci U S A 2007; 104:9375-80. [PMID: 17517634 PMCID: PMC1890502 DOI: 10.1073/pnas.0703678104] [Citation(s) in RCA: 291] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Indexed: 11/18/2022] Open
Abstract
Leishmaniasis is a geographically widespread severe disease, with an increasing incidence of two million cases per year and 350 million people from 88 countries at risk. The causative agents are species of Leishmania, a protozoan flagellate. Visceral leishmaniasis, the most severe form of the disease, lethal if untreated, is caused by species of the Leishmania donovani complex. These species are morphologically indistinguishable but have been identified by molecular methods, predominantly multilocus enzyme electrophoresis. We have conducted a multifactorial genetic analysis that includes DNA sequences of protein-coding genes as well as noncoding segments, microsatellites, restriction-fragment length polymorphisms, and randomly amplified polymorphic DNAs, for a total of approximately 18,000 characters for each of 25 geographically representative strains. Genotype is strongly correlated with geographical (continental) origin, but not with current taxonomy or clinical outcome. We propose a new taxonomy, in which Leishmania infantum and L. donovani are the only recognized species of the L. donovani complex, and we present an evolutionary hypothesis for the origin and dispersal of the species. The genus Leishmania may have originated in South America, but diversified after migration into Asia. L. donovani and L. infantum diverged approximately 1 Mya, with further divergence of infraspecific genetic groups between 0.4 and 0.8 Mya. The prevailing mode of reproduction is clonal, but there is evidence of genetic exchange between strains, particularly in Africa.
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Affiliation(s)
- Julius Lukeš
- *Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and
- Faculty of Biology, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Isabel L. Mauricio
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Gabriele Schönian
- Institute of Microbiology and Hygiene, Charité University Medicine, D-10117 Berlin, Germany
| | - Jean-Claude Dujardin
- Department of Molecular Parasitology, Institute of Tropical Medicine, B-2000 Antwerpen, Belgium
| | - Ketty Soteriadou
- Molecular Parasitology Laboratory, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Jean-Pierre Dedet
- **Laboratoire de Parasitologie, Université Montpellier 1, 34090 Montpellier, France; and
| | - Katrin Kuhls
- Institute of Microbiology and Hygiene, Charité University Medicine, D-10117 Berlin, Germany
| | | | - Milan Jirků
- *Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and
| | - Eva Chocholová
- *Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and
| | - Christos Haralambous
- Molecular Parasitology Laboratory, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Francine Pratlong
- **Laboratoire de Parasitologie, Université Montpellier 1, 34090 Montpellier, France; and
| | - Miroslav Oborník
- *Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and
- Faculty of Biology, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Aleš Horák
- *Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and
| | - Francisco J. Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697
| | - Michael A. Miles
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
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209
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Coimbra VC, Yamamoto D, Khusal KG, Atayde VD, Fernandes MC, Mortara RA, Yoshida N, Alves MJM, Rabinovitch M. Enucleated L929 cells support invasion, differentiation, and multiplication of Trypanosoma cruzi parasites. Infect Immun 2007; 75:3700-6. [PMID: 17502387 PMCID: PMC1951981 DOI: 10.1128/iai.00194-07] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Cell infection with Trypanosoma cruzi, the agent of Chagas' disease, begins with the uptake of infective trypomastigotes within phagosomes and their release into the cytosol, where they transform into replicating amastigotes; the latter, in turn, differentiate into cytolytically released and infective trypomastigotes. We ask here if the T. cruzi infection program can develop in enucleated host cells. Monolayers of L929 cells, enucleated by centrifugation in the presence of cytochalasin B and kept at 34 degrees C to extend the survival of cytoplasts, were infected with parasites of the CL strain. Percent infection, morphology, stage-specific markers, and numbers of parasites per cell were evaluated in nucleated and enucleated cells, both of which were present in the same preparations. Parasite uptake, differentiation and multiplication of amastigotes, development of epimastigote- and trypomastigote-like forms, and initial cytolytic release of parasites were all documented for cytoplasts and nucleated cells. Although the doubling times were similar, parasite loads at 48 and 72 h were significantly lower in the cytoplasts than in nucleated cells. Similar results were obtained with the highly virulent strain Y as well as with strains CL-14 and G, which exhibit low virulence for mice. Cytoplasts could also be infected with the CL strain 24 or 48 h after enucleation. Thus, infection of cells by T. cruzi can take place in enucleated host cells, i.e., in the absence of modulation of chromosomal and nucleolar gene transcription and of RNA modification and processing in the nucleus.
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Affiliation(s)
- Vanessa C Coimbra
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Escola Paulista de Medicina, Rua Botucatu 862, 6th Andar, São Paulo, SP 04023-062, Brazil
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210
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Lee SH, Stephens JL, Englund PT. A fatty-acid synthesis mechanism specialized for parasitism. Nat Rev Microbiol 2007; 5:287-97. [PMID: 17363967 DOI: 10.1038/nrmicro1617] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Most cells use either a type I or type II synthase to make fatty acids. Trypanosoma brucei, the sleeping sickness parasite, provides the first example of a third mechanism for this process. Trypanosomes use microsomal elongases to synthesize fatty acids de novo, whereas other cells use elongases to make long-chain fatty acids even longer. The modular nature of the pathway allows synthesis of different fatty-acid end products, which have important roles in trypanosome biology. Indeed, this newly discovered mechanism seems ideally suited for the parasitic lifestyle.
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Affiliation(s)
- Soo Hee Lee
- Department of Biological Chemistry, Johns Hopkins School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, USA
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211
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Genest PA, ter Riet B, Cijsouw T, van Luenen HG, Borst P. Telomeric localization of the modified DNA base J in the genome of the protozoan parasite Leishmania. Nucleic Acids Res 2007; 35:2116-24. [PMID: 17329373 PMCID: PMC1874636 DOI: 10.1093/nar/gkm050] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Base J or β-d-glucosylhydroxymethyluracil is a DNA modification replacing a fraction of thymine in the nuclear DNA of kinetoplastid parasites and of Euglena. J is located in the telomeric sequences of Trypanosoma brucei and in other simple repeat DNA sequences. In addition, J was found in the inactive variant surface glycoprotein (VSG) expression sites, but not in the active expression site of T. brucei, suggesting that J could play a role in transcription silencing in T. brucei. We have now looked at the distribution of J in the genomes of other kinetoplastid parasites. First, we analyzed the DNA sequences immunoprecipitated with a J-antiserum in Leishmania major Friedlin. Second, we investigated the co-migration of J- and telomeric repeat-containing DNA sequences of various kinetoplastids using J-immunoblots and Southern blots of fragmented DNA. We find only ∼1% of J outside the telomeric repeat sequences of Leishmania sp. and Crithidia fasciculata, in contrast to the substantial fraction of non-telomeric J found in T. brucei, Trypanosoma equiperdum and Trypanoplasma borreli. Our results suggest that J is a telomeric base modification, recruited for other (unknown) functions in some kinetoplastids and Euglena.
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Affiliation(s)
| | | | | | | | - Piet Borst
- *To whom Correspondence should be addressed. +31 20 512 2880+31 20 669 1383
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212
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Breglia SA, Slamovits CH, Leander BS. Phylogeny of Phagotrophic Euglenids (Euglenozoa) as Inferred from Hsp90 Gene Sequences. J Eukaryot Microbiol 2007; 54:86-92. [PMID: 17300525 DOI: 10.1111/j.1550-7408.2006.00233.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Molecular phylogenies of euglenids are usually based on ribosomal RNA genes that do not resolve the branching order among the deeper lineages. We addressed deep euglenid phylogeny using the cytosolic form of the heat-shock protein 90 gene (hsp90), which has already been employed with some success in other groups of euglenozoans and eukaryotes in general. Hsp90 sequences were generated from three taxa of euglenids representing different degrees of ultrastructural complexity, namely Petalomonas cantuscygni and wild isolates of Entosiphon sulcatum, and Peranema trichophorum. The hsp90 gene sequence of P. trichophorum contained three short introns (ranging from 27 to 31 bp), two of which had non-canonical borders GG-GG and GG-TG and two 10-bp inverted repeats, suggesting a structure similar to that of the non-canonical introns described in Euglena gracilis. Phylogenetic analyses confirmed a closer relationship between kinetoplastids and diplonemids than to euglenids, and supported previous views regarding the branching order among primarily bacteriovorous, primarily eukaryovorous, and photosynthetic euglenids. The position of P. cantuscygni within Euglenozoa, as well as the relative support for the nodes including it were strongly dependent on outgroup selection. The results were most consistent when the jakobid Reclinomonas americana was used as the outgroup. The most robust phylogenies place P. cantuscygni as the most basal branch within the euglenid clade. However, the presence of a kinetoplast-like mitochondrial inclusion in P. cantuscygni deviates from the currently accepted apomorphy-based definition of the kinetoplastid clade and highlights the necessity of detailed studies addressing the molecular nature of the euglenid and diplonemid mitochondrial genome.
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Affiliation(s)
- Susana A Breglia
- Program in Evolutionary Biology, Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
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213
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Waki K, Dutta S, Ray D, Kolli BK, Akman L, Kawazu SI, Lin CP, Chang KP. Transmembrane molecules for phylogenetic analyses of pathogenic protists: Leishmania-specific informative sites in hydrophilic loops of trans- endoplasmic reticulum N-acetylglucosamine-1-phosphate transferase. EUKARYOTIC CELL 2006; 6:198-210. [PMID: 17142569 PMCID: PMC1797956 DOI: 10.1128/ec.00282-06] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A sequence database was created for the Leishmania N-acetylglucosamine-1-phosphate transferase (nagt) gene from 193 independent isolates. PCR products of this single-copy gene were analyzed for restriction fragment length polymorphism based on seven nagt sequences initially available. We subsequently sequenced 77 samples and found 19 new variants (genotypes). Alignment of all 26 nagt sequences is gap free, except for a single codon addition or deletion. Phylogenetic analyses of the sequences allow grouping the isolates into three subgenera, each consisting of recognized species complexes, i.e., subgenus Leishmania (L. amazonensis-L. mexicana, L. donovani-L. infantum, L. tropica, L. major, and L. turanica-L. gerbilli), subgenus Viannia (L. braziliensis, L. panamensis), and one unclassified (L. enriettii) species. This hierarchy of grouping is also supported by sequence analyses of selected samples for additional single-copy genes present on different chromosomes. Intraspecies divergence of nagt varies considerably with different species complexes. Interestingly, species complexes with less subspecies divergence are more widely distributed than those that are more divergent. The relevance of this to Leishmania evolutionary adaptation is discussed. Heterozygosity of subspecies variants contributes to intraspecies diversity, which is prominent in L. tropica but not in L. donovani-L. infantum. This disparity is thought to result from the genetic recombination of the respective species at different times as a rare event during their predominantly clonal evolution. Phylogenetically useful sites of nagt are restricted largely to several extended hydrophilic loops predicted from hypothetical models of Leishmania NAGT as an endoplasmic reticulum transmembrane protein. In silico analyses of nagt from fungi and other protozoa further illustrate the potential value of this and, perhaps, other similar transmembrane molecules for phylogenetic analyses of single-cell eukaryotes.
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Affiliation(s)
- Kayoko Waki
- Department of Microbiology/Immunology, Chicago Medical School, Rosalind Franklin University, North Chicago, IL 60064, USA
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214
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Cruickshank RH, Paterson AM. The great escape: do parasites break Dollo's law? Trends Parasitol 2006; 22:509-15. [PMID: 16971179 DOI: 10.1016/j.pt.2006.08.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Revised: 08/03/2006] [Accepted: 08/30/2006] [Indexed: 11/17/2022]
Abstract
A long-held assumption in evolutionary studies is that a character that changes from a complex to a simple state is unlikely to return to the same complex state. The extreme version of this assumption has been codified as Dollo's law. Unfortunately, this paradigm has supported the idea that simple and complex traits are qualitatively different, when it is more sensible to suggest that there is a quantitative difference. Dollo's law has been the predominant paradigm in parasitology, where a move from a free-living state to parasitism has been considered a unidirectional pathway or 'one-way trip' because organisms lose the structures required to return to the free-living state. Several recent studies have suggested that complex structures can be regained from simple traits, and we suggest that this is also possible for parasites.
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Affiliation(s)
- Robert H Cruickshank
- Bio-Protection and Ecology Division, Lincoln University, PO Box 84, Lincoln, Canterbury 7647, New Zealand
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215
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Besteiro S, Coombs GH, Mottram JC. The SNARE protein family of Leishmania major. BMC Genomics 2006; 7:250. [PMID: 17026746 PMCID: PMC1626469 DOI: 10.1186/1471-2164-7-250] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Accepted: 10/06/2006] [Indexed: 11/21/2022] Open
Abstract
Background Leishmania major is a protozoan parasite with a highly polarised cell shape that depends upon endocytosis and exocytosis from a single area of the plasma membrane, the flagellar pocket. SNAREs (soluble N-ethylmaleimide-sensitive factor adaptor proteins receptors) are key components of the intracellular vesicle-mediated transports that take place in all eukaryotic cells. They are membrane-bound proteins that facilitate the docking and fusion of vesicles with organelles. The recent availability of the genome sequence of L. major has allowed us to assess the complement of SNAREs in the parasite and to investigate their location in comparison with metazoans. Results Bioinformatic searches of the L. major genome revealed a total of 27 SNARE domain-containing proteins that could be classified in structural groups by phylogenetic analysis. 25 of these possessed the expected features of functional SNAREs, whereas the other two could represent kinetoplastid-specific proteins that might act as regulators of the SNARE complexes. Other differences of Leishmania SNAREs were the absence of double SNARE domain-containing and of the brevin classes of these proteins. Members of the Qa group of Leishmania SNAREs showed differential expressions profiles in the two main parasite forms whereas their GFP-tagging and in vivo expression revealed localisations in the Golgi, late endosome/lysosome and near the flagellar pocket. Conclusion The early-branching eukaryote L. major apparently possess a SNARE repertoire that equals in number the one of metazoans such as Drosophila, showing that the machinery for vesicle fusion is well conserved throughout the eukaryotes. However, the analysis revealed the absence of certain types of SNAREs found in metazoans and yeast, while suggesting the presence of original SNAREs as well as others with unusual localisation. This study also presented the intracellular localisation of the L. major SNAREs from the Qa group and reveals that these proteins could be useful as organelle markers in this parasitic protozoon.
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Affiliation(s)
- Sébastien Besteiro
- Wellcome Centre for Molecular Parasitology and Division of Infection & Immunity, Institute of Biomedical and Life Sciences, University of Glasgow, G12 8TA, UK
| | - Graham H Coombs
- Wellcome Centre for Molecular Parasitology and Division of Infection & Immunity, Institute of Biomedical and Life Sciences, University of Glasgow, G12 8TA, UK
| | - Jeremy C Mottram
- Wellcome Centre for Molecular Parasitology and Division of Infection & Immunity, Institute of Biomedical and Life Sciences, University of Glasgow, G12 8TA, UK
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216
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Schumacher MA, Karamooz E, Zíková A, Trantírek L, Lukes J. Crystal structures of T. brucei MRP1/MRP2 guide-RNA binding complex reveal RNA matchmaking mechanism. Cell 2006; 126:701-11. [PMID: 16923390 DOI: 10.1016/j.cell.2006.06.047] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Revised: 05/19/2006] [Accepted: 06/23/2006] [Indexed: 11/19/2022]
Abstract
The mitochondrial RNA binding proteins MRP1 and MRP2 form a heteromeric complex that functions in kinetoplastid RNA editing. In this process, MRP1/MRP2 serves as a matchmaker by binding to guide RNAs and facilitating their hybridization with cognate preedited mRNAs. To understand the mechanism by which this complex performs RNA matchmaking, we determined structures of Trypanosoma brucei apoMRP1/MRP2 and an MRP1/MRP2-gRNA complex. The structures show that MRP1/MRP2 is a heterotetramer and, despite little sequence homology, each MRP subunit exhibits the same "Whirly" transcription-factor fold. The gRNA molecule binds to the highly basic beta sheet surface of the MRP complex via nonspecific, electrostatic contacts. Strikingly, while the gRNA stem/loop II base is anchored to the basic surface, stem/loop I (the anchor sequence) is unfolded and its bases exposed to solvent. Thus, MRP1/MRP2 acts as an RNA matchmaker by stabilizing the RNA molecule in an unfolded conformation suitable for RNA-RNA hybridization.
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MESH Headings
- Amino Acid Sequence
- Animals
- Crystallography, X-Ray
- Mitochondrial Proteins/chemistry
- Mitochondrial Proteins/genetics
- Mitochondrial Proteins/metabolism
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Binding
- Protein Folding
- Protein Structure, Quaternary
- Protein Structure, Secondary
- Protozoan Proteins/chemistry
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
- RNA, Guide, Kinetoplastida/chemistry
- RNA, Guide, Kinetoplastida/genetics
- RNA, Guide, Kinetoplastida/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Sequence Alignment
- Trypanosoma brucei brucei/chemistry
- Trypanosoma brucei brucei/metabolism
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry and Molecular Biology, University of Texas, M.D. Anderson Cancer Center, Unit 1000, Houston, 77030, USA.
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217
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Michels PAM, Bringaud F, Herman M, Hannaert V. Metabolic functions of glycosomes in trypanosomatids. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:1463-77. [PMID: 17023066 DOI: 10.1016/j.bbamcr.2006.08.019] [Citation(s) in RCA: 232] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2006] [Revised: 08/17/2006] [Accepted: 08/18/2006] [Indexed: 11/25/2022]
Abstract
Protozoan Kinetoplastida, including the pathogenic trypanosomatids of the genera Trypanosoma and Leishmania, compartmentalize several important metabolic systems in their peroxisomes which are designated glycosomes. The enzymatic content of these organelles may vary considerably during the life-cycle of most trypanosomatid parasites which often are transmitted between their mammalian hosts by insects. The glycosomes of the Trypanosoma brucei form living in the mammalian bloodstream display the highest level of specialization; 90% of their protein content is made up of glycolytic enzymes. The compartmentation of glycolysis in these organelles appears essential for the regulation of this process and enables the cells to overcome short periods of anaerobiosis. Glycosomes of all other trypanosomatid forms studied contain an extended glycolytic pathway catalyzing the aerobic fermentation of glucose to succinate. In addition, these organelles contain enzymes for several other processes such as the pentose-phosphate pathway, beta-oxidation of fatty acids, purine salvage, and biosynthetic pathways for pyrimidines, ether-lipids and squalenes. The enzymatic content of glycosomes is rapidly changed during differentiation of mammalian bloodstream-form trypanosomes to the forms living in the insect midgut. Autophagy appears to play an important role in trypanosomatid differentiation, and several lines of evidence indicate that it is then also involved in the degradation of old glycosomes, while a population of new organelles containing different enzymes is synthesized. The compartmentation of environment-sensitive parts of the metabolic network within glycosomes would, through this way of organelle renewal, enable the parasites to adapt rapidly and efficiently to the new conditions.
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Affiliation(s)
- Paul A M Michels
- Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Université catholique de Louvain, ICP-TROP 74.39, Avenue Hippocrate 74, B-1200 Brussels, Belgium.
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218
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Yurchenko VY, Lukes J, Jirku M, Zeledón R, Maslov DA. Leptomonas costaricensis sp. n. (Kinetoplastea: Trypanosomatidae), a member of the novel phylogenetic group of insect trypanosomatids closely related to the genus Leishmania. Parasitology 2006; 133:537-46. [PMID: 16834819 DOI: 10.1017/s0031182006000746] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2006] [Revised: 03/21/2006] [Accepted: 05/17/2006] [Indexed: 11/06/2022]
Abstract
A flagellate isolated from the intestinal tract of a reduviid bug Ricolla simillima (Heteroptera) in Costa Rica was found to represent a new trypanosomatid species by the phylogenetic analysis of small subunit ribosomal RNA (SSU rRNA), glyceraldehyde phosphate dehydrogenase (GAPDH) and large subunit of RNA polymerase II (RPOIILS) genes. The phylogenetic position of this trypanosomatid, together with its typical promastigote morphology and the host identity, allowed its classification as a species that belongs to the polyphyletic genus Leptomonas. Interestingly, the new species was revealed as a member of the novel phylogenetic clade representing the closest known relative of Leishmania. With the new species used as an outgroup to root the Leishmania RPOIILS phylogenetic tree, the lineage of the Neotropical species L. enriettii was found to branch off early, and was followed by a deep split between the Old World and the remaining New World species. This tree topology supports the hypothesis that the initial transition to dixenous parasitism in this group pre-dated the continental split and that afterwards the Neotropical and the Old World groups evolved largely independently.
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Affiliation(s)
- V Y Yurchenko
- Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA
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