Causes and effects of loss of classical non-homologous end joining pathway in parasitic eukaryotes

We report frequent losses of components of the classical nonhomologous end joining pathway (C-NHEJ), one of the main eukaryotic tools for end joining repair of DNA double-strand breaks, in several lineages of parasitic protists. Moreover, we have identified a single lineage among trypanosomatid flagellates that has lost Ku70 and Ku80, the core C-NHEJ components, and accumulated numerous insertions in many protein-coding genes. We propose a correlation between these two phenomena and discuss the possible impact of the C-NHEJ loss on genome evolution and transition to the parasitic lifestyle

Genome of Ca. Pandoraea novymonadis, an Endosymbiotic Bacterium of the Trypanosomatid Novymonas esmeraldas

We have sequenced, annotated, and analyzed the genome of Ca. Pandoraea novymonadis, a recently described bacterial endosymbiont of the trypanosomatid Novymonas esmeraldas. When compared with genomes of its free-living relatives, it has all the hallmarks of the endosymbionts’ genomes, such as significantly reduced size, extensive gene loss, low GC content, numerous gene rearrangements, and low codon usage bias. In addition, Ca. P. novymonadis lacks mobile elements, has a strikingly low number of pseudogenes, and almost all genes are single copied. This suggests that it already passed the intensive period of host adaptation, which still can be observed in the genome of Polynucleobacter necessarius, a certainly recent endosymbiont. Phylogenetically, Ca. P. novymonadis is more related to P. necessarius, an intracytoplasmic bacterium of free-living ciliates, than to Ca. Kinetoplastibacterium spp., the only other known endosymbionts of trypanosomatid flagellates. As judged by the extent of the overall genome reduction and the loss of particular metabolic abilities correlating with the increasing dependence of the symbiont on its host, Ca. P. novymonadis occupies an intermediate position P. necessarius and Ca. Kinetoplastibacterium spp. We conclude that the relationships between Ca. P. novymonadis and N. esmeraldas are well-established, although not as fine-tuned as in the case of Strigomonadinae and their endosymbionts

Selection of suitable reference genes for gene expression studies in myxosporean (Myxozoa, Cnidaria) parasites

Myxozoans (Cnidaria: Myxozoa) are an extremely diversified group of endoparasites some of which are causative agents of serious diseases in fish. New methods involving gene expression studies have emerged over the last years to better understand and control myxozoan diseases. Quantitative RT-PCR is the most extensively used approach for gene expression studies. However, the accuracy of the results depends on the normalization of the data to reference genes. We studied the expression of eight commonly used reference genes, adenosylhomocysteinase (AHC1), beta actin (ACTB), eukaryotic translation elongation factor 2 (EF2), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), hypoxanthine-guanine phosphoribosyltransferase 1 (HPRT1), DNA-directed RNA polymerase II (RPB2), 18S ribosomal RNA (18S), 28S ribosomal RNA (28S) across different developmental stages of three myxozoan species, Sphaerospora molnari, Myxobolus cerebralis and Ceratonova shasta, representing the three major myxozoan linages from the largest class Myxosporea. The stable reference genes were identified using four algorithms: geNorm, NormFinder, Bestkeeper and ΔCq method. Additionally, we analyzed transcriptomic data from S. molnari proliferative and spore-forming stages to compare the relative amount of expressed transcripts with the most stable reference genes suggested by RT-qPCR. Our results revealed that GAPDH and EF2 are the most uniformly expressed genes across the different developmental stages of the studied myxozoan species.Fil: Kosakyan, Anush. Academy of Sciences of the Czech Republic. Biology Centre. Institute of Parasitology; República ChecaFil: Alama Bermejo, Gema. Universidad Nacional del Comahue. Centro de Investigación Aplicada y Transferencia Tecnológica en Recursos Marinos "Almirante Storni". - Provincia de Río Negro. Ministerio de Agricultura, Ganadería y Pesca. Centro de Investigación Aplicada y Transferencia Tecnológica en Recursos Marinos "Almirante Storni". Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet Centro Nacional Patagónico. Centro de Investigación Aplicada y Transferencia Tecnológica en Recursos Marinos "Almirante Storni"; Argentina. Academy of Sciences of the Czech Republic. Biology Centre. Institute of Parasitology; República Checa. State University of Oregon; Estados UnidosFil: Bartošová-Sojková, Pavla. Academy of Sciences of the Czech Republic. Biology Centre. Institute of Parasitology; República ChecaFil: Born-Torrijos, Ana. Academy of Sciences of the Czech Republic. Biology Centre. Institute of Parasitology; República ChecaFil: Šíma, Radek. Academy of Sciences of the Czech Republic. Biology Centre. Institute of Parasitology; República ChecaFil: Nenarokova, Anna. Academy of Sciences of the Czech Republic. Biology Centre. Institute of Parasitology; República Checa. University of South Bohemia; República ChecaFil: Eszterbauer, Edit. Hungarian Academy Of Sciences; HungríaFil: Bartholomew, Jerri. State University of Oregon; Estados UnidosFil: Holzer, Astrid Sybylle. Academy of Sciences of the Czech Republic. Biology Centre. Institute of Parasitology; República Chec

Schematic representation of carbon source metabolism in the bloodstream form of <i>T</i>. <i>brucei</i>.

<p>Red arrows represent enzymatic steps that were experimentally shown to be active in BSF. Green arrows represent enzymatic steps that might be active in BSF because the enzymes (in green) were identified in BSF proteomic data. Glucose-derived metabolites (acetate, pyruvate, succinate, alanine, aspartate) are on a blue background. NADH molecules are on a pink background. Dashed arrows indicate enzymatic steps for which no experimental proof exists. The glycosomal and mitochondrial compartments are indicated. 2-OGDH, 2-oxoglutarate dehydrogenase; AAC, ADP/ATP carrier; AAT, amino acid transporter; ACH, acetyl-CoA thioesterase; AKCT, 2-amino-3-ketobutyrate coenzyme A ligase; Ala TR, alanine transaminase; AOX, alternative oxidase; ASCT, acetate:succinate CoA-transferase; Asp TR, aspartate transaminase; BSF, bloodstream form; cI, complex I (NADH:ubiquinone oxidoreductase); cII, complex II (succinate dehydrogenase); cIII, complex III (cytochrome bc1 complex); cIV, complex IV (cytochrome c oxidase); cV, complex V (F_oF₁ ATPase); cyt, cytosolic; DHAP, dihydroxyacetone phosphate; FH, fumarate hydratase (i.e., fumarase); FR, fumarate reductase; G3P, glyceraldehyde 3-phosphate; GluDH, glutamate dehydrogenase; gly, glycosomal; Gly3P, glycerol 3-phosphate; Gly-3-PDH, glycerol-3-phosphate dehydrogenase; m, mitochondrial; MDH, malate dehydrogenase; PDH, pyruvate dehydrogenase; PEP, phosphoenolpyruvate; PEPCK, phosphoenolpyruvate carboxykinase; PiC, phosphate carrier; ProDH, proline dehydrogenase.</p

A paradigm shift: The mitoproteomes of procyclic and bloodstream <i>Trypanosoma brucei</i> are comparably complex

A paradigm shift: The mitoproteomes of procyclic and bloodstream <i>Trypanosoma brucei</i> are comparably comple