Category: Papers by CGEB labs

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PLoS One. 2015;10(6):e0128773
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Bayesian long branch attraction bias and corrections.
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A large number of nuclear genes in the human parasite blastocystis require mRNA polyadenylation to create functional termination codons.

Genome Biol Evol. 2014 Aug;6(8):1956-61

Authors: Klimeš V, Gentekaki E, Roger AJ, Eliáš M

Abstract
Termination codons in mRNA molecules are typically specified directly by the sequence of the corresponding gene. However, in mitochondria of a few eukaryotic groups, some mRNAs contain the termination codon UAA deriving one or both adenosines from transcript polyadenylation. Here, we show that a similar phenomenon occurs for a substantial number of nuclear genes in Blastocystis spp., divergent unicellular eukaryote gut parasites. Our analyses of published genomic data from Blastocystis sp. subtype 7 revealed that polyadenylation-mediated creation of termination codons occurs in approximately 15% of all nuclear genes. As this phenomenon has not been noticed before, the procedure previously employed to annotate the Blastocystis nuclear genome sequence failed to correctly define the structure of the 3′-ends of hundreds of genes. From sequence data we have obtained from the distantly related Blastocystis sp. subtype 1 strain, we show that this phenomenon is widespread within the Blastocystis genus. Polyadenylation in Blastocystis appears to be directed by a conserved GU-rich element located four nucleotides downstream of the polyadenylation site. Thus, the highly precise positioning of the polyadenylation in Blastocystis has allowed reduction of the 3′-untranslated regions to the point that, in many genes, only one or two nucleotides of the termination codon are left.

PMID: 25015079 [PubMed – indexed for MEDLINE]

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On the age of eukaryotes: evaluating evidence from fossils and molecular clocks.
Cold Spring Harb Perspect Biol. 2014 Aug;6(8)
Authors: Eme L, Sharpe SC, Brown MW, Roger AJ
Abstract
…

An ancestral bacterial division system is widespread in eukaryotic mitochondria.

Proc Natl Acad Sci U S A. 2015 Mar 23;

Authors: Leger MM, Petrů M, Žárský V, Eme L, Vlček Č, Harding T, Lang BF, Eliáš M, Doležal P, Roger AJ

Abstract
Bacterial division initiates at the site of a contractile Z-ring composed of polymerized FtsZ. The location of the Z-ring in the cell is controlled by a system of three mutually antagonistic proteins, MinC, MinD, and MinE. Plastid division is also known to be dependent on homologs of these proteins, derived from the ancestral cyanobacterial endosymbiont that gave rise to plastids. In contrast, the mitochondria of model systems such as Saccharomyces cerevisiae, mammals, and Arabidopsis thaliana seem to have replaced the ancestral α-proteobacterial Min-based division machinery with host-derived dynamin-related proteins that form outer contractile rings. Here, we show that the mitochondrial division system of these model organisms is the exception, rather than the rule, for eukaryotes. We describe endosymbiont-derived, bacterial-like division systems comprising FtsZ and Min proteins in diverse less-studied eukaryote protistan lineages, including jakobid and heterolobosean excavates, a malawimonad, stramenopiles, amoebozoans, a breviate, and an apusomonad. For two of these taxa, the amoebozoan Dictyostelium purpureum and the jakobid Andalucia incarcerata, we confirm a mitochondrial localization of these proteins by their heterologous expression in Saccharomyces cerevisiae. The discovery of a proteobacterial-like division system in mitochondria of diverse eukaryotic lineages suggests that it was the ancestral feature of all eukaryotic mitochondria and has been supplanted by a host-derived system multiple times in distinct eukaryote lineages.

PMID: 25831547 [PubMed – as supplied by publisher]

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Ultrastructure and molecular phylogenetic position of Neometanema parovale sp. nov. (Neometanema gen. nov.), a Marine phagotrophic euglenid with skidding motility.

Protist. 2014 Aug;165(4):452-72

Authors: Lee WJ, Simpson AG

Abstract
Heteronema is a commonly encountered genus of phagotrophic euglenids that contains very different morphotypes, including elongate gliding species and ovoid skidding forms. We report the first ultrastructural and sequence data from a culture of an ovoid skidding heteronemid, KM051. Cells were 8-23.5 μm long with 22 pellicular strips and a fibrous extracellular layer. The tubular extrusomes had dense centre sections. The feeding apparatus was barely visible by light microscopy, but included two microtubule-supported rods. The flagella had hollow, inflated transition zones, heteromorphic paraxonemal rods, and sheaths of flagellar hairs. The posterior flagellum bore a knob that, unusually, sat >2 μm distal to the flagellar base. No ultrastructural features were uniquely shared by KM051 and the elongate, gliding species Heteronema scaphurum. Conversely, the pellicular microtubule array resembles that in deep-branching primary osmotrophs (Aphagea). 18S ribosomal DNA (18S rDNA) phylogenies showed that KM051 is related to a recently obtained Heteronema c.f. exaratum sequence. These skidding heteronemids are not closely related to H. scaphurum, and instead are closely related to Dinema, Anisonema and specifically, Aphagea. The skidding species in Heteronema are transferred to Neometanema gen. nov. (along with most species of Metanema Klebs, 1893), with KM051 described as Neometanema parovale sp. nov.

PMID: 24945929 [PubMed – indexed for MEDLINE]

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Creneis carolina gen. et sp. nov. (Heterolobosea), a novel marine anaerobic protist with strikingly derived morphology and life cycle.

Protist. 2014 Aug;165(4):542-67

Authors: Pánek T, Simpson AG, Hampl V, Cepička I

Abstract
We report the light-microscopic morphology and ultrastructure of a novel free-living, heterotrophic protist, Creneis carolina gen. et sp. nov. isolated from marine anoxic sediments. C. carolina is a heterotrophic, obligately anaerobic amoeboid flagellate, and superficially resembles Mastigamoeba (Amoebozoa: Archamoebae) or Breviata (Breviatea) by possessing a single anterior flagellum closely associated with the nucleus, and because it appears to be an anaerobe. However, its life cycle contains multiflagellate cells with an unusual morphology. The structure of the mastigont of C. carolina is unique and not readily comparable with any eukaryotic group. Unexpectedly, phylogenetic analyses of SSU rDNA and of a concatenate of α- and β-tubulin genes with SSU rDNA convincingly showed that C. carolina is a member of Heterolobosea and belongs to the taxon Tetramitia.

PMID: 24999602 [PubMed – indexed for MEDLINE]