Author's posts
Apr 08
A large number of nuclear genes in the human parasite blastocystis require mRNA polyadenylation to create functional termination codons.
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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]
Apr 05
Plastid genome-based phylogeny pinpointed the origin of the green-colored plastid in the dinoflagellate Lepidodinium chlorophorum.
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Plastid genome-based phylogeny pinpointed the origin of the green-colored plastid in the dinoflagellate Lepidodinium chlorophorum.
Genome Biol Evol. 2015 Apr 2;
Authors: Kamikawa R, Tanifuji G, Kawa…
Apr 04
On the age of eukaryotes: evaluating evidence from fossils and molecular clocks.
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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
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Apr 02
An ancestral bacterial division system is widespread in eukaryotic mitochondria.
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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]
Apr 01
An orthology-based analysis of pathogenic protozoa impacting global health: an improved comparative genomics approach with prokaryotes and model eukaryote orthologs.
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An orthology-based analysis of pathogenic protozoa impacting global health: an improved comparative genomics approach with prokaryotes and model eukaryote orthologs.
OMICS. 2014 Aug;18(8):524-38
Authors: Cuadrat RR, da Serra Cruz SM, Tschoeke DA, Silva E, Tosta F, Jucá H, Jardim R, Campos ML, Mattoso M, Dávila AM
Abstract
A key focus in 21(st) century integrative biology and drug discovery for neglected tropical and other diseases has been the use of BLAST-based computational methods for identification of orthologous groups in pathogenic organisms to discern orthologs, with a view to evaluate similarities and differences among species, and thus allow the transfer of annotation from known/curated proteins to new/non-annotated ones. We used here a profile-based sensitive methodology to identify distant homologs, coupled to the NCBI’s COG (Unicellular orthologs) and KOG (Eukaryote orthologs), permitting us to perform comparative genomics analyses on five protozoan genomes. OrthoSearch was used in five protozoan proteomes showing that 3901 and 7473 orthologs can be identified by comparison with COG and KOG proteomes, respectively. The core protozoa proteome inferred was 418 Protozoa-COG orthologous groups and 704 Protozoa-KOG orthologous groups: (i) 31.58% (132/418) belongs to the category J (translation, ribosomal structure, and biogenesis), and 9.81% (41/418) to the category O (post-translational modification, protein turnover, chaperones) using COG; (ii) 21.45% (151/704) belongs to the categories J, and 13.92% (98/704) to the O using KOG. The phylogenomic analysis showed four well-supported clades for Eukarya, discriminating Multicellular [(i) human, fly, plant and worm] and Unicellular [(ii) yeast, (iii) fungi, and (iv) protozoa] species. These encouraging results attest to the usefulness of the profile-based methodology for comparative genomics to accelerate semi-automatic re-annotation, especially of the protozoan proteomes. This approach may also lend itself for applications in global health, for example, in the case of novel drug target discovery against pathogenic organisms previously considered difficult to research with traditional drug discovery tools.
PMID: 24960463 [PubMed – indexed for MEDLINE]
Apr 01
A population genetic model for the initial spread of partially resistant malaria parasites under anti-malarial combination therapy and weak intrahost competition.
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A population genetic model for the initial spread of partially resistant malaria parasites under anti-malarial combination therapy and weak intrahost competition.
PLoS One. 2014;9(7):e101601
Author…
Mar 31
Ultrastructure and molecular phylogenetic position of Neometanema parovale sp. nov. (Neometanema gen. nov.), a Marine phagotrophic euglenid with skidding motility.
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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]
Mar 31
Creneis carolina gen. et sp. nov. (Heterolobosea), a novel marine anaerobic protist with strikingly derived morphology and life cycle.
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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]
Mar 20
Microbial diversity: a bonanza of phyla.
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Microbial diversity: a bonanza of phyla.
Curr Biol. 2015 Mar 16;25(6):R227-30
Authors: Eme L, Doolittle WF
Abstract
Metagenomics and single-cell genomics are now the gold standard fo…
Mar 19
Intra-genomic variation in symbiotic dinoflagellates: recent divergence or recombination between lineages?
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Intra-genomic variation in symbiotic dinoflagellates: recent divergence or recombination between lineages?
BMC Evol Biol. 2015 Dec;15(1):325
Authors: Wilkinson SP, Fisher PL, van Oppen MJ, Davy SK
Abstract
BACKGROUND: The symbiosis between corals and the dinoflagellate alga Symbiodinium is essential for the development and survival of coral reefs. Yet this fragile association is highly vulnerable to environmental disturbance. A coral’s ability to tolerate temperature stress depends on the fitness of its resident symbionts, whose thermal optima vary extensively between lineages. However, the in hospite population genetic structure of Symbiodinium is poorly understood and mostly based on analysis of bulk DNA extracted from thousands to millions of cells. Using quantitative single-cell PCR, we enumerated DNA polymorphisms in the symbionts of the reef-building coral Pocillopora damicornis, and applied a model selection approach to explore the potential for recombination between coexisting Symbiodinium populations.
RESULTS: Two distinct Symbiodinium ITS2 sequences (denoted C100 and C109) were retrieved from all P. damicornis colonies analysed. However, the symbiont assemblage consisted of three distinct Symbiodinium populations: cells featuring pure arrays of ITS2 type C109, near-homogeneous cells of type C100 (with trace ITS2 copies of type C109), and those with co-dominant C100 and C109 ITS2 repeats. The symbiont consortia of some colonies consisted almost entirely of these putative C100 × C109 recombinants.
CONCLUSIONS: Our results are consistent with the occurrence of sexual recombination between Symbiodinium types C100 and C109. While the multiple-copy nature of the ITS2 dictates that the observed pattern of intra-genomic co-dominance may be a result of incomplete concerted evolution of intra-genomic polymorphisms, this is a less likely explanation given the occurrence of homogeneous cells of the C109 type. Conclusive evidence for inter-lineage recombination and introgression in this genus will require either direct observational evidence or a single-cell genotyping approach targeting multiple, single-copy loci.
PMID: 25776334 [PubMed – in process]
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