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Genomic perspectives on the birth and spread of plastids.
Proc Natl Acad Sci U S A. 2015 Apr 20;
Authors: Archibald JM
Abstract
The endosymbiotic origin of plastids from cyanobacteri…
April 2015 archive
Apr 24
Genomic perspectives on the birth and spread of plastids.
Apr 23
Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate.
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Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate.
Proc Natl Acad Sci U S A. 2015 Apr 20;
Authors: Gornik SG, Febrimarsa, Cassin AM, MacRae JI, Ramaprasad A, …
Apr 20
Intra-genomic variation in symbiotic dinoflagellates: recent divergence or recombination between lineages?
Intra-genomic variation in symbiotic dinoflagellates: recent divergence or recombination between lineages?
BMC Evol Biol. 2015;15(1):46
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: 25887753 [PubMed – as supplied by publisher]
Apr 19
Eukaryogenesis, how special really?
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Eukaryogenesis, how special really?
Proc Natl Acad Sci U S A. 2015 Apr 16;
Authors: Booth A, Doolittle WF
Abstract
Eukaryogenesis is widely viewed as an improbable evolutionary trans…
Apr 17
Bayesian long branch attraction bias and corrections.
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Bayesian long branch attraction bias and corrections.
Syst Biol. 2015 Mar;64(2):243-55
Authors: Susko E
Abstract
Previous work on the star-tree paradox has shown that Bayesian metho…
Apr 08
DNA repair mechanisms and their biological roles in the malaria parasite Plasmodium falciparum.
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DNA repair mechanisms and their biological roles in the malaria parasite Plasmodium falciparum.
Microbiol Mol Biol Rev. 2014 Sep;78(3):469-86
Authors: Lee AH, Symington LS, Fidock DA
Abstra…
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
…
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]
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