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Sep 25

New insights into the evolutionary history of Plasmodium falciparum from mitochondrial genome sequence analyses of Indian isolates.

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New insights into the evolutionary history of Plasmodium falciparum from mitochondrial genome sequence analyses of Indian isolates.

Mol Ecol. 2014 Jun;23(12):2975-87

Authors: Tyagi S, Pande V, Das A

Abstract
Estimating genetic diversity and inferring the evolutionary history of Plasmodium falciparum could be helpful in understanding origin and spread of virulent and drug-resistant forms of the malaria pathogen and therefore contribute to malaria control programme. Genetic diversity of the whole mitochondrial (mt) genome of P. falciparum sampled across the major distribution ranges had been reported, but no Indian P. falciparum isolate had been analysed so far, even though India is highly endemic to P. falciparum malaria. We have sequenced the whole mt genome of 44 Indian field isolates and utilized published data set of 96 genome sequences to present global genetic diversity and to revisit the evolutionary history of P. falciparum. Indian P. falciparum presents high genetic diversity with several characteristics of ancestral populations and shares many of the genetic features with African and to some extent Papua New Guinean (PNG) isolates. Similar to African isolates, Indian P. falciparum populations have maintained high effective population size and undergone rapid expansion in the past with oldest time to the most recent common ancestor (TMRCA). Interestingly, one of the four single nucleotide polymorphisms (SNPs) that differentiates P. falciparum from P. falciparum-like isolates (infecting non-human primates in Africa) was found to be segregating in five Indian P. falciparum isolates. This SNP was in tight linkage with other two novel SNPs that were found exclusively in these five Indian isolates. The results on the mt genome sequence analyses of Indian isolates on the whole add to the current understanding on the evolutionary history of P. falciparum.

PMID: 24845521 [PubMed – indexed for MEDLINE]

Sep 24

Connecting alveolate cell biology with trophic ecology in the marine plankton using the ciliate Favella as a model.

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Connecting alveolate cell biology with trophic ecology in the marine plankton using the ciliate Favella as a model.
FEMS Microbiol Ecol. 2014 Jul 19;
Authors: Echevarria ML, Wolfe GV, Strom SL, Tay…

Sep 24

Are Niemann-Pick type C proteins key players in cnidarian-dinoflagellate endosymbioses?

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Are Niemann-Pick type C proteins key players in cnidarian-dinoflagellate endosymbioses?

Mol Ecol. 2014 Sep;23(18):4527-40

Authors: Dani V, Ganot P, Priouzeau F, Furla P, Sabourault C

Abstract
The symbiotic interaction between cnidarians, such as corals and sea anemones, and the unicellular algae Symbiodinium is regulated by yet poorly understood cellular mechanisms, despite the ecological importance of coral reefs. These mechanisms, including host-symbiont recognition and metabolic exchange, control symbiosis stability under normal conditions, but also lead to symbiosis breakdown (bleaching) during stress. This study describes the repertoire of the sterol-trafficking proteins Niemann-Pick type C (NPC1 and NPC2) in the symbiotic sea anemone Anemonia viridis. We found one NPC1 gene in contrast to the two genes (NPC1 and NPC1L1) present in vertebrate genomes. While only one NPC2 gene is present in many metazoans, this gene has been duplicated in cnidarians, and we detected four NPC2 genes in A. viridis. However, only one gene (AvNPC2-d) was upregulated in symbiotic relative to aposymbiotic sea anemones and displayed higher expression in the gastrodermis (symbiont-containing tissue) than in the epidermis. We performed immunolabelling experiments on tentacle cross sections and demonstrated that the AvNPC2-d protein was closely associated with symbiosomes. In addition, AvNPC1 and AvNPC2-d gene expression was strongly downregulated during stress. These data suggest that AvNPC2-d is involved in both the stability and dysfunction of cnidarian-dinoflagellate symbioses.

PMID: 25066219 [PubMed – in process]

Sep 24

Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region.

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Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region.
Mol Ecol. 2014 Sep;23(17):4418-33
Authors: Arif C, Daniels C, Bayer…

Sep 24

A genomic approach to coral-dinoflagellate symbiosis: studies of Acropora digitifera and Symbiodinium minutum.

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A genomic approach to coral-dinoflagellate symbiosis: studies of Acropora digitifera and Symbiodinium minutum.
Front Microbiol. 2014;5:336
Authors: Shinzato C, Mungpakdee S, Satoh N, Shoguchi E
…

Sep 24

Genomic Insights in Processes Driving the Infection of Alexandrium tamarense by the Parasitoid Amoebophrya sp.

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Genomic Insights in Processes Driving the Infection of Alexandrium tamarense by the Parasitoid Amoebophrya sp.

Eukaryot Cell. 2014 Sep 19;

Authors: Lu Y, Wohlrab S, Glöckner G, Guillou L, John U

Abstract
The regulatory circuits during infection of dinoflagellates by their parasites are largely unknown on the molecular level. Here we provide molecular insights into these infection dynamics. Alexandrium tamarense is one of the most prominent Harmful Algal Bloom dinoflagellate. Its pathogen, the dinoflagellate parasitoid Amoebophrya spp., has been observed to infect and control the blooms of this species. We generated a dataset of transcripts from three time points during the infection of this parasite-host system (0, 6 and 96 hours). Assembly of all transcript data from the parasitoid (>900.000 reads/313MBp with 454/Roche NGS) yielded 14,455 contigs, to which we mapped the raw transcript reads of each time point of the infection cycle. We show that particular surface lectins are expressed at the beginning of the infection cycle, which likely mediate the attachment to the host cell. In a later phase signal transduction related genes together with transmembrane transport and cytoskeleton proteins point to a high integration of processes involved in host recognition, adhesion, and invasion. At the final maturation stage, cell division and proliferation related genes were highly expressed, reflecting the fast cell growth and nuclear division of the parasitoid. Our molecular insights in dinoflagellate parasitoid interaction point to general mechanisms also known from other eukaryotic parasites, especially from the Alveolata. These similarities indicate the presence of fundamental processes of parasitoid infection that have remained stable throughout evolution within different phyla.

PMID: 25239978 [PubMed – as supplied by publisher]

Sep 24

Evidence for a hydrogenosomal-type anaerobic ATP generation pathway in Acanthamoeba castellanii.

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Evidence for a hydrogenosomal-type anaerobic ATP generation pathway in Acanthamoeba castellanii.
PLoS One. 2013;8(9):e69532
Authors: Leger MM, Gawryluk RM, Gray MW, Roger AJ
Abstract
…

Sep 24

Defining structural and evolutionary modules in proteins: a community detection approach to explore sub-domain architecture.

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Defining structural and evolutionary modules in proteins: a community detection approach to explore sub-domain architecture.

BMC Struct Biol. 2013;13:20

Authors: Hleap JS, Susko E, Blouin C

Abstract
BACKGROUND: Assessing protein modularity is important to understand protein evolution. Still the question of the existence of a sub-domain modular architecture remains. We propose a graph-theory approach with significance and power testing to identify modules in protein structures. In the first step, clusters are determined by optimizing the partition that maximizes the modularity score. Second, each cluster is tested for significance. Significant clusters are referred to as modules. Evolutionary modules are identified by analyzing homologous structures. Dynamic modules are inferred from sets of snapshots of molecular simulations. We present here a methodology to identify sub-domain architecture robustly, biologically meaningful, and statistically supported.
RESULTS: The robustness of this new method is tested using simulated data with known modularity. Modules are correctly identified even when there is a low correlation between landmarks within a module. We also analyzed the evolutionary modularity of a data set of α-amylase catalytic domain homologs, and the dynamic modularity of the Niemann-Pick C1 (NPC1) protein N-terminal domain.The α-amylase contains an (α/β)8 barrel (TIM barrel) with the polysaccharides cleavage site and a calcium-binding domain. In this data set we identified four robust evolutionary modules, one of which forms the minimal functional TIM barrel topology.The NPC1 protein is involved in the intracellular lipid metabolism coordinating sterol trafficking. NPC1 N-terminus is the first luminal domain which binds to cholesterol and its oxygenated derivatives. Our inferred dynamic modules in the protein NPC1 are also shown to match functional components of the protein related to the NPC1 disease.
CONCLUSIONS: A domain compartmentalization can be found and described in correlation space. To our knowledge, there is no other method attempting to identify sub-domain architecture from the correlation among residues. Most attempts made focus on sequence motifs of protein-protein interactions, binding sites, or sequence conservancy. We were able to describe functional/structural sub-domain architecture related to key residues for starch cleavage, calcium, and chloride binding sites in the α-amylase, and sterol opening-defining modules and disease-related residues in the NPC1. We also described the evolutionary sub-domain architecture of the α-amylase catalytic domain, identifying the already reported minimum functional TIM barrel.

PMID: 24131821 [PubMed – indexed for MEDLINE]

Sep 24

Evolution of the cytosolic iron-sulfur cluster assembly machinery in Blastocystis species and other microbial eukaryotes.

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Evolution of the cytosolic iron-sulfur cluster assembly machinery in Blastocystis species and other microbial eukaryotes.
Eukaryot Cell. 2014 Jan;13(1):143-53
Authors: Tsaousis AD, Gentekaki E, Em…

Sep 24

Being Aquifex aeolicus: Untangling a hyperthermophile's checkered past.

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Being Aquifex aeolicus: Untangling a hyperthermophile’s checkered past.
Genome Biol Evol. 2013;5(12):2478-97
Authors: Eveleigh RJ, Meehan CJ, Archibald JM, Beiko RG
Abstract
Latera…