September 2014 archive

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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
…

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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]

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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…

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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…

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Supertrees Based on the Subtree Prune-and-Regraft Distance.
Syst Biol. 2014 Jul;63(4):566-81
Authors: Whidden C, Zeh N, Beiko RG
Abstract
Supertree methods reconcile a set of phylo…

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Compositional complexity of the mitochondrial proteome of a unicellular eukaryote (Acanthamoeba castellanii, supergroup Amoebozoa) rivals that of animals, fungi, and plants.
J Proteomics. 2014 Jul 12;109C:4…

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Alignment Errors Strongly Impact Likelihood-Based Tests for Comparing Topologies.
Mol Biol Evol. 2014 Aug 1;
Authors: Levy Karin E, Susko E, Pupko T
Abstract
Estimating phylogenetic …

Characterisation of Tulamoeba bucina n. sp., an Extremely Halotolerant Amoeboflagellate Heterolobosean Belonging to the Tulamoeba-Pleurostomum Clade (Tulamoebidae n. fam.).

J Eukaryot Microbiol. 2014 Sep 17;

Authors: Kirby WA, Tikhonenkov DV, Mylnikov AP, Janouškovec J, Lax G, Simpson AG

Abstract
Most protozoans that have been cultivated recently from high salinity waters appear to be obligate halophiles. Phylogenetic analyses indicate that these species mostly represent independent lineages. Here we report the cultivation, morphological characterisation, and phylogenetic analysis of two strains (XLG1 and HLM-8) of a new extremely halotolerant heterolobosean amoeboflagellate. This species is closely related to the obligate halophiles Tulamoeba peronaphora and Pleurostomum flabellatum, and more specifically to the former. Like Tulamoeba, the new species has a monopodial limax amoeba stage, however, its cyst stage lacks an intrusive pore plug. The flagellate stage bears a combination of a planar spiral feeding apparatus and unequal heterodynamic flagella, which discriminate it from described Pleurostomum species. Strain XLG1 grows at salinities from 35‰ to 225‰. This degree of halotolerance is uncommon in protozoa, as most species showing growth in seawater are unable to grow at 200‰ salinity. The unrelatedness of most halophilic protozoa suggested that independent colonization of the hypersaline environment is more common than speciation within it. However, this study supports the idea that the Tulamoeba-Pleurostomum clade underwent an adaptive radiation within the hypersaline environment. A new species Tulamoeba bucina n. sp. is described, with Tulamoebidae n. fam. proposed for the Tulamoeba-Pleurostomum clade. This article is protected by copyright. All rights reserved.

PMID: 25227416 [PubMed – as supplied by publisher]

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Seasonal assemblages and short-lived blooms in coastal northwest Atlantic Ocean bacterioplankton.
Environ Microbiol. 2014 Sep 22;
Authors: El-Swais H, Dunn KA, Bielawski JP, Li WK, Walsh DA
…