Category: Papers by CGEB labs

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Getting “function” right.
Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3365
Authors: Brunet TD, Doolittle WF
PMID: 25107292 [PubMed – indexed for MEDLINE]

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Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome.

Int J Syst Evol Microbiol. 2014 Sep;64(Pt 9):3254-63

Authors: Hahn MW, Schmidt J, Taipale SJ, Doolittle WF, Koll U

Abstract
A pure culture of an actinobacterium previously described as ‘Candidatus Rhodoluna lacicola’ strain MWH-Ta8 was established and deposited in two public culture collections. Strain MWH-Ta8(T) represents a free-living planktonic freshwater bacterium obtained from hypertrophic Meiliang Bay, Lake Taihu, PR China. The strain was characterized by phylogenetic and taxonomic investigations, as well as by determination of its complete genome sequence. Strain MWH-Ta8(T) is noticeable due to its unusually low values of cell size (0.05 µm(3)), genome size (1.43 Mbp), and DNA G+C content (51.5 mol%). Phylogenetic analyses based on 16S rRNA gene and RpoB sequences suggested that strain MWH-Ta8(T) is affiliated with the family Microbacteriaceae with Pontimonas salivibrio being its closest relative among the currently described species within this family. Strain MWH-Ta8(T) and the type strain of Pontimonas salivibrio shared a 16S rRNA gene sequence similarity of 94.3 %. The cell-wall peptidoglycan of strain MWH-Ta8(T) was of type B2β (B10), containing 2,4-diaminobutyric acid as the diamino acid. The predominant cellular fatty acids were anteiso-C15 : 0 (36.5 %), iso-C16 : 0 (16.5 %), iso-C15 : 0 (15.6 %) and iso-C14 : 0 (8.9 %), and the major (>10 %) menaquinones were MK-11 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The combined phylogenetic, phenotypic and chemotaxonomic data clearly suggest that strain MWH-Ta8(T) represents a novel species of a new genus in the family Microbacteriaceae, for which the name Rhodoluna lacicola gen. nov., sp. nov. is proposed. The type strain of the type species is MWH-Ta8(T) ( = DSM 23834(T) = LMG 26932(T)).

PMID: 24984700 [PubMed – indexed for MEDLINE]

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A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria.
Genome Biol Evol. 2014 Mar;6(3):703-13
Authors: Meehan CJ, Beiko RG
…

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Reduced nuclear genomes maintain high gene transcription levels.
Mol Biol Evol. 2014 Mar;31(3):625-35
Authors: Tanifuji G, Onodera NT, Moore CE, Archibald JM
Abstract
Reductive geno…

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Mitochondrial tRNA 5′-editing in Dictyostelium discoideum and Polysphondylium pallidum.
J Biol Chem. 2014 May 30;289(22):15155-65
Authors: Abad MG, Long Y, Kinchen RD, Schindel ET, Gray MW, Jackman…

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Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle.
Proc Natl Acad Sci U S A. 2014 Aug 5;111(31):11407-12
Authors: Nakayama T…

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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…