Category: Papers by CGEB labs

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Rapid identification of high-confidence taxonomic assignments for metagenomic data.
Nucleic Acids Res. 2012 Aug;40(14):e111
Authors: MacDonald NJ, Parks DH, Beiko RG
Abstract
Determining the…

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Aggregative multicellularity evolved independently in the eukaryotic supergroup Rhizaria.
Curr Biol. 2012 Jun 19;22(12):1123-7
Authors: Brown MW, Kolisko M, Silberman JD, Roger AJ
Abstract
Mu…

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Population genomics: how bacterial species form and why they don’t exist.
Curr Biol. 2012 Jun 5;22(11):R451-3
Authors: Doolittle WF
Abstract
Two processes suggested to drive bacterial speciat…

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Evolutionary origin of RNA editing.
Biochemistry. 2012 Jul 3;51(26):5235-42
Authors: Gray MW
Abstract
The term “RNA editing” encompasses a wide variety of mechanistically and phylogenetically…

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Composition of the mitochondrial electron transport chain in acanthamoeba castellanii: structural and evolutionary insights.

Biochim Biophys Acta. 2012 Nov;1817(11):2027-37

Authors: Gawryluk RM, Chisholm KA, Pinto DM, Gray MW

Abstract
The mitochondrion, derived in evolution from an α-proteobacterial progenitor, plays a key metabolic role in eukaryotes. Mitochondria house the electron transport chain (ETC) that couples oxidation of organic substrates and electron transfer to proton pumping and synthesis of ATP. The ETC comprises several multiprotein enzyme complexes, all of which have counterparts in bacteria. However, mitochondrial ETC assemblies from animals, plants and fungi are generally more complex than their bacterial counterparts, with a number of ‘supernumerary’ subunits appearing early in eukaryotic evolution. Little is known, however, about the ETC of unicellular eukaryotes (protists), which are key to understanding the evolution of mitochondria and the ETC. We present an analysis of the ETC proteome from Acanthamoeba castellanii, an ecologically, medically and evolutionarily important member of Amoebozoa (sister to Opisthokonta). Data obtained from tandem mass spectrometric (MS/MS) analyses of purified mitochondria as well as ETC complexes isolated via blue native polyacrylamide gel electrophoresis are combined with the results of bioinformatic queries of sequence databases. Our bioinformatic analyses have identified most of the ETC subunits found in other eukaryotes, confirming and extending previous observations. The assignment of proteins as ETC subunits by MS/MS provides important insights into the primary structures of ETC proteins and makes possible, through the use of sensitive profile-based similarity searches, the identification of novel constituents of the ETC along with the annotation of highly divergent but phylogenetically conserved ETC subunits.

PMID: 22709906 [PubMed – indexed for MEDLINE]

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Absence of a universal element for tRNAHis identity in Acanthamoeba castellanii.
Nucleic Acids Res. 2012 Dec 14;
Authors: Rao BS, Mohammad F, Gray MW, Jackman JE
Abstract
The additional G(-1) …

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Evolution of Fe/S cluster biogenesis in the anaerobic parasite Blastocystis.
Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10426-31
Authors: Tsaousis AD, Ollagnier de Choudens S, Gentekaki E, Long S, Gaston …

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Human microbiome: a genetic bazaar for microbes?
Curr Biol. 2012 Jan 10;22(1):R20-2
Authors: Langille MG, Meehan CJ, Beiko RG
Abstract
A recent study suggests that lateral gene transfer has b…

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Genome sequence of Shigella flexneri serotype 5a strain M90T Sm.
J Bacteriol. 2012 Jun;194(11):3022
Authors: Onodera NT, Ryu J, Durbic T, Nislow C, Archibald JM, Rohde JR
Abstract
Bacteria of…

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Likelihood-based clustering (LiBaC) for codon models, a method for grouping sites according to similarities in the underlying process of evolution.
Mol Biol Evol. 2008 Sep;25(9):1995-2007
Authors: Bao L, Gu …