Proteomic Properties Reveal Phyloecological Clusters of Archaea 英文参考文献.docVIP

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Proteomic Properties Reveal Phyloecological Clusters of Archaea 英文参考文献.doc

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Proteomic Properties Reveal Phyloecological Clusters of Archaea 英文参考文献

ProteomicPropertiesRevealPhyloecologicalClustersof Archaea NelaNikolic1,2,3,ZlatkoSmole1,4,AnitaKrisko1* 1Mediterranean Institute for Life Sciences, Split, Croatia, 2Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zurich, Switzerland, 3Department of EnvironmentalMicrobiology,Eawag,Duebendorf,Switzerland,4InstituteofCellBiology,ETHZurich,Zurich,Switzerland Abstract Inthisstudy,weproposeanovelwaytodescribethevarietyofenvironmentaladaptationsofArchaea.Wehaveclustered 57Archaeabyusinganon-redundantsetofproteomicfeatures,andverifiedthattheclusterscorrespondtoenvironmental adaptationstothearchaealhabitats.Thefirstclusterconsistsdominantlyofhyperthermophilesandhyperthermoacidophilic aerobes. The second cluster joins together halophilic and extremely halophilic Archaea, while the third cluster contains mesophilic (mostly methanogenic) Archaea together with thermoacidophiles. The non-redundant subset of proteomic featureswasfoundtoconsistoffivefeatures:theratioofchargedresiduestouncharged,averageproteinsize,normalized frequencyofbeta-sheet,normalizedfrequencyofextendedstructureandnumberofhydrogenbonddonors.Wepropose this clustering to be termed phyloecological clustering. This approach could give additional insights into relationships amongarchaealspeciesthatmaybehiddenbysolephylogeneticanalysis. Citation: Nikolic N, Smole Z, Krisko A (2012) Proteomic Properties Reveal Phyloecological Clusters of Archaea. PLoS ONE 7(10): e48231. doi:10.1371/ journal.pone.0048231 Editor:VasilisJ.Promponas,UniversityofCyprus,Cyprus ReceivedOctober26,2011;AcceptedSeptember28,2012;PublishedOctober25,2012 Copyright: ? 2012 Nikolic et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:NelaNikolicwasfundedbyUnityThroughKnowledge‘‘Gainingexperience’’Grant,number2Aforher3-monthstayatTheSwissFederalInsti