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Rare Codons Cluster 英文参考文献.doc

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Rare Codons Cluster 英文参考文献

RareCodonsCluster ThomasF.ClarkeIV,PatriciaL.Clark* DepartmentofChemistryBiochemistry,UniversityofNotreDame,NotreDame,Indiana,UnitedStatesofAmerica Abstract Mostaminoacidsareencodedbymorethanonecodon.Thesesynonymouscodonsarenotusedwithequalfrequency:in everyorganism,somecodonsareusedmorecommonly,whileothersaremorerare.Thoughtheencodedproteinsequence is identical, selective pressures favor more common codons for enhanced translation speed and fidelity. However, rare codonspersist,presumablyduetoneutraldrift.Here,wedeterminewhetherother,unknownfactors,beyondneutraldrift, affect theselectionand/or distribution ofrare codons. Wehavedeveloped anovel algorithm thatevaluates therelative rarenessofanucleotidesequenceusedtoproduceagivenproteinsequence.Weshowthatrarecodons,ratherthanbeing randomlyscatteredacrossgenes,oftenoccurinlargeclusters.Theseclustersoccurinnumerouseukaryoticandprokaryotic genomes,andarenotconfinedtounusualorrarelyexpressedgenes:manyhighlyexpressedgenes,includinggenesfor ribosomalproteins,containrarecodonclusters.Ararecodonclustercanimpederibosometranslationoftherarecodon sequence.Theseresultsindicateadditionalselectivepressuresgoverntheuseofsynonymouscodons,andspecificallythat localpausesintranslationcanbebeneficialforproteinbiogenesis. Citation:ClarkeTFIV,ClarkPL(2008)RareCodonsCluster.PLoSONE3(10):e3412.doi:10.1371/journal.pone.0003412 Editor:Dong-YanJin,UniversityofHongKong,China ReceivedSeptember12,2008;AcceptedSeptember19,2008;PublishedOctober15,2008 Copyright: ? 2008 Clarke IV 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:ThisprojectwassupportedbyanawardfromtheNIH(GM74807).TheNIHhadnoroleinstudydesign,datacollectionandanalysis,decisiontopublish, orpreparationofthemanuscript. CompetingInterests:Theauthorshavedeclaredthatnocompetinginterestsexist. *E-mail:pcla