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Association of purine asymmetry, strand-biased gene distribution and PolC within Firmicutes and beyond: a new appraisal

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Title Association of purine asymmetry, strand-biased gene distribution and PolC within Firmicutes and beyond: a new appraisal
 
Creator Saha, Sanjoy Kumar
Goswami, Aranyak
Dutta, Chitra
 
Subject Structural Biology & Bioinformatics
 
Description strands of replication, Strand-biased Gene Distribution (SGD) and presence of two isoforms of DNA polymerase III alpha subunit, PolC and DnaE. Despite considerable research efforts, it is not clear whether the co-existence of PAS, PolC and/or SGD is an essential and exclusive characteristic of the Firmicutes. The nature of
correlations, if any, between these three features within and beyond the lineages of Firmicutes has also remained
elusive. The present study has been designed to address these issues. A large-scale analysis of diverse bacterial genomes indicates that PAS, PolC and SGD are neither essentialnor exclusive features of the Firmicutes. PolC prevails in four bacterial phyla: Firmicutes, Fusobacteria, Tenericutes and Thermotogae, while PAS occurs only in subsets of Firmicutes, Fusobacteria and Tenericutes. There are five major compositional trends in Firmicutes: (I) an explicit PAS or G + A-dominance along the entire leading strand (II) only G-dominance in the leading strand, (III) alternate stretches of purine-rich and pyrimidine-rich sequences, (IV) G + T dominance along the leading strand, and (V) no identifiable patterns in base usage. Presence of strong SGD has been observed not only in genomes having PAS, but also in genomes with G-dominance along their leading strands – an observation that defies the notion of co-occurrence of PAS and SGD in Firmicutes. The PolC-containing non-Firmicutes organisms often have alternate stretches of R-dominant and Y-dominant sequences along their
genomes and most of them show relatively weak, but significant SGD. Firmicutes having G + A-dominance or
G-dominance along LeS usually show distinct base usage patterns in three codon sites of genes. Probable
molecular mechanisms that might have incurred such usage patterns have been proposed.Co-occurrence of PAS, strong SGD and PolC should not be regarded as a genome signature of the Firmicutes. Presence of PAS in a species may warrant PolC and strong SGD, but PolC and/or SGD not necessarily
implies PAS.
 
Publisher BioMed Central
 
Date 2014
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://www.eprints.iicb.res.in/2167/1/BMC_GENOMICS__V_15___Article_Number_430;2014[92].pdf
Saha, Sanjoy Kumar and Goswami, Aranyak and Dutta, Chitra (2014) Association of purine asymmetry, strand-biased gene distribution and PolC within Firmicutes and beyond: a new appraisal. BMC Genomics, 15 (430).
 
Relation http://www.eprints.iicb.res.in/2167/