Abstract
BackgroundThe Firmicutes often possess three conspicuous genome features: marked Purine Asymmetry (PAS) across two 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.ResultsA large-scale analysis of diverse bacterial genomes indicates that PAS, PolC and SGD are neither essential nor 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.ConclusionCo-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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-430) contains supplementary material, which is available to authorized users.
Highlights
The Firmicutes often possess three conspicuous genome features: marked Purine Asymmetry (PAS) across two strands of replication, Strand-biased Gene Distribution (SGD) and presence of two isoforms of DNA polymerase III alpha subunit, PolC and DnaE
In order to rule out any ambiguity while identifying such trends in skew trajectories, we have examined the scatter plots of the local GC-skew and AT-skew values for each species under study
In most of the Trend I organisms, more than 70% of the 10 kb leading strand (LeS) segments have exceptionally high frequencies of both guanine and adenine as compared to cytosine and thymine respectively (Tables 1 and 2), while the number of LeS segments of other three possible combinations (b), (c) or (d) are significantly low in most cases
Summary
The Firmicutes often possess three conspicuous genome features: marked Purine Asymmetry (PAS) across two strands of replication, Strand-biased Gene Distribution (SGD) and presence of two isoforms of DNA polymerase III alpha subunit, PolC and DnaE. A correlation between PAS and SGD might exist [1] It is worth mentioning at this point that a different type of strand-specific compositional bias - an enrichment of guanine and thymine (G + T) in the LeSs – has earlier been observed in many non-Firmicutes bacterial species [14,15,16]. This trait, which is more frequent among the strictly host-associated endosymbionts or pathogens with reduced genomes [17,18,19,20], has been attributed to the strand-biased deamination and 5-methylation of cytosine [9,21]
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