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

Background

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. 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.

Results

A 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.

Conclusion

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.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-430) contains supplementary material, which is available to authorized users.     

虎斑颈槽蛇肠道微生物组成和分布特征

蛇类是一种研究能量平衡的模型动物,而肠道微生物则帮助宿主获取能量和营养。大多数肠道微生物的研究集中在圈养动物上,而对于野生蛇类的研究很少。本研究从3只野生虎斑颈槽蛇（Rhabdophis tigrinus）的大肠、小肠和泄殖腔内容物提取微生物总DNA,进行16S rRNA基因V4区域扩增子测序,分析虎斑颈槽蛇肠道核心微生物组成和分布特征。结果表明,阿尔法指数在不同肠道区域的多样性不存在显著性差异。大肠、小肠和泄殖腔3个肠道部位共享534个操作分类单元（OTUs）,大肠包含最多特有OTUs（388个）。门水平,梭杆菌门（Fusobacteria）在小肠（52.87% ± 14.49%）、大肠（41.12% ± 22.60%）和泄殖腔（65.70% ± 10.44%）均为优势菌。属水平,鲸杆菌属（Cetobacterium）在小肠（46.36% ± 13.86%）、大肠（21.95% ± 9.82%）和泄殖腔（58.18% ± 14.29%）为优势菌,柠檬酸杆菌属（Citrobacter）在小肠和泄殖腔中有显著性差异。此外,在其肠道检测到很多潜在的致病菌,例如,柠檬酸杆菌属、明串珠菌属（Trichococcus）和丹毒丝菌属（Erysipelothrix）,了解了潜在致病菌在虎斑颈槽蛇肠道中的分布情况。在聚类分析中发现泄殖腔的数据重复性较好,将本研究泄殖腔数据与前人研究过的食鱼蝮（Agkistrodon piscivorus）泄殖腔高通量测序数据进行联合分析,为更广泛开展不同蛇类肠道微生物组成的差异性分析提供理论借鉴依据。