Analysis of genome content evolution in pvc bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle.
Analysis of genome content evolution in pvc bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle.
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DOI：
10.1093/gbe/evs113
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发表时间：
2012
影响因子：
3.3
通讯作者：
Ward NL
中科院分区：
文献类型：
--
作者：
Kamneva OK;Knight SJ;Liberles DA;Ward NL
浮游菌、疣微菌、衣原体（PVC）超门包含具有复杂细胞组织或简单细胞结构的细菌;它还包括不同生活方式的生物体（病原体、互利主义者、寄生虫和自由生活）。这组基因组内容的演变还没有进行系统的研究，这将揭示潜在的PVC特异性表型的出现基因。在这里，我们分析了26 PVC基因组和几个外类群物种的进化动力学。我们通过27，123个基因树与物种遗传学的调和来推断HGT，重复和损失。我们发现，基因组的扩张和收缩分别驱动了浮游菌和衣原体的进化，并在疣微菌和慢球菌中相互平衡。我们还发现，对于PVC基因组中的大量基因，酸杆菌中存在最相似的序列，这表明这些群体的生物体之间过去和/或当前的生态相互作用。我们还发现了粘蛋白降解人类肠道嗜粘蛋白阿克曼氏菌中的碳水化合物降解基因与来自酸杆菌和拟杆菌的序列之间的共同祖先的证据，这表明糖苷水解酶在肠道微生物之间横向转移，并且碳水化合物降解过程对人类消化系统内的微生物生存至关重要。此外，我们确定了一个高度保守的遗传模块，优先存在于区室化的PVC物种，并可能与这些生物体中的复杂细胞计划。这种保守的机制可能是膜靶向的，并参与电子传递，尽管其确切功能尚不清楚。这些基因代表了未来功能研究的良好候选者。
The Planctomycetes, Verrucomicrobia, Chlamydiae (PVC) super-phylum contains bacteria with either complex cellular organization or simple cell structure; it also includes organisms of different lifestyles (pathogens, mutualists, commensal, and free-living). Genome content evolution of this group has not been studied in a systematic fashion, which would reveal genes underlying the emergence of PVC-specific phenotypes. Here, we analyzed the evolutionary dynamics of 26 PVC genomes and several outgroup species. We inferred HGT, duplications, and losses by reconciliation of 27,123 gene trees with the species phylogeny. We showed that genome expansion and contraction have driven evolution within Planctomycetes and Chlamydiae, respectively, and balanced each other in Verrucomicrobia and Lentisphaerae. We also found that for a large number of genes in PVC genomes the most similar sequences are present in Acidobacteria, suggesting past and/or current ecological interaction between organisms from these groups. We also found evidence of shared ancestry between carbohydrate degradation genes in the mucin-degrading human intestinal commensal Akkermansia muciniphila and sequences from Acidobacteria and Bacteroidetes, suggesting that glycoside hydrolases are transferred laterally between gut microbes and that the process of carbohydrate degradation is crucial for microbial survival within the human digestive system. Further, we identified a highly conserved genetic module preferentially present in compartmentalized PVC species and possibly associated with the complex cell plan in these organisms. This conserved machinery is likely to be membrane targeted and involved in electron transport, although its exact function is unknown. These genes represent good candidates for future functional studies.
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影响因子：
10.7
作者：
Cohen, Ofir;Gophna, Uri;Pupko, Tal
通讯作者：
Pupko, Tal
影响因子：
5.2
作者：
Derrien M;Van Baarlen P;Hooiveld G;Norin E;Müller M;de Vos WM
通讯作者：
de Vos WM
影响因子：
2.8
作者：
Domman, Daryl B.;Steven, Blaire T.;Ward, Naomi L.
通讯作者：
Ward, Naomi L.
影响因子：
4.4
作者：
Fieseler, L;Horn, M;Hentschel, U
通讯作者：
Hentschel, U
DOI：
10.1126/science.1127573
发表时间：
2007-01-26
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Fraser C;Hanage WP;Spratt BG
通讯作者：
Spratt BG