Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria.
Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria.
复制标题
DOI：
10.1186/1471-2164-13-670
复制
发表时间：
2012-11-27
期刊：
影响因子：
4.4
通讯作者：
Sockett RE
中科院分区：
文献类型：
--
作者：
Hobley L;Lerner TR;Williams LE;Lambert C;Till R;Milner DS;Basford SM;Capeness MJ;Fenton AK;Atterbury RJ;Harris MA;Sockett RE
进化使噬菌弧菌捕食性细菌能够侵入其他细菌，消化和复制，并将其密封在细菌内部，从而阻止与周围环境中的生物体共享营养。蛭弧菌以前被描述为“专性捕食者”，因为仅通过突变（通常发生在基因 bd0108 中），大约 1x107 的捕食性蛭弧菌实验室菌株中就有 1 株转化为不依赖猎物的生长。之前对噬菌芽孢杆菌 HD100 菌株的基因组分析表明，通过裂解酶捕食猎物 DNA，使得噬菌弧菌比其他细菌更不可能通过横向基因转移 (LGT) 获得 DNA。然而，Doolittle 和 Pan 小组在计算机模拟中预测，古代和现代的基因都会转移到 B. bacteriovorus HD100 基因组中。为了验证这些预测，我们通过用大肠杆菌猎物细胞进行富集培养，从台伯河中分离出了一种捕食性细菌，这是 LGT 的良好潜在来源，因为它富含多种细菌和有机污染物。该分离株被鉴定为食菌芽孢杆菌并命名为Tiberius菌株。不同寻常的是，这种提比略菌株同时表现出对有机营养物的猎物独立生长和对活猎物的捕食性生长。尽管生长不依赖于猎物，bd0108的同源物并不具有典型的不依赖于猎物的突变。双重生长模式可能反映了河流的高碳含量，并使 B. bacteriovorus Tiberius 能够与其他存在的细菌进行更长时间的非捕食性接触。 HD100 和 Tiberius 基因组具有广泛的同线性，尽管它们的陆地培养/新分离的水生历史不同。但指示基因组通量和 LGT 的基因含量存在显着差异。基因内容比较支持之前发表的 HD100 菌株中 LGT 的计算机预测，其中预测具有古老 LGT 起源的基因具有大量保守性，但预测最近获得的富含 AT 的基因几乎没有保守性。食菌芽孢杆菌 Tiberius 菌株的自然生态位和双重捕食性以及不依赖猎物的生长使其能够与其他海洋和淡水细菌进行广泛的非捕食性接触，而这些细菌的 LGT 在其基因组中是明显的。因此，尽管他们有 DNA 裂解酶的武器库；蛭弧菌在自然生态位中并不总是具有掠夺性，它们的基因组是通过从其他细菌获取完整基因而形成的。
Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as “obligate predators” because only by mutations, often in gene bd0108, are 1 in ~1x107 of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome. To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. Despite the prey-independent growth, the homolog of bd0108 did not have typical prey-independent-type mutations. The dual growth mode may reflect the high carbon content of the river, and gives B. bacteriovorus Tiberius extended non-predatory contact with the other bacteria present. The HD100 and Tiberius genomes were extensively syntenic despite their different cultured-terrestrial/freshly-isolated aquatic histories; but there were significant differences in gene content indicative of genomic flux and LGT. Gene content comparisons support previously published in silico predictions for LGT in strain HD100 with substantial conservation of genes predicted to have ancient LGT origins but little conservation of AT-rich genes predicted to be recently acquired. The natural niche and dual predatory, and prey-independent growth of the B. bacteriovorus Tiberius strain afforded it extensive non-predatory contact with other marine and freshwater bacteria from which LGT is evident in its genome. Thus despite their arsenal of DNA-lytic enzymes; Bdellovibrio are not always predatory in natural niches and their genomes are shaped by acquiring whole genes from other bacteria.
登录
查看更多内容
影响因子：
6.7
作者：
Hobley L;Fung RK;Lambert C;Harris MA;Dabhi JM;King SS;Basford SM;Uchida K;Till R;Ahmad R;Aizawa S;Gomelsky M;Sockett RE
通讯作者：
Sockett RE
影响因子：
3.2
作者：
Novichkov, Pavel S.;Wolf, Yuri I.;Koonin, Eugene V.
通讯作者：
Koonin, Eugene V.
影响因子：
3.2
作者：
Evans, Katy J.;Lambert, Carey;Sockett, R. Elizabeth
通讯作者：
Sockett, R. Elizabeth
影响因子：
14.9
作者：
Lagesen K;Hallin P;Rødland EA;Staerfeldt HH;Rognes T;Ussery DW
通讯作者：
Ussery DW
影响因子：
3.2
作者：
Fenton, A. K.;Kanna, M.;Sockett, R. E.
通讯作者：
Sockett, R. E.