The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons.
The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons.
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DOI：
10.3389/fmicb.2012.00125
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发表时间：
2012
影响因子：
5.2
通讯作者：
Zhao J
中科院分区：
文献类型：
--
作者：
Hickey WJ;Chen S;Zhao J
细菌是多环芳烃（PAH）生物降解的关键，多环芳烃是广泛存在的环境污染物。至少六种 PAH 降解剂基因型可通过启动细菌 PAH 代谢的环羟基化双加氧酶 (RHD) 的系统发育来区分。多种细菌属都可以拥有给定的 RHD 基因型，这表明水平基因转移 (HGT) 是 PAH 降解基因传播的重要过程。但是，大多数 RHD 基因型的 HGT 机制尚不清楚。在这里，我们报告了菲降解细菌 Delftia sp 的计算机模拟和功能分析。 Cs1-4，phnAFK2 RHD 组的代表。 phnAFK2 基因型在一些土壤和沉积物中的 PAH 降解菌群落中占主导地位，但迄今为止，其基因组生物学尚未得到探索。在本研究中，整个菲分解代谢途径的基因是在一种新的约中发现的。 232 kb 基因组岛 (GEI)，现在称为 phn 岛。该GEI具有整合和共轭元件的特征，具有类似于SXT/R391型GEI的动员/稳定系统。但是，它不能与任何已知的 GEI 归为一类，并且是新 GEI 类别的第一个成员。该岛还携带预计编码的基因：群体感应信号分子的合成、脂肪酸/聚羟基脂肪酸酯生物合成、IV 型分泌系统、PRRTC 系统、DNA 动员功能和超过 50 种假设蛋白质。 phn基因簇的50％G + C含量与整个岛和菌株Cs1-4染色体的66.7％G + C水平显着不同，表明phn基因的系统发育起源不同。总的来说，这些研究为影响微生物群落 PAH 生物降解能力的遗传因素以及 HGT 的潜在载体提供了新的见解。
Bacteria are key in the biodegradation of polycyclic aromatic hydrocarbons (PAH), which are widespread environmental pollutants. At least six genotypes of PAH degraders are distinguishable via phylogenies of the ring-hydroxylating dioxygenase (RHD) that initiates bacterial PAH metabolism. A given RHD genotype can be possessed by a variety of bacterial genera, suggesting horizontal gene transfer (HGT) is an important process for dissemination of PAH-degrading genes. But, mechanisms of HGT for most RHD genotypes are unknown. Here, we report in silico and functional analyses of the phenanthrene-degrading bacterium Delftia sp. Cs1-4, a representative of the phnAFK2 RHD group. The phnAFK2 genotype predominates PAH degrader communities in some soils and sediments, but, until now, their genomic biology has not been explored. In the present study, genes for the entire phenanthrene catabolic pathway were discovered on a novel ca. 232 kb genomic island (GEI), now termed the phn island. This GEI had characteristics of an integrative and conjugative element with a mobilization/stabilization system similar to that of SXT/R391-type GEI. But, it could not be grouped with any known GEI, and was the first member of a new GEI class. The island also carried genes predicted to encode: synthesis of quorum sensing signal molecules, fatty acid/polyhydroxyalkanoate biosynthesis, a type IV secretory system, a PRTRC system, DNA mobilization functions and >50 hypothetical proteins. The 50% G + C content of the phn gene cluster differed significantly from the 66.7% G + C level of the island as a whole and the strain Cs1-4 chromosome, indicating a divergent phylogenetic origin for the phn genes. Collectively, these studies added new insights into the genetic elements affecting the PAH biodegradation capacity of microbial communities specifically, and the potential vehicles of HGT in general.
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影响因子：
64.8
作者：
Beaber, JW;Hochhut, B;Waldor, MK
通讯作者：
Waldor, MK
影响因子：
3.6
作者：
Basu, Aditya;Phale, Prashant S.
通讯作者：
Phale, Prashant S.
影响因子：
3.2
作者：
Beaber, JW;Hochhut, B;Waldor, MK
通讯作者：
Waldor, MK
影响因子：
4.4
作者：
HICKEY, WJ;FOCHT, DD
通讯作者：
FOCHT, DD
影响因子：
11.3
作者：
Juhas M;van der Meer JR;Gaillard M;Harding RM;Hood DW;Crook DW
通讯作者：
Crook DW