Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis
Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis
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DOI：
10.1038/ismej.2009.76
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发表时间：
2009-12-01
期刊：
影响因子：
11
通讯作者：
Miyazaki, Kentaro
中科院分区：
文献类型：
--
作者：
Suenaga, Hikaru;Koyama, Yoshinori;Miyazaki, Kentaro
已经鉴定了几种类型的可以有氧降解各种芳香族化合物的环境细菌。这些细菌中的分解代谢基因通常被发现形成操纵子，其促进有效和完全的降解。然而，人们对实验室中难以培养的细菌的降解途径知之甚少。通过功能筛选从活性污泥中创建的宏基因组文库，我们早先已经确定了91个携带extradiol双加氧酶（EDO）基因的fosmid克隆，EDO是芳香族化合物降解的关键酶。在这项研究中，我们分析了38个这些fossils的存在和组织的新基因的芳烃降解。只有两个宏基因组克隆包含与已知的芳香族化合物利用细菌中发现的类似的完整降解途径。其余的克隆只包含途径基因的子集，具有新的基因排列。一个环状的36.7 kb的DNA形式组装从克隆的序列携带属于一个新的EDO亚家族的基因。这种质粒样DNA形式，命名为pSKYE 1，具有DNA复制和稳定维持的基因以及一小部分苯酚降解基因;编码的酶，苯酚羟化酶和EDO，能够对芳香族化合物进行解毒。在38个被分析的克隆体中，有20个发现了这种基因组，这表明这种“解毒装置”可能在环境中广泛存在。The ISME Journal（2009）3，1335-1348; doi：10.1038/ismej.2009.76; 2009年7月9日在线发表
Several types of environmental bacteria that can aerobically degrade various aromatic compounds have been identified. The catabolic genes in these bacteria have generally been found to form operons, which promote efficient and complete degradation. However, little is known about the degradation pathways in bacteria that are difficult to culture in the laboratory. By functionally screening a metagenomic library created from activated sludge, we had earlier identified 91 fosmid clones carrying genes for extradiol dioxygenase (EDO), a key enzyme in the degradation of aromatic compounds. In this study, we analyzed 38 of these fosmids for the presence and organization of novel genes for aromatics degradation. Only two of the metagenomic clones contained complete degradation pathways similar to those found in known aromatic compound-utilizing bacteria. The rest of the clones contained only subsets of the pathway genes, with novel gene arrangements. A circular 36.7-kb DNA form was assembled from the sequences of clones carrying genes belonging to a novel EDO subfamily. This plasmid-like DNA form, designated pSKYE1, possessed genes for DNA replication and stable maintenance as well as a small set of genes for phenol degradation; the encoded enzymes, phenol hydroxylase and EDO, are capable of the detoxification of aromatic compounds. This gene set was found in 20 of the 38 analyzed clones, suggesting that this 'detoxification apparatus' may be widespread in the environment. The ISME Journal (2009) 3, 1335-1348; doi: 10.1038/ismej.2009.76; published online 9 July 2009