A new classification system for bacterial Rieske non-heme iron aromatic ring-hydroxylating oxygenases.
A new classification system for bacterial Rieske non-heme iron aromatic ring-hydroxylating oxygenases.
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DOI：
10.1186/1471-2091-9-11
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发表时间：
2008-04-03
期刊：
影响因子：
--
通讯作者：
Cerniglia CE
中科院分区：
文献类型：
--
作者：
Kweon O;Kim SJ;Baek S;Chae JC;Adjei MD;Baek DH;Kim YC;Cerniglia CE
Rieske 非血红素铁芳香环羟基化加氧酶 (RHO) 是多组分酶系统，在从不同栖息地分离的细菌中具有显着的多样性。自1990年首次分类以来，需要为这些酶设计新的分类方案，因为已经发现了许多RHO，它们不属于先前分类中的任何组。在这里，我们提出了一种 RHO 分类方案，反映了新的序列信息和 RHO 酶组分之间的相互作用。我们总共分析了 130 种 RHO 酶，其中 25 种经过充分表征的 RHO 酶被用作标准来检验我们对所提出的分类系统的假设。从标准 RHO 的电子传递链 (ETC) 组件的序列分析中，我们提取了分类键，该分类键不仅反映了每个组件内的系统发育关系，而且还反映了组件之间的关系。标准 RHO 的加氧酶组件在系统发育上分为 10 组，分类键源自 ETC 组件。该系统发育分类方案被转换为由 5 种不同类型组成的新系统分类。新的分类系统经过统计检验以证明其稳定性。 I 型代表由加氧酶和 FNRC 型还原酶组成的双组分 RHO 系统。 II 型包含其他双组分 RHO 系统，由加氧酶和 FNRN 型还原酶组成。 III 型代表一组三组分 RHO 系统，由加氧酶、[2Fe-2S] 型铁氧还蛋白和 FNRN 型还原酶组成。 IV型代表另一种三组分系统，由加氧酶、[2Fe-2S]型铁氧还蛋白和GR型还原酶组成。 V型代表另一种不同的三组分系统，由加氧酶、[3Fe-4S]型铁氧还蛋白和GR型还原酶组成。新的分类系统具有以下特点。首先，新的分类系统对RHO酶进行整体分析。其次，新的分类系统不是静态的，而是动态响应不断增长的 RHO 酶库。第三，我们的分类可以可靠地应用于不完整的 RHO 的分类。第四，分类对实验工作有直接的适用性。第五，该系统为基于酶相互作用的RHO系统的进化提供了新的见解。
Rieske non-heme iron aromatic ring-hydroxylating oxygenases (RHOs) are multi-component enzyme systems that are remarkably diverse in bacteria isolated from diverse habitats. Since the first classification in 1990, there has been a need to devise a new classification scheme for these enzymes because many RHOs have been discovered, which do not belong to any group in the previous classification. Here, we present a scheme for classification of RHOs reflecting new sequence information and interactions between RHO enzyme components. We have analyzed a total of 130 RHO enzymes in which 25 well-characterized RHO enzymes were used as standards to test our hypothesis for the proposed classification system. From the sequence analysis of electron transport chain (ETC) components of the standard RHOs, we extracted classification keys that reflect not only the phylogenetic affiliation within each component but also relationship among components. Oxygenase components of standard RHOs were phylogenetically classified into 10 groups with the classification keys derived from ETC components. This phylogenetic classification scheme was converted to a new systematic classification consisting of 5 distinct types. The new classification system was statistically examined to justify its stability. Type I represents two-component RHO systems that consist of an oxygenase and an FNRC-type reductase. Type II contains other two-component RHO systems that consist of an oxygenase and an FNRN-type reductase. Type III represents a group of three-component RHO systems that consist of an oxygenase, a [2Fe-2S]-type ferredoxin and an FNRN-type reductase. Type IV represents another three-component systems that consist of oxygenase, [2Fe-2S]-type ferredoxin and GR-type reductase. Type V represents another different three-component systems that consist of an oxygenase, a [3Fe-4S]-type ferredoxin and a GR-type reductase. The new classification system provides the following features. First, the new classification system analyzes RHO enzymes as a whole. RwithSecond, the new classification system is not static but responds dynamically to the growing pool of RHO enzymes. Third, our classification can be applied reliably to the classification of incomplete RHOs. Fourth, the classification has direct applicability to experimental work. Fifth, the system provides new insights into the evolution of RHO systems based on enzyme interaction.
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影响因子：
3.2
作者：
Fukumori, F;Saint, CP
通讯作者：
Saint, CP
DOI：
10.1016/j.bbrc.2004.12.060
发表时间：
2005-02-18
影响因子：
3.1
作者：
Cho, OY;Choi, KY;Kim, E
通讯作者：
Kim, E
影响因子：
3.6
作者：
Cerniglia, Carl E.
通讯作者：
Cerniglia, Carl E.
影响因子：
13.8
作者：
Jeanmougin, F;Thompson, JD;Gibson, TJ
通讯作者：
Gibson, TJ
影响因子：
2.8
作者：
DEHMEL, U;ENGESSER, KH;DWYER, DF
通讯作者：
DWYER, DF