Molecular evolution of urea amidolyase and urea carboxylase in fungi.
Molecular evolution of urea amidolyase and urea carboxylase in fungi.
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DOI：
10.1186/1471-2148-11-80
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发表时间：
2011-03-29
影响因子：
3.4
通讯作者：
Moriyama EN
中科院分区：
文献类型：
--
作者：
Strope PK;Nickerson KW;Harris SD;Moriyama EN
尿素酰胺酶通过两步的过程将尿素分解成氨和二氧化碳，而另一种酶脲酶则通过一步的过程完成这一过程。在真核生物中，尿素酶仅存在于某些真菌中。它包含两个主要结构域：酰胺酶和尿素羧化酶结构域。尿素酰胺酶的一种较短形式被称为尿素羧化酶，它没有酰胺酶结构域。真核尿素羧化酶仅在几种真菌和绿藻中发现。为了阐明尿素酰胺酶和尿素羧化酶的进化起源，我们研究了尿素酰胺酶、尿素羧化酶以及包括脲酶在内的其他蛋白质在不同王国的分布。在我们检测的64种真菌中，只有两个子囊菌纲（Sordariomycetes和Saccharomycetes）具有尿素酰胺酶序列。脲羧化酶存在于担子菌门和子囊菌门的许多种中，但不是全部。在酵母菌纲（子囊菌门；酵母菌亚门）中完全不存在。我们检测的四种sordariomyetes同时具有尿素羧化酶和尿素酰胺酶序列。系统发育分析表明，这两种酶自细菌起源以来似乎经历了独立的进化。真菌尿素酰胺酶的氨基酶结构域和尿素羧化酶结构域序列与少量β -和γ -变形菌的氨基酶和尿素羧化酶序列强烈聚集在一起。另一方面，真菌尿素羧化酶蛋白与另一个广泛分布于细菌中的尿素羧化酶副本聚集在一起。除酵母菌亚门外，所有真菌种类均含有脲酶蛋白。我们的结论是，目前仅在真菌中发现的尿素酰胺酶基因是来自变形菌的β -， γ -或相关物种的水平基因转移事件的结果。这一事件发生在扁菌门和酵母菌门分化之前，而在霉菌门分化之后。目前在真菌和其他有限生物中发现的尿素羧化酶基因也可能来源于细菌中的另一个祖先基因。我们的研究提供了另一个重要的例子，表明细菌和真菌的可塑性和机会性基因组进化及其进化相互作用。
Urea amidolyase breaks down urea into ammonia and carbon dioxide in a two-step process, while another enzyme, urease, does this in a one step-process. Urea amidolyase has been found only in some fungal species among eukaryotes. It contains two major domains: the amidase and urea carboxylase domains. A shorter form of urea amidolyase is known as urea carboxylase and has no amidase domain. Eukaryotic urea carboxylase has been found only in several fungal species and green algae. In order to elucidate the evolutionary origin of urea amidolyase and urea carboxylase, we studied the distribution of urea amidolyase, urea carboxylase, as well as other proteins including urease, across kingdoms. Among the 64 fungal species we examined, only those in two Ascomycota classes (Sordariomycetes and Saccharomycetes) had the urea amidolyase sequences. Urea carboxylase was found in many but not all of the species in the phylum Basidiomycota and in the subphylum Pezizomycotina (phylum Ascomycota). It was completely absent from the class Saccharomycetes (phylum Ascomycota; subphylum Saccharomycotina). Four Sordariomycetes species we examined had both the urea carboxylase and the urea amidolyase sequences. Phylogenetic analysis showed that these two enzymes appeared to have gone through independent evolution since their bacterial origin. The amidase domain and the urea carboxylase domain sequences from fungal urea amidolyases clustered strongly together with the amidase and urea carboxylase sequences, respectively, from a small number of beta- and gammaproteobacteria. On the other hand, fungal urea carboxylase proteins clustered together with another copy of urea carboxylases distributed broadly among bacteria. The urease proteins were found in all the fungal species examined except for those of the subphylum Saccharomycotina. We conclude that the urea amidolyase genes currently found only in fungi are the results of a horizontal gene transfer event from beta-, gamma-, or related species of proteobacteria. The event took place before the divergence of the subphyla Pezizomycotina and Saccharomycotina but after the divergence of the subphylum Taphrinomycotina. Urea carboxylase genes currently found in fungi and other limited organisms were also likely derived from another ancestral gene in bacteria. Our study presented another important example showing plastic and opportunistic genome evolution in bacteria and fungi and their evolutionary interplay.
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影响因子：
4.4
作者：
Labadorf A;Link A;Rogers MF;Thomas J;Reddy AS;Ben-Hur A
通讯作者：
Ben-Hur A
DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
影响因子：
9.4
作者：
De Baere, T;Verhelst, R;Vaneechoutte, M
通讯作者：
Vaneechoutte, M
影响因子：
3.2
作者：
Navarathna DH;Harris SD;Roberts DD;Nickerson KW
通讯作者：
Nickerson KW
影响因子：
3.4
作者：
Fitzpatrick, David A.;Logue, Mary E.;Butler, Geraldine
通讯作者：
Butler, Geraldine