Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization.
Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization.
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DOI：
10.1186/1471-2164-10-78
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发表时间：
2009-02-10
期刊：
影响因子：
4.4
通讯作者：
Gladyshev VN
中科院分区：
文献类型：
--
作者：
Zhang Y;Rodionov DA;Gelfand MS;Gladyshev VN
镍(Ni)和钴(Co)是多种生物过程所需的微量元素。镍由蛋白质直接配位，而钴主要用作维生素B12的一种成分。虽然一些依赖镍和钴的酶已经被表征，但对这些金属的利用的系统进化分析是有限的。我们进行了比较基因组分析，在(I)运输系统和(Ii)金属蛋白质组的水平上研究了镍和钴的使用的发生和进化动力学。我们的数据显示，这两种金属在细菌和古菌中都被广泛使用。CbI/NikMNQO是最常见的原核镍/钴转运蛋白，镍依赖的尿素酶和镍铁氢酶、B12依赖的蛋氨酸合成酶、核苷酸还原酶和甲基丙二酰辅酶A变位酶分别是镍和钴最普遍的金属蛋白。其他金属酶的分布呈镶嵌分布，并预测了一个新的B12依赖蛋白家族。三角洲蛋白细菌和甲烷八叠球菌通常有更大的依赖镍和钴的蛋白质组。另一方面，这两种金属在真核生物中的利用是有限的，这些生物中很少同时利用这两种金属。利用镍的真核生物主要是真菌(酵母菌除外)和植物，而利用B12的大多数生物是动物。NICOT转运蛋白家族是真核细胞中分布最广泛的镍转运蛋白，而真核细胞中的尿素酶和甲基甲酸甲酯分别是最常见的依赖镍和B12的酶。最后，对环境和其他条件的调查以及显示对镍或钴有依赖关系的生物的特性表明，与宿主相关的生物(特别是专性胞内寄生虫和内共生菌)有丧失对镍/钴的利用的趋势。我们的数据提供了关于镍和钴利用的进化动态的信息，并强调了这些金属在生命的三个领域中的广泛使用，但只有有限数量的使用者蛋白质。
Nickel (Ni) and cobalt (Co) are trace elements required for a variety of biological processes. Ni is directly coordinated by proteins, whereas Co is mainly used as a component of vitamin B12. Although a number of Ni and Co-dependent enzymes have been characterized, systematic evolutionary analyses of utilization of these metals are limited. We carried out comparative genomic analyses to examine occurrence and evolutionary dynamics of the use of Ni and Co at the level of (i) transport systems, and (ii) metalloproteomes. Our data show that both metals are widely used in bacteria and archaea. Cbi/NikMNQO is the most common prokaryotic Ni/Co transporter, while Ni-dependent urease and Ni-Fe hydrogenase, and B12-dependent methionine synthase (MetH), ribonucleotide reductase and methylmalonyl-CoA mutase are the most widespread metalloproteins for Ni and Co, respectively. Occurrence of other metalloenzymes showed a mosaic distribution and a new B12-dependent protein family was predicted. Deltaproteobacteria and Methanosarcina generally have larger Ni- and Co-dependent proteomes. On the other hand, utilization of these two metals is limited in eukaryotes, and very few of these organisms utilize both of them. The Ni-utilizing eukaryotes are mostly fungi (except saccharomycotina) and plants, whereas most B12-utilizing organisms are animals. The NiCoT transporter family is the most widespread eukaryotic Ni transporter, and eukaryotic urease and MetH are the most common Ni- and B12-dependent enzymes, respectively. Finally, investigation of environmental and other conditions and identity of organisms that show dependence on Ni or Co revealed that host-associated organisms (particularly obligate intracellular parasites and endosymbionts) have a tendency for loss of Ni/Co utilization. Our data provide information on the evolutionary dynamics of Ni and Co utilization and highlight widespread use of these metals in the three domains of life, yet only a limited number of user proteins.