SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases.
SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases.
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发表时间：
2002
影响因子：
1.2
通讯作者：
Vivek Anantharaman;E. Koonin;L. Aravind
中科院分区：
文献类型：
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作者：
Vivek Anantharaman;E. Koonin;L. Aravind
核苷酸修饰是rna，特别是rrna和trna结构和生化多样性的主要来源（Rozenski et al., 1999）。碱基特异性甲基化是与假尿嘧啶化和硫代尿嘧啶化一起流行的转录后修饰模式之一。大多数RNA甲基化酶的催化结构域属于Rossmanfo酶的巨大超类（Lo Conte et al., 2000）。这些罗斯曼折叠甲基化酶（RFM）通过该折叠典型的核苷酸结合环与s -腺苷- l-蛋氨酸（SAM）结合，并催化其甲基转移到DNA， RNA，蛋白质或小分子等底物上。然而，分别由大肠杆菌蛋白SpoU （TrmH）和TrmD表征的两个RNA甲基化酶家族似乎与rfm无关。SpoU家族蛋白在大肠杆菌和葡萄球菌中被表征为tRNA (G)甲基转移酶（Cavaille等，1999；Koonin等，1993；Persson等，1997），而TrmD则负责细菌特有的G位tRNA甲基化（Bjork等，1989；Li等，1999）。在这里，我们为TrmD和SpoU甲基化酶超家族的共同进化起源提供了证据，这些超家族以前被认为是不相关的。我们发现，SpoU超家族包含比以前认识到的更大的（预测的）甲基化酶多样性，并且包含两个以前未被发现的家族，它们是古细菌和嗜热细菌所特有的。此外，我们分别从古细菌和细菌中发现了两个以前未被注意到的蛋白质超家族，它们被预测为与TrmD和SpoU超家族相关的甲基化酶。这四个超家族共同定义了RNA甲基化酶活性的新结构支架。作为参与RNA代谢的酶（VA， EVK和LA，未发表）的系统调查的一部分，我们使用PSI-BLAST程序（Altschul et al., 1997）通过非冗余数据库（National Center for Biotechnology Information， NIH, Bethesda）的迭代搜索调查了SpoU和TrmD家族。这种以大肠杆菌SpoU序列为种子的搜索（图谱包含期望(E)值阈值为0.01）不仅检测到细菌、古细菌和真核生物中明显的SpoU同源物和先前描述的同源物（Koonin, 1996），而且还检测到来自古细菌（以MJ1385为典型）和嗜热细菌Aquifex和Thermotoga（以aq_054为典型）的一些未被鉴定的蛋白质。这些蛋白呈现显著的e值(10!3!10！7)在第一次检测时，保留了SpoU蛋白的典型保守模式（图1），表明它们是该超家族的真正成员。此外，在这些搜索中，我们检测到一些未表征的古菌蛋白，以AF2226为典型，TrmD甲基化酶具有显著的e值（0.06 - 0.1）。从AF2226序列开始进行互反搜索，发现TrmD甲基化酶和SpoU超家族成员具有相似的边界e值。另一项基于Aquifex aeolicus（2983865）的TrmD同源基因的PSIBLAST验证搜索不仅检测到af2226样古细菌蛋白，还检测到一个高度保守的以细菌蛋白为主的超家族成员，以大肠杆菌的YbeA为典型，e值显著（<0.001）。TrmD甲基化酶、SpoU甲基化酶以及新检测到的af2226样蛋白和ybea样蛋白在SpoU超家族中预测的sam结合环区域显示出惊人的保守性（Koonin, 1996）（图1）。此外，在古细菌af2226样蛋白中，假定的甲基化酶结构域与最近描述的RNA结合结构域THUMP融合，该结构域也被发现与经典的Rossmann-fold RNA甲基化酶、硫脲合酶和假尿嘧啶合酶融合（Aravind et al., 2001）。这些观察结果表明，SpoU超家族、TrmD超家族以及新发现的af2226样和ybea样超家族属于一类具有共同结构折叠的甲基转移酶，该结构折叠不包括任何结构特征蛋白，与经典的罗斯曼折叠不同。为了进一步研究这种关系，我们使用Gibbs抽样程序搜索了SpoU、TrmD、YbeA和AF2226超家族的全部成员，寻找潜在的保守基序（Neuwald et al., 1997）。检测到两个基序，一个与预测的sam结合环对应，另一个位于sam结合环的c端，与*For对应。电子邮件。aravind@ncbi.nlm.nih.gov微生物学。Biotechnol。（2002） 4(1): 71-75。JMMB沟通
Nucleotide modification is a major source of structural and biochemical diversity of RNAs, particularly of rRNAs and tRNAs (Rozenski et al., 1999). Basespecific methylation is one of the prevalent modes of post-transcriptional modification along with pseudouridylation and thio-uridylation. The catalytic domains of the majority of RNA methylases belong to the vast la rge superc lass o f Rossmanfo ld enzymes (Lo Conte et al., 2000). These Rossman-fold methylases (RFM) bind S-adenosyl-L-methionine (SAM) via the nucleotide-binding loop typical of this fold and catalyze the transfer of its methyl group to substrates such as DNA, RNA, proteins or small molecules. However, two families of RNA methylases, typified, respectively, by Escherichia coli proteins SpoU (TrmH) and TrmD, appear to be unrelated to the RFMs. SpoU family proteins have been characterized as tRNA (G) methyltransferases in E. coli and S. cerevisiae (Cavaille et al., 1999; Koonin et al., 1993; Persson et al., 1997), whereas TrmD is responsible for the bacteriaspecific tRNA methylation at the G position (Bjork et al., 1989; Li et al., 1999). Here, we provide evidence for a common evolutionary origin of the TrmD and SpoU methylase superfamilies that were previously considered unrelated. We show that the SpoU superfamily encompasses a greater diversity of (predicted) methylases than previously appreciated and contains two previously undetected families that are specific to the archaea and thermophilic bacteria. Additionally, we identify two previously unnoticed superfamilies of proteins from archaea and bacteria, respectively, that are predicted to be methylases related to both the TrmD and SpoU superfamilies. These four superfamilies together define a new structural scaffold for RNA methylase activity. As part of a systematic survey of the enzymes involved in RNA metabolism (VA, EVK and LA, unpublished), we investigated the SpoU and TrmD families by iterative searches of the Non-redundant database (National Center for Biotechnology Information, NIH, Bethesda) using the PSI-BLAST program (Altschul et al., 1997). Such a search (profile inclusion expectation (E) value threshold of 0.01) seeded with the E. coli SpoU sequence detected not only the obvious SpoU orthologs and previously described homologs (Koonin, 1996) from bacteria, archaea, and eukaryotes, but also several uncharacterized proteins from archaea (typified by MJ1385) and the thermophilic bacteria Aquifex and Thermotoga (typified by aq_054). These proteins showed significant E-values (10!3!10!7) on first detection and retained the conservation pattern typical of the SpoU proteins (Figure 1), suggesting that they were bona fide members of this superfamily. Additionally, in these searches we detected several uncharacterized archaeal proteins, typified by AF2226, and the TrmD methylases with marginally significant E-values (.06-.1). A reciprocal search started with the AF2226 sequence recovered the TrmD methylases and SpoU superfamily members with similar borderline E-values. Another confirmatory PSIBLAST search initiated with the TrmD ortholog from Aquifex aeolicus (2983865) detected not only the AF2226-like archaeal proteins, but also members of a highly conserved superfamily of predominantly bacterial proteins, typified by YbeA from E. coli, with significant E-values (<0.001). The TrmD methylases, the SpoU methylases, and the newly detected AF2226like, and YbeA-like proteins showed striking conservation in the region predicted to be the SAM-binding loop in the SpoU superfamily (Koonin, 1996) (Figure 1). Furthermore, in the archaeal AF2226-like proteins, the putative methylase domain is fused with a recently described RNA-binding domain, THUMP, that has also been found fused to classic, Rossmann-fold RNA methylases, thiouridine synthases and pseudouridine synthases (Aravind et al., 2001). These observations suggested that the SpoU superfamily, the TrmD superfamily, and the newly detected AF2226-like and YbeA-like superfamilies, belong to a class of methyltransferases with a common structural fold that does not include any structurally characterized proteins and is distinct from the classic Rossmann fold. To investigate this relationship further, we searched the entire set of members of the SpoU, TrmD, YbeA and AF2226 superfamilies for potential conserved motifs using the Gibbs sampling procedure (Neuwald et al., 1997). Two motifs were detected, one corresponding to the predicted SAM-binding loop and the other located directly C-terminal of it, with the *For correspondence. Email. aravind@ncbi.nlm.nih.gov J. Mol. Microbiol. Biotechnol. (2002) 4(1): 71–75. JMMB Communication