Finding Protein Sequence Motifs--Methods and Application

寻找蛋白质序列基序--方法与应用

• 批准号: 6988455
• 负责人: Eugene V Koonin
• 金额: --
• 依托单位: NATIONAL LIBRARY OF MEDICINE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/6988455
• 关键词: acid anhydride hydrolase; biochemical evolution; bioinformatics; computer assisted sequence analysis; computer system design /evaluation; enzyme structure; information retrieval; molecular biology information system; protein folding; protein sequence; protein structure function; replicon; statistics /biometry

In the last few years, rapid accumulation of genome sequences and protein structures has been paralleled by major advances in sequence database search methods. The powerful Position-Specific Iterating BLAST (PSI-BLAST) method developed at the NCBI formed the basis of our work on protein motif analysis. During last year, we made further progress in detailed analysis of the classification, evolution, and functions of several classes of proteins. In particular, a new major class of P-loop NTPases was described, the so-called STAND class, after signal transduction ATPases with numerous domains. The STAND class includes the AP-ATPases (animal apoptosis regulators CED4/Apaf-1, plant disease resistance proteins, and bacterial AfsR-like transcription regulators) and NACHT NTPases (e.g. NAIP, TLP1, Het-E-1) that have been studied extensively in the context of apoptosis, pathogen response in animals and plants, and transcriptional regulation in bacteria. We show that, in addition to these well-characterized protein families, the STAND class includes several other groups of (predicted) NTPase domains from diverse signaling and transcription regulatory proteins from bacteria and eukaryotes, and three Archaea-specific families. We identified the STAND domain in several biologically well-characterized proteins that have not been suspected to have NTPase activity, including soluble adenylyl cyclases, nephrocystin 3 (implicated in polycystic kidney disease), and Rolling pebble (a regulator of muscle development); these findings are expected to facilitate elucidation of the functions of these proteins. The STAND class belongs to the additional strand, catalytic E division of P-loop NTPases together with the AAA+ ATPases, RecA/helicase-related ATPases, ABC-ATPases, and VirD4/PilT-like ATPases. The STAND proteins are distinguished from other P-loop NTPases by the presence of unique sequence motifs associated with the N-terminal helix and the core strand-4, as well as a C-terminal helical bundle that is fused to the NTPase domain. This helical module contains a signature GxP motif in the loop between the two distal helices. With the exception of the archaeal families, almost all STAND NTPases are multidomain proteins containing three or more domains. In addition to the NTPase domain, these proteins typically contain DNA-binding or protein-binding domains, superstructure-forming repeats, such as WD40 and TPR, and enzymatic domains involved in signal transduction, including adenylate cyclases and kinases. By analogy to the AAA+ ATPases, it can be predicted that STAND NTPases use the C-terminal helical bundle as a "lever" to transmit the conformational changes brought about by NTP hydrolysis to effector domains. STAND NTPases represent a novel paradigm in signal transduction, whereby adaptor, regulatory switch, scaffolding, and, in some cases, signal-generating moieties are combined into a single polypeptide. The STAND class consists of 14 distinct families, and the evolutionary history of most of these families is riddled with dramatic instances of lineage-specific expansion and apparent horizontal gene transfer. The STAND NTPases are most abundant in developmentally and organizationally complex prokaryotes and eukaryotes. Transfer of genes for STAND NTPases from bacteria to eukaryotes on several occasions might have played a significant role in the evolution of eukaryotic signaling systems. Additionally, we identified a previously uncharacterized family of P-loop NTPases, which includes the neuronal membrane protein and receptor tyrosine kinase substrate Kidins220/ARMS, which is conserved in animals, the F-plasmid PifA protein involved in phage T7 exclusion, and several uncharacterized bacterial proteins. We refer to these (predicted) NTPases as the KAP family, after Kidins220/ARMS and PifA. The KAP family NTPases are sporadically distributed across a wide phylogenetic range in bacteria but ammong the eukaryotes are represented only in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side. We show that the KAP family belongs to the same major division of the P-loop NTPase fold with the AAA+, ABC, RecA-like, VirD4-like, PilT-like, and AP/NACHT-like NTPase classes. In addition to the KAP family, we identified another small family of predicted bacterial NTPases, with two transmembrane helices inserted into the P-loop domain. This family is not specifically related to the KAP NTPases, suggesting independent acquisition of the transmembrane helices. CONCLUSIONS: We predict that KAP family NTPases function principally in the NTP-dependent dynamics of protein complexes, especially those associated with the intracellular surface of cell membranes. Animal KAP NTPases, including Kidins220/ARMS, are likely to function as NTP-dependent regulators of the assembly of membrane-associated signaling complexes involved in neurite growth and development. One possible function of the prokaryotic KAP NTPases might be in the exclusion of selfish replicons, such as viruses, from the host cells. Phylogenetic analysis and phyletic patterns suggest that the common ancestor of the animals acquired a KAP NTPase via lateral transfer from bacteria. However, an earlier transfer into eukaryotes followed by multiple losses in several eukaryotic lineages cannot be ruled out.

在过去的几年中，基因组序列和蛋白质结构的快速积累与序列数据库搜索方法的重大进步并行。 NCBI 开发的强大的位置特异性迭代 BLAST (PSI-BLAST) 方法构成了我们蛋白质基序分析工作的基础。去年，我们在几类蛋白质的分类、进化和功能的详细分析方面取得了进一步进展。特别是，在具有多个结构域的信号转导 ATP 酶之后，描述了 P 环 NTP 酶的新主要类别，即所谓的 STAND 类。 STAND 类包括已研究的 AP-ATPase（动物凋亡调节因子 CED4/Apaf-1、植物抗病蛋白和细菌 AfsR 样转录调节因子）和 NACHT NTPase（例如 NAIP、TLP1、Het-E-1）广泛应用于细胞凋亡、动物和植物的病原体反应以及细菌的转录调控。我们表明，除了这些充分表征的蛋白质家族之外，STAND 类还包括来自细菌和真核生物的不同信号传导和转录调节蛋白的其他几组（预测的）NTPase 结构域，以及三个古生菌特异性家族。我们在几种生物学特性良好的蛋白质中鉴定了 STAND 结构域，这些蛋白质未被怀疑具有 NTPase 活性，包括可溶性腺苷酸环化酶、肾囊肿素 3（与多囊肾病有关）和 Rolling pebble（肌肉发育的调节因子）；预计这些发现将有助于阐明这些蛋白质的功能。 STAND 类属于 P 环 NTP 酶的附加链、催化 E 分裂以及 AAA+ ATP 酶、RecA/解旋酶相关 ATP 酶、ABC-ATP 酶和 VirD4/PilT 样 ATP 酶。 STAND 蛋白与其他 P 环 NTPase 的区别在于存在与 N 端螺旋和核心链 4 相关的独特序列基序，以及与 NTPase 结构域融合的 C 端螺旋束。该螺旋模块在两个远端螺旋之间的环中包含标志性 GxP 基序。除古细菌家族外，几乎所有 STAND NTPase 都是包含三个或更多结构域的多结构域蛋白。除了 NTPase 结构域外，这些蛋白质通常还包含 DNA 结合或蛋白质结合结构域、超结构形成重复序列（例如 WD40 和 TPR）以及参与信号转导的酶结构域（包括腺苷酸环化酶和激酶）。通过类比AAA+ ATP酶，可以预测STAND NTP酶利用C端螺旋束作为“杠杆”，将NTP水解带来的构象变化传递到效应域。 STAND NTPase代表了信号转导中的一种新范例，其中接头、调节开关、支架以及在某些情况下的信号产生部分被组合成单个多肽。 STAND类由14个不同的家族组成，其中大多数家族的进化史充满了谱系特异性扩张和明显的水平基因转移的戏剧性实例。 STAND NTPase 在发育和组织复杂的原核生物和真核生物中最为丰富。 STAND NTPase 基因多次从细菌转移到真核生物，可能在真核信号系统的进化中发挥了重要作用。 此外，我们还鉴定了一个以前未表征的 P 环 NTPase 家族，其中包括动物中保守的神经元膜蛋白和受体酪氨酸激酶底物 Kidins220/ARMS、参与噬菌体 T7 排除的 F 质粒 PifA 蛋白，以及一些未表征的 P 环 NTPase 家族。细菌蛋白质。我们将这些（预测的）NTPase 称为 KAP 家族，仅次于 Kidins220/ARMS 和 PifA。 KAP 家族 NTPase 零星分布在细菌的广泛系统发育范围内，但在真核生物中仅在动物中出现。许多原核 KAP NTP 酶是在质粒中编码的，并且往往会受到破坏而形成假基因。所有真核生物和某些细菌 KAP NTPase 的一个独特特征是存在插入 P 环 NTPase 结构域的两个或四个跨膜螺旋。这些跨膜螺旋将 KAP NTPase 锚定在膜上，使得 P 环结构域位于细胞内侧。我们表明，KAP 家族与 AAA+、ABC、RecA 样、VirD4 样、PilT 样和 AP/NACHT 样 NTPase 类属于 P 环 NTPase 折叠的相同主要部分。除了 KAP 家族之外，我们还鉴定了另一个预测细菌 NTPase 的小家族，其中两个跨膜螺旋插入到 P 环结构域中。该家族与 KAP NTPase 没有特定关系，表明跨膜螺旋的独立获得。结论：我们预测 KAP 家族 NTP 酶主要在蛋白质复合物的 NTP 依赖性动力学中发挥作用，尤其是与细胞膜的细胞内表面相关的蛋白质复合物。动物 KAP NTPase，包括 Kidins220/ARMS，可能作为参与神经突生长和发育的膜相关信号复合物组装的 NTP 依赖性调节因子。原核 KAP NTP 酶的一种可能的功能可能是从宿主细胞中排除自私的复制子，例如病毒。系统发育分析和系统发育模式表明，动物的共同祖先通过细菌的横向转移获得了 KAP NTPase。然而，不能排除较早转移到真核生物中，随后在几个真核细胞谱系中发生多次损失的可能性。