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.

在过去的几年里，基因组序列和蛋白质结构的快速积累已经被序列数据库搜索方法的重大进展所取代。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。在过去的一年中，我们在详细分析几类蛋白质的分类，进化和功能方面取得了进一步的进展。特别地，在具有许多结构域的信号转导ATP酶之后，描述了一种新的主要类别的P-环NTPases，即所谓的STAND类别。STAND类包括AP-ATP酶（动物细胞凋亡调节剂CED4/Apaf-1、植物抗病蛋白和细菌AfsR样转录调节剂）和NACHT NTP酶（例如NAIP、TLP1、Het-E-1），其已经在细胞凋亡、动物和植物中的病原体应答以及细菌中的转录调节的背景下被广泛研究。我们发现，除了这些良好的特征蛋白质家族，STAND类包括其他几组（预测）NTR结构域从不同的信号和转录调控蛋白的细菌和真核生物，和三个特定的家族。我们确定了STAND结构域在几个生物学特征良好的蛋白质，尚未怀疑有NTR活性，包括可溶性腺苷酸环化酶，肾囊蛋白3（牵连在多囊肾病），和滚动卵石（肌肉发育的调节器）;这些发现有望促进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NTPases的区别在于存在与N-末端螺旋和核心链-4相关的独特序列基序，以及与NTPases结构域融合的C-末端螺旋束。该螺旋模块在两个远端螺旋之间的环中包含签名GxP基序。除了古细菌家族，几乎所有的STAND NTPases都是含有三个或更多结构域的多结构域蛋白。除了NTR结构域之外，这些蛋白质通常含有DNA结合或蛋白质结合结构域、超结构形成重复序列（例如WD 40和TPR）和参与信号转导的酶结构域（包括腺苷酸环化酶和激酶）。与AAA + ATP酶类似，可以预测STAND NTP酶使用C末端螺旋束作为"杠杆"，将NTP水解引起的构象变化传递到效应结构域。STAND NTPases代表了信号转导中的一种新范式，其中衔接子、调节开关、支架以及在某些情况下信号产生部分组合成单个多肽。STAND类由14个不同的家族组成，这些家族中的大多数家族的进化历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例子。STAND NTPases在发育和组织复杂的原核生物和真核生物中最丰富。STAND NTPases的基因从细菌转移到真核生物中，在真核生物信号系统的进化中可能发挥了重要作用。 此外，我们确定了一个以前未表征的家庭的P-环NTPases，其中包括神经元膜蛋白和受体酪氨酸激酶底物Kidins220/ARMS，这是保守的动物，F-质粒PifA蛋白参与噬菌体T7排斥，和几个未表征的细菌蛋白。我们将这些（预测的）NTPases称为KAP家族，位于Kidins220/ARMS和PifA之后。KAP家族NTPases在细菌中广泛分布，但在真核生物中仅存在于动物中。许多原核KAP NTPases在质粒中编码，并且倾向于经历破坏以形成假基因。所有真核生物和某些细菌KAP NTPases的独特特征是存在两个或四个跨膜螺旋插入P环NTPases结构域。这些跨膜螺旋将锚KAP NTPases锚定在膜中，使得P环结构域位于细胞内侧。我们表明，KAP家族属于相同的主要部门的P-环NTR折叠与AAA+，ABC，RecA样，VirD4样，PilT样，AP/NACHT样NTR类。除了KAP家族外，我们还鉴定了另一个预测的细菌NTPases小家族，其具有插入到P环结构域中的两个跨膜螺旋。该家族与KAP NTPases没有特异性相关，表明跨膜螺旋的独立获得。结论：我们预测，KAP家族NTPases的功能主要是在蛋白质复合物的NTP依赖的动力学，特别是那些与细胞膜的细胞内表面。动物KAP NTPases，包括Kidins 220/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依赖性调节剂发挥作用。原核KAP NTPases的一个可能的功能可能是从宿主细胞中排除自私的复制子，如病毒。系统发育分析和系统模式表明，动物的共同祖先获得了一个KAP NTR通过横向转移从细菌。然而，不能排除早期转移到真核生物中，随后在几个真核生物谱系中多次丢失的可能性。