Evolutionary Analysis and Comparative Genomics of Protein Superfamilies

蛋白质超家族的进化分析和比较基因组学

• 批准号: 7735093
• 负责人: Aravind Iyer
• 金额: $ 22.42万
• 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/7735093
• 关键词: ATP phosphohydrolase; ATPase Domain; Active Sites; Adenoviruses; Anatomy; Animal Model; Animals; Architecture; Bacteria; Binding; Biological; Biological Process; Biology; C-terminal; Catalysis; Chromatin; Chromatin Structure; Chromosomes; Classification; Code; Comparative Genomic Analysis; Complex; Cysteine; DNA; DNA Binding Domain; DNA Modification Process; DNA Packaging; DNA Viruses; Demography; Drosophila genus; Elements; Entamoeba histolytica; Enzymatic Biochemistry; Enzymes; Epigenetic Process; Eukaryota; Eukaryotic Cell; Evolution; Family; Future; Genes; Genetic Transcription; Genomics; Giardia; Helix-Turn-Helix Motifs; Histidine; Histone Code; Histones; Individual; Investigation; Life; Ligase; Lipids; Location; Mechanics; Mediating; Membrane; Membrane Lipids; Methyltransferase; Microscopic; Modification; Molecular; Motor; Naegleria; Neighborhoods; Nucleic Acids; Nucleosomes; Numbers; Oomycetes; Organism; Parasites; Pathway interactions; Peptides; Phytophthora; Play; Portal System; Positioning Attribute; Poxviridae; Protein Analysis; Protein Binding; Protein Isoforms; Proteins; Proteome; Pump; Reaction; Recording of previous events; Relative (related person); Reporting; Research Personnel; Role; SWI2/SNF2; Shapes; Signal Transduction; Sister; Structure; Surgical Flaps; System; Tail; Tertiary Protein Structure; Trichomonas; Trichomonas vaginalis; Ubiquitin; Ubiquitin Like Proteins; Viral; Viral Packaging; Viral Proteins; Virus; base; chromatin protein; chromatin remodeling; comparative; genome sequencing; histone acetyltransferase; histone methyltransferase; innovation; member; novel; nuclease; protein protein interaction; reconstruction; research study; scaffold; size; terminase; transcription factor; transposon/insertion element; viral DNA

1)Comparative Genomics and Evolutionary Trajectories of Viral ATP Dependent DNA-Packaging Systems. We performed a comparative genomics study of ATP-dependent DNA packaging systems of viruses. Several distinct ATPase motors and accessory proteins have been identified in DNA-packaging systems of viruses such as terminase-portal systems, the phi29-like packaging apparatus, and packaging systems of lipid inner-membrane-containing viruses. Sequence and structure analysis of these proteins suggest that there were two major independent innovations of ATP-dependent DNA packaging systems in the viral universe. The first of these utilizes a HerA/FtsK superfamily ATPase and is seen in prokaryotic viruses with inner lipid membranes, large eukaryotic nucleo-cytoplasmic DNA viruses (including poxviruses) and a group of eukaryotic mobile DNA transposons. We showed that ATPases of the phi29-like packaging system are also divergent versions of the HerA/FtsK superfamily that functions in viruses without an inner membrane. The second system, the terminase-portal system, is dominant in prokaryotic tailed viruses and typically functions with linear chromosomes. The large subunit of this system contains a distinct ATPase domain and a C-terminal nuclease domain of the RNAse H fold. We developed the classification of these ATPases within the P-loop NTPases, genomic demography and positioning of their genes in the viral chromosome. We showed that diverse portal proteins utilized by these systems share a common evolutionary origin and might have frequently displaced each other in evolution. Examination of conserved gene neighborhoods indicates repeated acquisition of Helix-turn-Helix domaincontaining terminase small subunits and a third accessory component, the MuF protein. Adenoviruses appear to have evolved a third packaging ATPase, unique to their lineage. Relationship between one major type of packaging ATPases and cellular chromosome pumps like FtsK suggests an ancient common origin for viral packaging and cellular chromosome partitioning systems. 2)Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes. Comparative genomics of parasitic protists and their free-living relatives are profoundly impacting our understanding of the regulatory systems involved in transcription and chromatin dynamics. While some parts of these systems are highly conserved, other parts are rapidly evolving, thereby providing the molecular basis for the variety in the regulatory adaptations of eukaryotes. The gross number of specific transcription factors and chromatin proteins are positively correlated with proteome size in eukaryotes. However, the individual types of specific transcription factors show an enormous variety across different eukaryotic lineages. The dominant families of specific transcription factors even differ between sister lineages, and have been shaped by gene loss and lineage-specific expansions. Recognition of this principle has helped in identifying the hitherto unknown, major specific transcription factors of several parasites, such as apicomplexans, Entamoeba histolytica, Trichomonas vaginalis, Phytophthora and ciliates. Comparative analysis of predicted chromatin proteins from protists allows reconstruction of the early evolutionary history of histone and DNA modification, nucleosome assembly and chromatin-remodeling systems. Many key catalytic, peptide-binding and DNA-binding domains in these systems ultimately had bacterial precursors, but were put together into distinctive regulatory complexes that are unique to the eukaryotes. In the case of histone methylases, histone demethylases and SWI2/SNF2 ATPases, proliferation of paralogous families followed by acquisition of novel domain architectures, seem to have played a major role in producing a diverse set of enzymes that create and respond to an epigenetic code of modified histones. The diversification of histone acetylases and DNA methylases appears to have proceeded via repeated emergence of new versions, most probably via transfers from bacteria to different eukaryotic lineages, again resulting in lineage-specific diversity in epigenetic signals. Even though the key histone modifications are universal to eukaryotes, domain architectures of proteins binding post-translationally modified-histones vary considerably across eukaryotes. This indicates that the histone code might be "interpreted" differently from model organisms in parasitic protists and their relatives. The complexity of domain architectures of chromatin proteins appears to have increased during eukaryotic evolution. Thus, Trichomonas, Giardia, Naegleria and kinetoplastids have relatively simple domain architectures, whereas apicomplexans and oomycetes have more complex architectures. RNA-dependent post-transcriptional silencing systems, which interact with chromatin-level regulatory systems, show considerable variability across parasitic protists, with complete loss in many apicomplexans and partial loss in Trichomonas vaginalis. This evolutionary synthesis offers a robust scaffold for future investigation of transcription and chromatin structure in parasitic protists. 3)Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation. The configuration of the active site of E2 ligases, central enzymes in the ubiquitin/ubiquitin-like protein (Ub/Ubl) conjugation systems, has long puzzled researchers. Taking advantage of the wealth of newly available structures and sequences of E2s from diverse organisms, we performed a large-scale comparative analysis of these proteins. As a result we identified a previously under-appreciated diversity in the active site of these enzymes, in particular, the spatial location of the catalytic cysteine and a constellation of associated conserved residues that potentially contributes to catalysis. We observed structural innovations of differing magnitudes occurring in various families across the E2 fold that might correlate in part with differences in target interaction. A key finding was the independent emergence on multiple occasions of a polar residue, often a histidine, in the vicinity of the catalytic cysteine in different E2 families. We propose that these convergently emerging polar residues have a common function, such as in the stabilization of oxyanion holes during Ub/Ubl transfer and spatial localization of the Ub/Ubl tails in the active site. Thus, the E2 ligases represent a rare example in enzyme evolution of high structural diversity of the active site and position of the catalytic residue despite all characterized members catalyzing a similar reaction. Our studies also indicated certain evolutionarily conserved features in all active members of the E2 superfamily that stabilize the unusual flap-like structure in the fold. These features are likely to form a critical mechanical element of the fold required for catalysis. The results presented here could aid in new experiments to understand E2 catalysis. BEN: a novel domain in chromatin factors and DNA viral proteins. We reported a previously uncharacterized alpha-helical module, the BEN domain, in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Contextual analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organization and transcription. The presence of BEN domains in a poxviral early virosomal protein and in polydnaviral proteins also suggests a possible role for them in organization of viral DNA during replication or transcription.

1）病毒ATP依赖性DNA包装系统的比较基因组学和进化轨迹。 我们对病毒的ATP依赖性DNA包装系统进行了比较基因组学研究。已经在病毒的DNA包装系统中鉴定出几种不同的ATPase Motor和辅助蛋白，例如末端酶 - 门膜系统，类似PHI29的包装设备以及含脂质内膜内膜病毒的包装系统。这些蛋白质的序列和结构分析表明，病毒宇宙中ATP依赖性DNA包装系统的两个主要独立创新。其中的第一个利用HERA/FTSK超家族ATPase，在具有内部脂质膜的原核病毒中可见，大型真核神经核细胞质DNA病毒（包括痘病毒）和一组真核生物移动的移动DNA tryposons。我们表明，类似Phi29的包装系统的ATPase也是HERA/FTSK超家族的不同版本，该版本在没有内膜的病毒中起作用。第二个系统是末端 - 体积系统，在原核尾病毒中占主导地位，通常与线性染色体起作用。该系统的大量亚基包含一个不同的ATPase结构域和RNase H折叠的C末端核酸酶结构域。我们在P环NTPases，基因组人口统计学及其基因在病毒染色体中的定位中开发了这些ATPases的分类。我们表明，这些系统使用的多种门户蛋白具有共同的进化起源，并且可能经常在进化中相互流离失所。对保守基因邻域的检查表明，反复采集螺旋螺旋螺旋结构域的末端酶小亚基和第三个附件成分MUF蛋白。腺病毒似乎已经进化出了第三个包装ATPase，其谱系是其谱系所特有的。一种主要类型的包装ATPase与FTSK（例如FTSK）等细胞染色体泵之间的关系表明，病毒包装和细胞染色体分配系统的古老起源。 2）寄生虫和其他真核生物中转录因子和染色质蛋白的比较基因组学。 寄生生物及其自由生活亲戚的比较基因组学对我们对参与转录和染色质动力学涉及的调节系统的理解产生了深远的影响。尽管这些系统的某些部分是高度保守的，但其他部分正在迅速发展，从而为真核生物的调节适应性提供了分子基础。特定转录因子和染色质蛋白的总数与真核生物中的蛋白质组大小呈正相关。但是，特定转录因子的各个类型显示在不同的真核谱系中种类繁多。特定转录因子的主要家族甚至在姊妹谱系之间也有所不同，并且已经由基因丧失和谱系特异性扩张来塑造。对这一原则的认识有助于确定迄今未知的几种寄生虫的主要特定转录因子，例如apicomplexans，sentamoeba histolytica，trichomonas vaginalis，phytophthora和ciliates。对生物学家预测的染色质蛋白的比较分析允许重建组蛋白和DNA修饰的早期进化史，核小体组装和染色质 - 复发系统。这些系统中的许多关键催化，肽结合和DNA结合结构域最终都具有细菌前体，但被放入真核生物独有的独特调节复合物中。在组蛋白甲基酶，组蛋白脱甲基酶和SWI2/SNF2 ATPases的情况下，寄生虫家族的增殖随后是获得新型结构架构的，似乎在产生一系列酶创造和响应的酶方面起着重要作用。组蛋白乙酰酶和DNA甲基酶的多样化似乎是通过反复出现新版本进行的，这很可能是通过从细菌到不同真核谱系的转移，再次导致表观遗传信号的谱系特异性多样性。即使关键的组蛋白修饰与真核生物是普遍的，但在真核生物中，蛋白质结合后的蛋白质结构构建域也有很大差异。这表明组蛋白代码可能与寄生虫及其亲戚的模型生物“解释”不同。在真核进化过程中，染色质蛋白的结构域结构的复杂性似乎有所增加。因此，毛毛虫，贾迪亚，纳格勒菌和动型塑料具有相对简单的结构架构，而Apicomplexans和Oomycetes具有更复杂的结构。与染色质级调节系统相互作用的RNA依赖性后沉默系统显示出寄生虫生物的可变性很大，许多Apicomplexans的损失完全损失，而Trichomonas阴道中的部分损失则显示出。该进化合成为寄生虫的转录和染色质结构的未来研究提供了强大的支架。 3）E2连接酶褶皱的解剖：对泛素/UB样蛋白结合的酶学和演变的影响。 E2连接酶的活性位点的构型，泛素/泛素样蛋白（UB/UBL）共轭系统中的中央酶长期以来一直困惑研究人员。利用来自不同生物体的E2的新可用结构和序列的优势，我们对这些蛋白质进行了大规模的比较分析。结果，我们确定了这些酶的活性位点中先前被低估的多样性，尤其是催化半胱氨酸的空间位置以及可能有助于催化的相关保守残基的星座。我们观察到在E2折叠各个家族中发生不同幅度的结构创新，这可能部分与目标相互作用的差异相关。一个关键的发现是在不同E2家族中催化半胱氨酸附近的极性残基（通常是组氨酸）的多次出现。我们提出，这些趋同的极性残基具有共同的功能，例如在UB/UBL转移期间的氧孔稳定和活性位点中UB/UBL尾巴的空间定位。因此，E2连接酶是活性位点高结构多样性的酶演化和催化残基的位置的罕见例子，尽管所有特征成员都催化了类似的反应。我们的研究还表明，在E2超家族的所有活性成员中，某些进化保守的特征可以稳定折叠中异常的襟翼样结构。这些特征可能会形成催化所需的折叠的关键机械元素。此处介绍的结果可以帮助进行新的实验以了解E2催化。 BEN：染色质因子和DNA病毒蛋白的新结构域。 我们报道了在多种动物蛋白（例如BANP/SMAR1，NAC1和果蝇MOD（MDG4）同工型C中，在多种动物蛋白E5R中的多种动物蛋白（例如BANP/SMAR1，NAC1）和果蝇Mod（MDG4）Mod（MDG4）中，BEN结构域的先前未表征。上下文分析表明，BEN域在染色质组织和转录过程中介导蛋白-DNA和蛋白质 - 蛋白质相互作用。 BEN域在早期的病毒体蛋白和多核蛋白中的存在也表明，在复制或转录过程中，它们在病毒DNA的组织中可能起作用。