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: 10269689
• 负责人: Aravind Iyer
• 金额: $ 145.81万
• 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/10269689
• 关键词: 2019-nCoV; Active Sites; Animals; Apoptosis; Architecture; B-Lymphocytes; Bacteria; Binding; Biochemistry; Biological; Biological Process; Biology; COVID-19; Calcineurin; Calcium; Cell physiology; Cells; Collaborations; Complex; Conflict (Psychology); Cysteine; DNA; DNA Binding; DNA Double Strand Break; DNA Repair; Defect; Dominant-Negative Mutation; Double Strand Break Repair; EF Hand Motifs; Endoplasmic Reticulum; Environment; Epigenetic Process; Eukaryota; Evolution; Family; Gene Family; Genes; Genome; Genomics; Guanosine Triphosphate Phosphohydrolases; Hematopoiesis; Human; Immune response; Immunoglobulin Class Switching; Immunoglobulin Domain; Immunoglobulin Switch Recombination; Immunoglobulins; Infection; Inherited; Ligand Binding; Lung diseases; Measures; Mediating; Microscopic; Mitochondria; Modification; Molecular Chaperones; Mus; Nucleic Acids; Pathogenesis; Pathway interactions; Peptide Hydrolases; Physical Containment; Positioning Attribute; Process; Prokaryotic Cells; Protein phosphatase; Proteins; RNA-Directed DNA Polymerase; Reporting; Risk; Role; SARS coronavirus; SOS Response; Signal Transduction; Site; Social Environment; Structure; System; Tertiary Protein Structure; Time; Triad Acrylic Resin; Virulence Factors; Virus; WFS1 gene; Wolfram Syndrome; Work; base; biomineralization; cell motility; comparative genomics; crosslink; embryonic stem cell; global health; innovation; novel; novel coronavirus; nucleoside triphosphatase; progenitor; recruit; response; social; stem; symbiont; transmission process; whole genome

The origin of eukaryotes was marked by the emergence of several novel subcellular systems. One such is the calcium (Ca2+)-stores system of the endoplasmic reticulum, which profoundly influences diverse aspects of cellular function including signal transduction, motility, division, and biomineralization. We used comparative genomics and sensitive sequence and structure analyses to investigate the evolution of this system. Our findings reconstruct the core form of the Ca2+-stores system in the last eukaryotic common ancestor as having at least 15 proteins that constituted a basic system for facilitating both Ca2+ flux across endomembranes and Ca2+-dependent signaling. We showed that the key EF-hand Ca2+-binding components had their origins in a likely bacterial symbiont other than the mitochondrial progenitor, whereas the protein phosphatase subunit of the ancestral calcineurin complex was likely inherited from the asgardarchaeal progenitor of the stem eukaryote. This further points to the potential origin of the eukaryotes in a Ca2+-rich biomineralized environment such as stromatolites. We further show that throughout eukaryotic evolution there were several acquisitions from bacteria of key components of the Ca2+-stores system, even though no prokaryotic lineage possesses a comparable system. Further, using quantitative measures derived from comparative genomics we show that there were several rounds of lineage-specific gene expansions, innovations of novel gene families, and gene losses correlated with biological innovation such as the biomineralized molluscan shells, coccolithophores, and animal motility. The burst of innovation of new genes in animals included the wolframin protein associated with Wolfram syndrome in humans. We showed for the first time that it contains previously unidentified Sel1, EF-hand, and OB-fold domains, which might have key roles in its biochemistry. HMCES (5hmC binding, embryonic stem cell-specific-protein) was originally identified as a protein capable of binding 5-hydroxymethylcytosine (5hmC), an epigenetic modification generated by TET proteins. Our work showed that it contains a catalytic triad that is likely to possess autopeptidase activity. This active site was also reported to covalently crosslink to DNA at abasic sites via its conserved cysteine. In a collaboration with Dr. Anjana Rao's lab we showed that Hmces-deficient mice display normal hematopoiesis without global alterations in 5hmC. HMCES specifically enables DNA double-strand break repair through the microhomology-mediated alternative-end-joining (Alt-EJ) pathway during class switch recombination (CSR) in B cells, and HMCES deficiency leads to a significant defect in CSR. HMCES mediates Alt-EJ through its SOS-response-associated-peptidase domain (SRAPd), a function that requires DNA binding but is independent of its autopeptidase and DNA-crosslinking activities. We showed that HMCES is recruited to switch regions of the immunoglobulin locus and provide a potential structural basis for the interaction of HMCES with long DNA overhangs generated by Alt-EJ during CSR. Our studies provided strong evidence for for HMCES as a novel player in eukaryotic DNA repair with an origin in bacteria. The novel coronavirus (SARS-CoV-2) is the causative agent of an emergent severe respiratory disease (COVID-19) in humans that has resulted in a global health crisis. By using genomic, sequence, structural and evolutionary analysis, we identified several rapidly evolving proteins in SARS-CoV-2 with potential roles in pathogenesis. In addition to the well-known spike protein, these include the triad of Macro domains predicted to process NAD+ an showed that Alpha- and Beta-CoVs possess several novel families of immunoglobulin (Ig) domain proteins, including ORF8 and ORF7a from SARS-related coronaviruses and two protein groups from certain Alpha-CoVs. Among them, ORF8 is distinguished in being rapidly evolving, possessing a unique insert and a hypervariable position among SARS-CoV-2 genomes in its predicted ligand-binding groove. We also uncovered many Ig proteins from several metazoan viruses, which are distinct in sequence and structure but share an architecture comparable to that of CoV Ig domain proteins. Hence, we propose that deployment of Ig domain proteins is a widely-used strategy by viruses, and SARS-CoV-2 ORF8 is a potential pathogenicity factor which evolves rapidly to counter the immune response and facilitate the transmission between hosts. Social cellular aggregation or multicellular organization pose increased risk of transmission of infections through the system upon infection of a single cell. The generality of the evolutionary responses to this outside of Metazoa remains unclear. We discovered several thematically unified, remarkable biological conflict systems preponderantly present in multicellular prokaryotes. These combine thresholding mechanisms utilizing NTPase chaperones (the MoxR-vWA couple), GTPases and proteolytic cascades with hypervariable effectors, which vary either by using a reverse transcriptase-dependent diversity-generating system or through a system of acquisition of diverse protein modules, typically in inactive form, from various cellular subsystems. Conciliant lines of evidence indicate their deployment against invasive entities, like viruses, to limit their spread in multicellular/social contexts via physical containment, dominant-negative interactions or apoptosis. Base on these findings we argue for both a similar operational 'grammar' and shared protein domains in the sensing and limiting of infections during the multiple emergences of multicellularity.

真核生物的起源以几种新的亚细胞系统的出现为标志。其中之一是内质网的钙 (Ca2+) 储存系统，它深刻影响细胞功能的各个方面，包括信号转导、运动、分裂和生物矿化。我们使用比较基因组学以及敏感的序列和结构分析来研究该系统的进化。我们的研究结果重建了最后一个真核生物共同祖先中 Ca2+ 储存系统的核心形式，该系统具有至少 15 种蛋白质，这些蛋白质构成了促进 Ca2+ 跨内膜流动和 Ca2+ 依赖性信号传导的基本系统。我们发现，关键的 EF 手 Ca2+ 结合成分起源于线粒体祖细胞之外的一种可能的细菌共生体，而祖先钙调神经磷酸酶复合物的蛋白磷酸酶亚基很可能继承自茎真核生物的阿斯加菌祖细胞。这进一步指出了真核生物在富含 Ca2+ 的生物矿化环境（如叠层石）中的潜在起源。我们进一步表明，在整个真核进化过程中，尽管没有原核细胞谱系拥有类似的系统，但从细菌中多次获得了 Ca2+ 储存系统的关键成分。此外，使用来自比较基因组学的定量测量，我们表明存在多轮谱系特异性基因扩展、新基因家族的创新以及与生物创新相关的基因丢失，例如生物矿化软体动物壳、颗石藻和动物运动性。动物新基因的创新爆发包括与人类沃尔夫勒姆综合征相关的沃尔夫勒明蛋白。我们首次证明它包含以前未识别的 Sel1、EF-hand 和 OB-fold 结构域，这些结构域可能在其生物化学中发挥关键作用。 HMCES（5hmC 结合，胚胎干细胞特异性蛋白）最初被鉴定为能够结合 5-羟甲基胞嘧啶 (5hmC) 的蛋白质，5-羟甲基胞嘧啶 (5hmC) 是由 TET 蛋白产生的表观遗传修饰。我们的工作表明它包含一个可能具有自肽酶活性的催化三联体。据报道，该活性位点还通过其保守的半胱氨酸与脱碱基位点的 DNA 共价交联。在与 Anjana Rao 博士实验室的合作中，我们发现 Hmces 缺陷小鼠表现出正常的造血功能，而 5hmC 没有发生整体改变。 HMCES 在 B 细胞的类转换重组 (CSR) 过程中通过微同源介导的替代末端连接 (Alt-EJ) 途径特异性地实现 DNA 双链断裂修复，而 HMCES 缺陷会导致 CSR 的显着缺陷。 HMCES 通过其 SOS 反应相关肽酶结构域 (SRAPd) 介导 Alt-EJ，该功能需要 DNA 结合，但独立于其自肽酶和 DNA 交联活性。我们表明，HMCES 被招募来转换免疫球蛋白基因座的区域，并为 HMCES 与 CSR 过程中 Alt-EJ 产生的长 DNA 突出端的相互作用提供潜在的结构基础。我们的研究为 HMCES 作为起源于细菌的真核 DNA 修复的新参与者提供了强有力的证据。 新型冠状病毒（SARS-CoV-2）是人类突发严重呼吸道疾病（COVID-19）的病原体，已导致全球健康危机。通过使用基因组、序列、结构和进化分析，我们鉴定了 SARS-CoV-2 中几种快速进化的蛋白质，这些蛋白质在发病机制中具有潜在作用。除了众所周知的刺突蛋白外，这些蛋白还包括预计可处理 NAD+ 的宏结构域三联体，并表明 Alpha 和 Beta-CoV 拥有几个新的免疫球蛋白 (Ig) 结构域蛋白家族，包括来自 SARS 相关冠状病毒的 ORF8 和 ORF7a 以及来自某些 Alpha-CoV 的两个蛋白组。其中，ORF8 的特点是快速进化，在 SARS-CoV-2 基因组中其预测的配体结合槽中拥有独特的插入片段和高度可变的位置。我们还发现了来自几种后生动物病毒的许多 Ig 蛋白，它们在序列和结构上不同，但具有与 CoV Ig 结构域蛋白相似的结构。因此，我们认为部署 Ig 结构域蛋白是病毒广泛使用的策略，而 SARS-CoV-2 ORF8 是一种潜在的致病因子，它快速进化以对抗免疫反应并促进宿主之间的传播。 社会细胞​​聚集或多细胞组织在单细胞感染后通过系统传播感染的风险增加。后生动物之外对此的进化反应的普遍性仍不清楚。我们发现了几个主题统一的、显着的生物冲突系统，主要存在于多细胞原核生物中。这些结合了利用 NTPase 伴侣（MoxR-vWA 对）、GTPase 和蛋白水解级联与高变效应器的阈值机制，这些效应器通过使用逆转录酶依赖性多样性生成系统或通过从各种细胞子系统获取通常以非活性形式的不同蛋白质模块的系统而变化。一致的证据表明，它们针对病毒等入侵实体进行部署，通过物理遏制、显性负相互作用或细胞凋亡来限制它们在多细胞/社会环境中的传播。基于这些发现，我们主张在多细胞生物的多次出现期间，在感知和限制感染方面存在相似的操作“语法”和共享的蛋白质结构域。