甾体激素受体功能特异性的结构基础

甾体激素受体家族包括雌激素受体、雄激素受体等五个亚家族,在机体组织细胞的生长分化、发育生殖、内环境稳定等几乎所有生理过程中都起着重要的作用。研究甾体激素受体亚家族的特异性可以加深对该家族功能的理解,并且具有潜在的临床应用价值。采用进化踪迹方法对该家族的配体结合域（LBD）进行分析,探讨了决定亚家族功能特异性的结构基础。结果表明,甾体激素受体的各亚家族可能同相应的内源性配体存在着共进化关系;配体结合处的踪迹残基决定了受体－配体间的氢键作用和疏水相互作用模式并导致了亚家族的配体结合特异性。上述结论可用于甾体激素受体的配体结合特异性的改造以及新型组织选择性配体（如选择性雌激素受体调节剂,SERM）的设计。     

Unc5基因家族多样性进化的研究

Uncoordinated-5(Unc5)基因家族属于经典的轴突导向基因家族。为了探讨Unc5的进化和分化规律,首先通过序列比对和蛋白质结构预测鉴定了Unc5基因家族成员的起源和分布,再利用PAML和DIVERGE软件分析了各基因亚型的进化选择压力和功能歧化。结果表明,Unc5基因家族在脊椎动物中受到了不同程度的选择压力,其中Unc5C基因型受到了纯化选择作用,而Unc5A、Unc5B和Unc5D基因型受到了正选择作用,并且在这3个基因型中分别检测到了8个、1个和6个正选择位点。此外,DIVERGE软件检测出38个I型功能歧化位点和97个Ⅱ型功能歧化位点。这些正选择位点和功能分歧位点为进一步研究Unc5蛋白的结构和功能提供了参考和依据。     

西瓜含有JmjC结构域的组蛋白去甲基化酶家族的生物信息学分析

利用生物信息学方法,对西瓜（Citrullus lanatus（Thunb.）Matsum.&Nakai）JmjC基因家族的成员进行鉴定,对该基因家族的染色体定位、基因结构、蛋白结构域、选择压力和酶活位点进行分析,并对该基因家族与其它物种的系统进化及共线性关系进行研究。结果显示：西瓜全基因组含有17个JmjC候选基因,核苷酸序列长度为1209~5541 bp;这些基因均含有JmjC结构域,分别位于9条染色体上,归属8个亚族。系统进化、选择压力以及共线性分析结果表明,西瓜与黄瓜（Cucumis sativus L.）亲缘关系较近,JmjC家族基因数量相同,其中14个成员呈现一对一的共线性关系;而西瓜与拟南芥（Arabidopsis thaliana（L.）Heynh）亲缘关系较远,但西瓜和拟南芥同一亚族中JmjC基因间K_a/K_s的比值均小于1,推测西瓜各个亚族成员的编码蛋白功能与同一亚族的拟南芥成员功能极为相似。酶活位点分析结果表明西瓜JmjC基因家族中有10个成员具有潜在的组蛋白去甲基化酶活性。     

基因组水平蝙蝠嗅觉受体基因的分子进化

翼手目动物（俗称蝙蝠）的食性分化显著,不同食性的蝙蝠具有显著不同的嗅球大小。为了研究嗅觉是否影响了蝙蝠食性的进化,我们利用网上已公布的10种蝙蝠基因组的数据,通过同源比对的方法鉴定出所有的嗅觉受体基因,并进行嗅觉受体基因亚家族的分类,进而比较嗅觉受体基因亚家族的数目差异。结果显示,蝙蝠的嗅觉受体基因与其它哺乳动物一样,都可以分为13个单系起源的亚家族;在Yinpterochiroptera亚目中,OR1/3/7、OR2/13、OR5/8/9等3个嗅觉受体亚家族在食果蝙蝠中均发生了不同程度的扩张,基因数目显著地多于食虫蝙蝠,提示嗅觉在食果蝙蝠取食过程中具有重要的作用。因此,本研究在基因组水平上重现了蝙蝠嗅觉受体基因的进化历史,揭示了3个嗅觉受体基因亚家族的功能可能与食果蝙蝠的食性相关,突出了嗅觉对动物食性的重要作用.     

雷蒙德氏棉和亚洲棉基因组数据中LPAAT基因家族的发掘及其同源基因在陆地棉材料中的表达分析

溶血磷脂酸酰基转移酶(Lysophosphatidic acid acyltransferase, LPAAT)是油脂合成途径中的一个关键酶,能催化溶血磷脂酸转变为磷脂酸。本研究从雷蒙德氏棉(G. raimondii, D5)和亚洲棉(G. arboreum, A2)的基因组数据中得到17个LPAAT基因家族成员。利用生物信息学方法对二倍体棉花LPAAT基因进行基因结构、染色体分布以及系统进化分析。结果表明,LPAAT基因家族根据亲缘关系的远近可以分为不同的亚家族,各亚家族中LPAAT基因具有相似的基因结构;LPAAT家族基因编码的氨基酸序列具有3个保守基序,其中包括ΦFPEGTR-G结合位点和Φ-NHQS-ΦDΦΦ催化位点;通过对不同物种的LPAAT基因家族进行系统进化分析可知,不同物种中的LPAAT在进化中存在较大差异。基于陆地棉(G. hirsutum)不同发育时期的胚珠RNA-seq数据库和qRT-PCR表达分析,发现LPAAT基因可能对脂肪积累起到积极作用。本研究结果有助于了解棉属植物LPAAT基因家族的功能,以期从中选取较好的LPAAT基因进行进一步功能验证。     

受体型酪氨酸激酶RON异构体:潜在的肿瘤治疗靶标北大核心CSCD

RON是MET原癌基因家族的一员,与特异性配体MSP结合后,能通过激活下游RAS/ERK、PI3K/AKT等信号通路调节细胞的增殖、分化和侵袭等。RON是跨膜蛋白,结构上可分为胞外、跨膜和胞内3个片段,各片段具有其特异性的功能区。近年研究发现,由于前体mRNA选择性剪接,蛋白酶解和选择性转录等产生了多种RON异构体及转录本。由于缺失、插入或突变的结构不同,产生的RON异构体的功能也不尽相同。在研究RON的亚结构功能时,具有不同甚至拮抗功能的异构体,能提供大量有益的帮助。但同时,这些异构体影响了对RON表达的定量分析以及其特异性治疗效果。更加深入了解不同RON异构体的结构及其亚单位的功能,也能为基于RON的靶向治疗提供更多有利的参考。     

雷蒙德氏棉HSP70基因家族的进化分析及其同源基因在陆地棉中的表达分析

热激蛋白70家族(HSP70)是一类在植物中高度保守的分子伴侣蛋白,在细胞中协助蛋白质正确折叠。文章利用隐马可链夫模型(HMM)在雷蒙德氏棉(Gossypium raimondii L.)全基因组范围内进行HSP70基因家族成员进化分析,共得到30个HSP70家族成员。利用生物信息学对雷蒙德氏棉HSP70基因的结构、染色体分布、基因倍增模式以及系统进化进行分析,结果表明,HSP70基因家族根据亚细胞定位结果可分为不同的基因亚家族,各亚家族中HSP70基因具有相对保守的基因结构;染色体片段重复和串联重复是雷蒙德氏棉HSP70基因家族扩增的主要方式。通过对不同物种的HSP70基因家族进行系统进化分析可知,HSP70亚组的分化发生在单细胞植物形成前,且细胞质型HSP70成员大量扩增。比较陆地棉棉纤维发育不同时期的深度测序表达谱,发现HSP70基因可能参与棉纤维的生长发育。本研究结果有助于了解棉属植物HSP70基因家族的功能,以期为深入研究棉纤维发育过程中的分子调控机理提供基础。     

哺乳动物锌指蛋白家族中KRAB功能域的进化

KRAB锌指基因是哺乳动物中最大的转录调控因子家族,它的多数成员在基因组上成簇分布,具有五种不同的亚家族,在功能行使上承担着不同的作用。本文通过对人类、黑猩猩、小鼠、大鼠和狗五种哺乳动物全蛋白质组序列及mRNA组织表达谱分析,验证了C2H2锌指结构在单个KRAB蛋白质中出现的数目多于一般锌指蛋白质;KRAB功能域在各物种中分布显著不同且与分化时间不成正比,这表明KRAB相关功能域多样性在灵长类进化过程中潜在的适应性进化。同时,提出KRAB亚家族进化的路线：即KRAB—Aa为起始家族,Ba由Aa直接演变形成,而Ca,blonga和XRCC-Z种亚型可能经过Ba或直接从Aa演变形成;此外,锌指结构在单个蛋白质中出现个数伴随KRAB功能域自身的进化路线逐渐递增,反映了KRAB功能域在形成新转录调控因子方面的积极作用。     

毛果杨nsLTP基因家族全基因组水平鉴定及其表达特性分析

植物非特异性脂质转移蛋白（non-specific lipid transfer proteins,nsLTP）是一类多基因家族编码碱性蛋白,负责脂肪酸体外结和与膜之间的磷脂转移,在植物生长发育和逆境胁迫响应中扮演着重要角色。目前为止,尚无模式植物毛果杨（Populus trichocarpa）nsLTP家族的研究报导。本研究从全基因组水平对PtrnsLTP家族成员的基因数量、亲缘关系、基因结构、编码蛋白保守基序等特性进行了分析,结果表明：PtrnsLTP家族共由39个基因组成,进化成5个亚家族,其中A亚族含有6个基因、B亚族含有2个、C亚族含有13个、D亚族含有3个、E亚族含有15个。PtrnsLTP家族包含7对旁系同源基因,其中1对大于1,6对Ka/Ks均远小于1,且这6对基因均处于同一个大的进化分支上,进化压力的不同导致基因间的功能出现了分化,编码蛋白均含有Motif 1和 Motif 2保守基序。利用qRT-PCR技术并结合杨树转录组数据对PtrnsLTP的组织表达与盐胁迫响应特性研究发现：各家族成员在毛果杨根、茎和叶中均有表达且经qRT-PCR技术验证后与网站预测结果基本吻合,有11、15和13个成员分别在根、茎和叶中有较高的表达,表明该基因家族参与了杨树不同组织的生长发育;NaCl胁迫下,该家族39个基因中分别有26个成员在根部、14个成员在叶部表达量随着胁迫时间的增加而升高,而32个基因在茎部表现为先升高后降低的趋势。本研究结果对于PtrnsLTP家族基因生物学功能的鉴定与盐胁迫响应基因资源的工作有着积极的推动作用。     

中粒咖啡萜类合成酶基因家族的生物信息学分析

萜类化合物具有重要的生理、生态作用和药用价值,萜类合成酶(TPS)是合成萜类化合物的关键酶。通过整合中粒咖啡(Coffee canephora)的基因组和转录组数据,利用生物信息学方法,鉴定出43个萜类合成酶全长基因,并对这些基因的分子进化、结构、复制、表达及功能分化的机理进行了探究。结果表明,中粒咖啡萜类合成酶基因可以分为5个亚家族(a、b、c、e/f、g),不同亚家族的基因结构差异很大;串联复制是基因家族扩增的主要原因;表达分析结果表明,萜类合成酶基因在不同组织中的表达差异明显;中粒咖啡萜类合成酶基因启动子区的顺式调控元件可能与基因的功能分化相关;不同亚家族之间的功能差异主要由亚家族特异的氨基酸决定。     

Evolution of the class C GPCR Venus flytrap modules involved positive selected functional divergence

Background  

Class C G protein-coupled receptors (GPCRs) represent a distinct group of the GPCR family, which structurally possess a characteristically distinct extracellular domain inclusive of the Venus flytrap module (VFTM). The VFTMs of the class C GPCRs is responsible for ligand recognition and binding, and share sequence similarity with bacterial periplasmic amino acid binding proteins (PBPs). An extensive phylogenetic investigation of the VFTMs was conducted by analyzing for functional divergence and testing for positive selection for five typical groups of the class C GPCRs. The altered selective constraints were determined to identify the sites that had undergone functional divergence via positive selection. In order to structurally demonstrate the pattern changes during the evolutionary process, three-dimensional (3D) structures of the GPCR VFTMs were modelled and reconstructed from ancestral VFTMs.     

Understanding the functional difference between growth arrest-specific protein 6 and protein S: an evolutionary approach

Although protein S (PROS1) and growth arrest-specific protein 6 (GAS6) proteins are homologous with a high degree of structural similarity, they are functionally different. The objectives of this study were to identify the evolutionary origins from which these functional differences arose. Bioinformatics methods were used to estimate the evolutionary divergence time and to detect the amino acid residues under functional divergence between GAS6 and PROS1. The properties of these residues were analysed in the light of their three-dimensional structures, such as their stability effects, the identification of electrostatic patches and the identification potential protein–protein interaction. The divergence between GAS6 and PROS1 probably occurred during the whole-genome duplications in vertebrates. A total of 78 amino acid sites were identified to be under functional divergence. One of these sites, Asn463, is involved in N-glycosylation in GAS6, but is mutated in PROS1, preventing this post-translational modification. Sites experiencing functional divergence tend to express a greater diversity of stabilizing/destabilizing effects than sites that do not experience such functional divergence. Three electrostatic patches in the LG1/LG2 domains were found to differ between GAS6 and PROS1. Finally, a surface responsible for protein–protein interactions was identified. These results may help researchers to analyse disease-causing mutations in the light of evolutionary and structural constraints, and link genetic pathology to clinical phenotypes.     

Determinants of Endogenous Ligand Specificity Divergence among Metabotropic Glutamate Receptors

To determine the structural origins of diverse ligand response specificities among metabotropic glutamate receptors (mGluRs), we combined computational approaches with mutagenesis and ligand response assays to identify specificity-determining residues in the group I receptor, mGluR1, and the group III receptors, mGluR4 and mGluR7. Among these, mGluR1 responds to l-glutamate effectively, whereas it binds weakly to another endogenous ligand, l-serine-O-phosphate (l-SOP), which antagonizes the effects of l-glutamate. In contrast, mGluR4 has in common with other group III mGluR that it is activated with higher potency and efficacy by l-SOP. mGluR7 differs from mGluR4 and other group III mGluR in that l-glutamate and l-SOP activate it with low potency and efficacy. Enhanced versions of the evolutionary trace (ET) algorithm were used to identify residues that when swapped between mGluR1 and mGluR4 increased the potency of l-SOP inhibition relative to the potency of l-glutamate activation in mGluR1 mutants and others that diminished the potency/efficacy of l-SOP for mGluR4 mutants. In addition, combining ET identified swaps from mGluR4 with one identified by computational docking produced mGluR7 mutants that respond with dramatically enhanced potency/efficacy to l-SOP. These results reveal that an early functional divergence between group I/II and group III involved variation at positions primarily at allosteric sites located outside of binding pockets, whereas a later divergence within group III occurred through sequence variation both at the ligand-binding pocket and at loops near the dimerization interface and interlobe hinge region. They also demonstrate the power of ET for identifying allosteric determinants of evolutionary importance.     

慢性低氧对大鼠左右心室的功能及TRPC亚家族表达的影响

目的：探讨慢性低氧3周对大鼠左右心室的影响以及规范性瞬时感受器电位亚家族（TRPC）在慢性低氧诱导的右心室心肌肥厚中的表达。方法：将SD雄性大鼠48只随机分为对照组（CON组）和慢性低氧肺动脉高压模型组（CH组）（n=24）,CH组将大鼠置于连续的慢性低氧（10％±0．2％）环境饲养三周以诱导大鼠发生心肌肥厚。通过左、右心室插管法测定右心室内压（RVSP）、左心室内压（LVSP）、心率（HR）、平均体循环动脉压（mSAP）、左、右心室内压力最大上升速率（＋dp／dtmax）、最大下降速率（-dp／dkmax）、右心肥大指数（RVMI）、左心肥大指数（LVMI）;HE染色观察左、右心室心肌组织切片;通过SYBR Green荧光定量PCR法检测CON组、CH组大鼠的肥厚侧心室心肌组织编码TRPC 1／3／4／5／6／7的rnRNA表达;结合real-time RT-PCR结果对mRNA表达有显著变化的TRPC亚型通过免疫印迹法检测相应蛋白的表达。结果：与CON组相比：CH组的RVSP、RVMI、右心室±dp／dtmax显著增高（P〈0．01）,LVSP、左心室±dp／dmax无显著变化,LVMI显著降低（P〈0．01）;CH组右心室心肌细胞显著增粗（P〈0．01）,细胞内肌原纤维数量增多,心肌纤维排列紊乱,细胞核深染,形状不整;左心室心肌纤维无明显改变;CH组编码TRPCI的mRNA和蛋白显著增高（P〈0．05）,而编码其余TRPC亚型的mRNA无显著变化。结论：慢性低氧3周可特异性诱导sD大鼠产生右心室心肌肥厚,上调了编码右心室心肌细胞TRPCI通道蛋白的mRNA和蛋白的表达,TRPCI可能参与了心肌肥厚的发生发展。     

Evolutionary analysis for functional divergence of Jak protein kinase domains and tissue-specific genes

Jak (Janus kinase) is a nonreceptor tyrosine kinase, which plays important roles in signal transduction pathways. The unique feature of Jak is that, in addition to a fully functional tyrosine kinase domain (JH1), Jak possesses a pseudokinase domain (JH2). Although JH2 lost its catalytic function, experimental evidence has shown that this domain may have acquired some new but unknown functions. This apparent functional divergence after the (internal) domain duplication may result in dramatic changes of selective constraints at some sites. We conducted a data analysis to test this hypothesis. Our result shows that shifted selective constraints (or shifted evolutionary rates) between the JH1 and the JH2 domains are statistically significant. Predicted amino acid sites by posterior analysis can be classified into two groups: very conserved in JH1 but highly variable in JH2, and vice versa. Moreover, we have studied the evolutionary pattern of four tissue-specific genes, Jak1, Jak2, Jak3, and Tyk2, which were generated in the early stages of vertebrates. We found that after the (first) gene duplication, site-specific rate shifts between Jak2/Jak3 and Jak1/Tyk are significant, presumably as a consequence of functional divergence among these genes. The implication of our study for functional genomics is discussed.     

Delineating a Ca2+ binding pocket within the venus flytrap module of the human calcium-sensing receptor

The Ca(2+)-sensing receptor (CaSR) belongs to the class III G-protein-coupled receptors (GPCRs), which include receptors for pheromones, amino acids, sweeteners, and the neurotransmitters glutamate and gamma-aminobutyric acid (GABA). These receptors are characterized by a long extracellular amino-terminal domain called a Venus flytrap module (VFTM) containing the ligand binding pocket. To elucidate the molecular determinants implicated in Ca(2+) recognition by the CaSR VFTM, we developed a homology model of the human CaSR VFTM from the x-ray structure of the metabotropic glutamate receptor type 1 (mGluR1), and a phylogenetic analysis of 14 class III GPCR VFTMs. We identified critical amino acids delineating a Ca(2+) binding pocket predicted to be adjacent to, but distinct from, a cavity reminiscent of the binding site described for amino acids in mGluRs, GABA-B receptor, and GPRC6a. Most interestingly, these Ca(2+)-contacting residues are well conserved within class III GPCR VFTMs. Our model was validated by mutational and functional analysis, including the characterization of activating and inactivating mutations affecting a single amino acid, Glu-297, located within the proposed Ca(2+) binding pocket of the CaSR and associated with autosomal dominant hypocalcemia and familial hypocalciuric hypercalcemia, respectively, genetic diseases characterized by perturbations in Ca(2+) homeostasis. Altogether, these data define a Ca(2+) binding pocket within the CaSR VFTM that may be conserved in several other class III GPCRs, thereby providing a molecular basis for extracellular Ca(2+) sensing by these receptors.     

神经元型一氧化氮合酶在Ⅱ组代谢型谷氨酸受体介导的脑缺血耐受中的作用

目的：探讨神经元型一氧化氮合酶（nNOS）催化产生的一氧化氮（NO）在Ⅱ组代谢型谷氨酸受体（mGluR2／3）介导的脑缺血预处理（CIP）保护机制中的作用。方法：36只永久凝闭椎动脉的SD大鼠随机分为6组（n=6）：sham、CIP、损伤性缺血、CIP4-损伤性缺血、MqPG＋CIP和MTPG＋CIP＋损伤性缺血组。采用硫堇染色和免疫组化观察海马CA1区迟发性神经元死亡（DND）和nNOS表达的变化。结果：与Sham组相比,CIP组海马nNOS表达出现一定程度的上调,而损伤性脑缺血组则出现nNOS表达的明显上调,预先给与CIP可一定程度上防止损伤性脑缺血所致的nNOS表达的过度升高。在MTPG4-CIP组,预先侧脑室注射mGluR2／3阻断剂MTPG,可阻断CIP引起的nNOS表达增加,但对神经元的存活无影响。而在MTPG＋CIP＋损伤性缺血组中,出现大量锥体神经元DND,同时nNOS的表达较MTPG＋CIP组明显增加,该增加为损伤性脑缺血所致,而非MTPG的作用。结论：nNOS催化产生的NO作为mGluR2／3的下游分子参与脑缺血预处理过程中mGluR2／3介导的脑缺血耐受的形成。     

国家自然科学基金委重大项目“禾本科植物的适应性辐射及其进化机制”结题综述

国家自然科学基金委重大项目"禾本科植物的适应性辐射及其进化机制"利用比较形态学、分子系统学、进化发育生物学、古生物学等多方面证据,通过多学科交叉的方法探讨了禾本科植物中出现的适应性辐射现象及其机制,在禾本科的系统发育关系以及适应性辐射的基本式样、生物和非生物环境因素在物种适应和分化以及物种快速形成中的作用、基因组大小及其结构变异以及突变、重复和调控模式变化对适应性辐射过程中关键性状(功能)的影响等方面取得了重要进展,在人才培养、国际合作和实验体系建立等方面极具特点。该项目的顺利完成为更好地阐明植物多样性形成的原因与机理奠定了良好的基础。     

Comparative analysis of sequence covariation methods to mine evolutionary hubs: Examples from selected GPCR families

Covariation between positions in a multiple sequence alignment may reflect structural, functional, and/or phylogenetic constraints and can be analyzed by a wide variety of methods. We explored several of these methods for their ability to identify covarying positions related to the divergence of a protein family at different hierarchical levels. Specifically, we compared seven methods on a model system composed of three nested sets of G‐protein‐coupled receptors (GPCRs) in which a divergence event occurred. The covariation methods analyzed were based on: χ² test, mutual information, substitution matrices, and perturbation methods. We first analyzed the dependence of the covariation scores on residue conservation (measured by sequence entropy), and then we analyzed the networking structure of the top pairs. Two methods out of seven—OMES (Observed minus Expected Squared) and ELSC (Explicit Likelihood of Subset Covariation)—favored pairs with intermediate entropy and a networking structure with a central residue involved in several high‐scoring pairs. This networking structure was observed for the three sequence sets. In each case, the central residue corresponded to a residue known to be crucial for the evolution of the GPCR family and the subfamily specificity. These central residues can be viewed as evolutionary hubs, in relation with an epistasis‐based mechanism of functional divergence within a protein family. Proteins 2014; 82:2141–2156. © 2014 Wiley Periodicals, Inc.