FAM3基因家族功能研究概况

蛋白序列相似度为3的类细胞因子家族(family with similarity 3,FAM3)是2002年发现的新基因家族,其包括四个成员FAM3A、FAM3B、FAM3C和FAM3D。因FAM3B高表达于胰腺胰岛细胞中,又被称为胰腺衍生因子(pancreatic derived factor,PANDER)。PANDER已被证实在胰岛素抵抗和2型糖尿病发展过程中起重要作用,其可能成为2型糖尿病的新干预靶点。FAM3C被发现在胚胎发育和视网膜功能调控,上皮细胞间充质转化及胰腺癌发生过程中起重要作用。FAM3D被发现可能介入了机体能量代谢异常、结肠癌及嗜睡等疾病的发生发展过程。目前尚未见有关FAM3A生物学功能的研究报道。总之,现有研究表明FAM3基因家族成员可能在包括糖尿病和肿瘤在内的多种重大疾病发生发展过程中起重要作用。本综述将对FAM3基因家族的最新研究进展进行简要总结及讨论。     

油菜EIN3/EIL基因家族的鉴定及结构分析

Ethylene-insensitive3(EIN3)和EIN3-like(EIL)蛋白是乙烯信号转导途径中重要的核转录因子。EIN3/EIL基因家族在高等植物中分布广泛,在植物的生长、发育等多个过程中有重要的作用。为了揭示油菜EIN3/EIL基因家族的生物学信息,利用生物信息学的方法鉴定了油菜EIN3/EIL基因家族的成员,并从理化性质、亚细胞定位、跨膜结构、二级结构等几个方面对油菜EIN3/EIL基因家族成员进行了预测和分析。这些研究结果有助于进一步研究油菜EIN3/EIL基因家族成员的功能,同时在生产实践中也具有一定的应用价值。     

谷子CPP基因家族鉴定及外源硒响应分析

【目的】探究谷子CPP家族成员基本特征及其在外源硒处理下的响应模式,为谷子富硒高叶酸新品种选育提供新的遗传材料。【方法】借助生物信息学工具鉴定谷子CPP家族成员,采用qRT-PCR技术对CPP基因在不同组织及外源硒处理下的表达水平进行检测,为揭示谷子CPP家族生物学功能及外源硒响应机制奠定基础。【结果】(1)谷子基因组中包含9个CPP基因,定位于6条染色体上,依照基因在染色体的排布命名为SiCPP1～SiCPP9,氨基酸数目在220～899之间,相对分子量为23624.32～97253.16Da,等电点介于6.64～9.17之间,内含子数目为3～11个不等,亚细胞预测显示该家族所有成员均能在细胞核定位到,蛋白质二级结构预测表明该家族中占比最大的是α-螺旋其次是无规则卷曲。(2)系统进化分析表明,谷子CPP蛋白可分为4个亚家族,相同亚家族之间保守基序和结构域的数目及分布相似。(3)启动子分析发现谷子CPP家族中存在大量光、生长发育、激素以及胁迫响应元件。(4)荧光定量结果显示,谷子CPP家族成员在根、茎、叶和穗中差异表达。谷子CPP家族9个成员均对外源硒存在响应,其中SiCPP5、SiCPP6、SiCPP7和SiCPP8响应程度最强。【结论】谷子CPP家族成员具有组织表达特异性且对外源硒存在不同程度响应。     

HLA-DQB1~*02、03基因及IFN-γ、IL-4与广西壮、瑶族肝癌家族聚集性的相关性

本研究探讨HLA-DQB1~*02、03等位基因及细胞因子IFN-γ和IL-4与广西壮、瑶族肝癌家庭聚集性的相关性。将来自肝癌高发区,民族为瑶族的肝癌高发家族成员、无癌家族成员各40例及民族为壮族的肝癌高发家族成员、无癌家族成员各48例作为研究对象(采用相同性别,年龄(±5岁)配对方法),采集研究对象外周血并提取全血DNA,采用PCR-SSP技术检测受试者的HLA-DQB1~*02和HLA-DQB1~*03等位基因,IFN-γ及IL-4细胞因子表达水平采用ELISA法检测。结果发现,HLA-DQB1~*02、03基因在壮族肝癌高发家族成员组的表达频率均低于无癌家族成员组(p0.05);HLA-DQB1~*02基因在瑶族肝癌高发家族成员组的表达频率高于无癌家族组(p=0.002),HLA-DQB1~*03在两组间的表达频率无明显差异(p0.05)。广西壮、瑶族人群HLA-DQB1~*02、03基因在乙肝病毒感染组及非感染组中的表达频率比较无显著性差异(p0.05)。壮、瑶族肝癌高发家族成员组IL-4平均表达水平均高于无癌家族成员组,肝癌高发家族成员组IFN-γ平均表达水平均低于无癌家族成员组,差异具有统计学意义(p0.05)。广西壮、瑶族人群中HLA-DQB1~*02基因阳性和阴性成员的IL-4平均表达水平无明显差异(p0.05)。广西壮族人群中HLA-DQB1~*03基因阳性成员的IFN-γ平均表达水平高于HLA-DQB1~*03阴性成员(p=0.011),HLA-DQB1~*03阳性和阴性成员的IL-4平均表达水平无明显差异(p0.05)。本课题得出结论,HLA-DQB1~*02、03基因与广西壮、瑶族肝癌家庭聚集性有关,但存在较大的民族差异;细胞因子IFN-γ及IL-4的表达水平失衡可能是广西壮、瑶族肝癌家族聚集性的危险因素。HLA-DQB1~*03基因导致广西壮族肝癌家族聚集性的发生可能是通过影响IFN-γ的表达水平来实现的。     

IFN-λ家族基因遗传多态性与HBV感染、病毒复制及清除的关系

乙型肝炎病毒(hepatitis B virus,HBV)感染是一个严重的全球性公共卫生问题.HBV感染后会引发肝炎,可进一步发展为肝硬化甚至恶化为肝癌.干扰素λ(interferon λ,IFN-λ)是干扰素家族的成员之一,是抗病毒防御的重要细胞因子.IFN-λ家族包括4个成员,分别为IFN-λ1、IFN-λ2、IF...     

植物miR159家族成员分子特性及其进化规律研究

为了解植物miR159家族成员的分子特性及其进化规律,该研究对miRBase数据库中登录的miR159家族成员进行分类统计、进化树构建、科间比较、二级结构预测及靶基因分析。结果表明:miR159家族在植物界分布非常广泛,蕨类植物可能是miR159家族的进化祖先;系统发育进化树分析显示,植物miR159家族成员间存在多个进化分支,且进化关系与植物属性有关,即植物亲缘关系越近的成员更易成枝,且具有相同进化方向的成员序列高度同源;Mfold预测显示,pre-miR159均会自发形成典型、稳定的茎环二级结构,并包含19~21个碱基为单位的功能片段,每个单位均有可能形成miR159成熟体;靶基因分析发现,miR159家族成员主要作用于MYB转录因子、转座因子和假定蛋白等,但在不同物种间及相同物种的不同成员间作用的靶标种类与靶基因ID数量均存在差异,尤其是miR159-3p与miR159-5p间的差异最为显著。     

FAM160A2功能缺失性突变可能诱发心房颤动

心房颤动(atrial fibrillation, AF)是临床最常见的心律失常,对AF致病基因的研究,有助于AF早期筛查。本文旨在家族性AF人群和散发性AF人群中筛选具有潜在发病意义的易感基因,并对其在AF发生机制进行初步探讨。首先对4名家族性AF进行全外显子组测序(WES),鉴定AF相关基因。然后用Sanger测序在非家族性AF人群和健康人群中证实易感基因突变情况,应用Western印迹分析其蛋白质表达情况,利用膜片钳技术分析突变基因对外向钾离子电流的影响。家族共有39人,其中有4人发生AF,这4名AF患者存在2个共有的突变基因FAM160A2(纯合突变,rs77726581 c.1375C>T)和MUC5B(杂合突变,rs199736618 c.12272C>T)。在52例非家族性AF患者中,有5例存在FAM160A2相同位点杂合突变,在健康人群中未发现此突变;而MUC5B在非家族性AF人群和健康人群中均发生杂合突变。FAM160A2蛋白在非家族性AF散发人群和健康人群中表达水平并无显著性差异。FAM160A2基因突变明显降低外向钾离子电流(与野生型比较,P<0...     

小立碗藓WRKY基因家族生物信息学分析

WRKY作为最先在植物中发现的转录因子,在植物生长发育等过程中发挥重要作用。为了更好地研究小立碗藓WRKY蛋白的结构与功能,该文以Pfam数据库中WRKY基因家族数据(登录号为PF03106)为材料,分析了小立碗藓(Physcomitrella patens)WRKY基因家族成员的理化性质、蛋白质的二级结构预测、染色体定位、内外显子分布及系统进化关系。结果表明:(1)小立碗藓WRKY基因家族成员共有38个基因,根据WRKY保守结构域个数和锌指结构类型分成Ⅰ、Ⅱ两大类,不含第Ⅲ类(锌指结构为C2HC型),其中部分基因WRKY保守结构域发生变异。(2)WRKY蛋白氨基酸长度在216~775 aa之间、相对分子质量在24.5~82.8 kDa之间,亚细胞定位显示WRKY家族成员蛋白质定位于细胞核中。(3)WRKY蛋白的二级结构以α-螺旋、延伸链、β-转角、无规卷曲四种构成元件构成,除PpWRKY11(α-螺旋为主)外,其余无规卷曲占比高达70%。(4)与拟南芥的系统进化关系表明,植物在进化过程中WRKY家族成员的数目与进化方式发生改变,WRKY基因家族成员外显子的个数为3~7个。(5)小立碗藓WRKY基因家族成员无规则分散于21条染色体上,并未形成基因簇。该研究通过分析WRKY基因家族的基本结构与性质,能为后续深入研究WRKY转录因子的功能奠定基础。     

促血管生成素的生物学特点和应用前景

促血管生成素（Ang）家族是调节血管生成的一类细胞因子,包括Ang-1、Ang-2、Ang-3和Ang-4等4个成员,Ang-1和Ang-2是其中最重要的成员。Tie-2是Ang家族的共同受体。Ang-1与Tie-2结合后激活下游信号通路,起到抑制内皮凋亡、促进内皮存活和迁移、维持血管完整性的作用;Ang-2则是Ang-1天然的抑制剂,其拮抗的效应与局部血管内皮生长因子（VEGF）的水平有关,VEGF存在时促进新生血管形成,VEGF缺乏时则有利于血管的消退。Ang参与生理和病理性的血管新生,与肿瘤和其他疾病有密切的关系,有广泛的应用前景。     

芥蓝miR172家族成员进化特性比较及时空表达分析

为了明确植物miR172家族成员的进化特性及其在不同组织部位的表达情况,该研究以芥蓝miR172a家族为例,通过芥蓝miR172a成熟体序列比对、前体(pre-miRNA)二级结构预测、系统发育进化树构建、靶基因预测及实时荧光定量等手段,对芥蓝miR172a和miR172b基因家族的进化特性及其在芥蓝不同组织部位中的表达规律进行分析。结果显示:(1)芥蓝miR172家族存在20个成熟体成员,通过比对发现20条序列都存在一个重叠区域,该区域中ACTAGATC 8个碱基高度保守,并且在芥蓝pre-miR172的3′和5′端均能形成成熟体。(2)mfold预测结果显示,miR172a家族5个前体成员的最小折叠自由能在-54.55~-78.60kal/mol之间,均能自发形成典型、稳定的茎环二级结构。(3)系统发育进化树显示,芥蓝miR172a家族的前体成员具有一定的保守性和多样性,并与番木瓜pre-miR172a亲缘关系较近。(4)靶基因预测发现芥蓝miR172a共有13个不同靶标基因,多个成员也可以作用于相同靶标基因。(5)实时荧光定量PCR显示,芥蓝pre-miR172a和pre-miR172b家族不同成员在不同组织部位表达量差异显著,10个成员在9个组织部位中的表达各不相同。其中,芥蓝pre-miR172a-1、pre-miR172a-2、premiR172a-3和pre-miR172b在芥蓝荚中大量表达;pre-miR172b-5p和pre-miR172b-5p-2在芥蓝花中大量表达。研究表明,miR172在芥蓝花和荚的发育过程中起着重要的作用。     

A Novel Predicted Calcium-Regulated Kinase Family Implicated in Neurological Disorders

The catalogues of protein kinases, the essential effectors of cellular signaling, have been charted in Metazoan genomes for a decade now. Yet, surprisingly, using bioinformatics tools, we predicted protein kinase structure for proteins coded by five related human genes and their Metazoan homologues, the FAM69 family. Analysis of three-dimensional structure models and conservation of the classic catalytic motifs of protein kinases present in four out of five human FAM69 proteins suggests they might have retained catalytic phosphotransferase activity. An EF-hand Ca²⁺-binding domain in FAM69A and FAM69B proteins, inserted within the structure of the kinase domain, suggests they may function as Ca²⁺-dependent kinases. The FAM69 genes, FAM69A, FAM69B, FAM69C, C3ORF58 (DIA1) and CXORF36 (DIA1R), are by large uncharacterised molecularly, yet linked to several neurological disorders in genetics studies. The C3ORF58 gene is found deleted in autism, and resides in the Golgi. Unusually high cysteine content and presence of signal peptides in some of the family members suggest that FAM69 proteins may be involved in phosphorylation of proteins in the secretory pathway and/or of extracellular proteins.     

Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals

Background

Hematopoiesis is a complex developmental process controlled by a large number of factors that regulate stem cell renewal, lineage commitment and differentiation. Secreted proteins, including the hematopoietic growth factors, play critical roles in these processes and have important biological and clinical significance. We have employed representational difference analysis to identify genes that are differentially expressed during experimentally induced myeloid differentiation in the murine EML hematopoietic stem cell line.

Results

One identified clone encoded a previously unidentified protein of 541 amino acids that contains an amino terminal signal sequence but no other characterized domains. This protein is a member of family of related proteins that has been named family with sequence similarity 20 (FAM20) with three members (FAM20A, FAM20B and FAM20C) in mammals. Evolutionary comparisons revealed the existence of a single FAM20 gene in the simple vertebrate Ciona intestinalis and the invertebrate worm Caenorhabditis elegans and two genes in two insect species, Drosophila melanogaster and Anopheles gambiae. Six FAM20 family members were identified in the genome of the pufferfish, Fugu rubripes and five members in the zebrafish, Danio rerio. The mouse Fam20a protein was ectopically expressed in a mammalian cell line and found to be a bona fide secreted protein and efficient secretion was dependent on the integrity of the signal sequence. Expression analysis revealed that the Fam20a gene was indeed differentially expressed during hematopoietic differentiation and that the other two family members (Fam20b and Fam20c) were also expressed during hematcpoiesis but that their mRNA levels did not vary significantly. Likewise FAM20A was expressed in more limited set of human tissues than the other two family members.

Conclusions

The FAM20 family represents a new family of secreted proteins with potential functions in regulating differentiation and function of hematopoietic and other tissues. The Fam20a mRNA was only expressed during early stages of hematopoietic development and may play a role in lineage commitment or proliferation. The expansion in gene number in different species suggests that the family has evolved as a result of several gene duplication events that have occurred in both vertebrates and invertebrates.     

Characterisation of the FAM69 family of cysteine-rich endoplasmic reticulum proteins

The FAM69 family of cysteine-rich type II transmembrane proteins comprises three members in all vertebrates except fish, and orthologues with a conserved structure are present throughout metazoa. All three murine FAM69 proteins (FAM69A, FAM69B, FAM69C) localise to the endoplasmic reticulum (ER) in cultured cells, probably via N-terminal di-arginine motifs. Mammalian FAM69A is ubiquitously expressed, FAM69B is strongly expressed in the brain and in peripheral endothelial cells, and FAM69C in the brain and eye. Antibodies against mouse FAM69B strongly stain the ER of a subset of neurons in the brain. FAM69 proteins are likely to play a fundamental and highly conserved role in the ER of most metazoan cells, with additional specialised roles in the vertebrate nervous system.     

A new gene family (FAM9) of low-copy repeats in Xp22.3 expressed exclusively in testis: implications for recombinations in this region

Illegitimate recombinations between low-copy repetitive elements (LCR) have been implicated in the pathogenesis of various chromosomal rearrangements. Two such duplicons have been reported previously on Xp22.3, the CRI-S232 elements, involved in the generation of deletions in the steroidsulfatase gene and five members of the G1.3 (DXF22S) repetitive sequence family. By molecular characterization of an Xp22/10q24 translocation, we identified one duplicon of the G1.3 family in the breakpoint region in Xp22.3. We show that G1.3 elements harbor at least three expressed genes, FAM9A, FAM9B, and FAM9C, and three putative pseudogenes, all mapped to Xp22.33-p22.31. The deduced amino acid sequence of the three novel proteins shows homology to SYCP3, a component of the synaptonemal complex located along the paired chromosomes during meiosis. FAM9A, FAM9B, and FAM9C are expressed exclusively in testis; their proteins are located in the nucleus, and FAM9A localizes to the nucleolus. The presence of genes within duplicons may represent putative recombination-promoting factors for actively transcribed genes in meiotic cells, with the resulting open chromatin structure facilitating unequal crossing-over events and chromosomal rearrangements.     

Characterisation of the biochemical and cellular roles of native and pathogenic amelogenesis imperfecta mutants of FAM83H

The majority of mutations identified in patients with amelogenesis imperfecta have been mapped to FAM83H. As FAM83H expression is not limited to the enamel, how FAM83H contributes to amelogenesis is still largely unknown. We previously reported that members of the FAM83 family of proteins interact with and regulate the subcellular distribution of the promiscuous serine-threonine protein kinase CK1 family, through their shared N-terminal DUF1669 domains. FAM83H co-localises with CK1 isoforms to speckle-like structures in both the cytoplasm and nucleus. In this report, we show FAM83H, unlike other FAM83 proteins, interacts and colocalises with NCK1/2 tyrosine kinase adaptor proteins. This interaction is mediated by proline-rich motifs within the C-terminus of FAM83H, specifically interacting with the second and third SH3 domains of NCK1/2. Moreover, FAM83H pathogenic AI mutant proteins, which trigger C-terminal truncations of FAM83H, retain their interactions with CK1 isoforms but lose interaction with NCK1/2. These AI mutant FAM83H proteins acquire a nuclear localisation, and recruit CK1 isoforms to the nucleus where CK1 retains its kinase activity. As understanding the constituents of the FAM83H-localised speckles may hold the key to unravelling potential substrates of FAM83H-associated CK1 substrates, we employed a TurboID-based proximity labelling approach and uncovered several proteins including Iporin and BAG3 as potential constituents of the speckles.     

Characterization of the FAM110 gene family

We have previously characterized the centrosome/spindle pole-associated protein (CSPP) involved in cell cycle progression. The open reading frame C20orf55 was identified in a yeast two-hybrid screen in a search for CSPP-interacting proteins. A homology search revealed that C20orf55 belongs to a gene family consisting of three members that have not yet been described. The HUGO Nomenclature Committee has assigned these genes the names FAM110A-FAM110C. Studies of transfectants showed that the FAM110 proteins localized to centrosomes and accumulated at the microtubule organization center in interphase and at spindle poles in mitosis. In addition, overexpression of FAM110C induced microtubule aberrancies. Our data also indicated a cell cycle-regulated expression of FAM110A. Moreover, ectopic expression of FAM110B and FAM110C proteins impaired cell cycle progression in G1 phase. To summarize, we have characterized a novel family of genes encoding proteins with distinct conserved motifs, of which all members localize to centrosomes and spindle poles.     

Cloning,expression, and initial characterization of a novel cytokine-like gene family

We report the identification and characterization of a novel cytokine-like gene family using structure-based methods to search for novel four-helix-bundle cytokines in genomics databases. There are four genes in this family, FAM3A, FAM3B, FAM3C, and FAM3D, each encoding a protein (224-235 amino acids) with a hydrophobic leader sequence. Northern analysis indicates that FAM3B is highly expressed in pancreas, FAM3D in placenta, and FAM3A and FAM3C in almost all tissues. Immunohistochemistry showed that FAM3A is expressed prominently in the vascular endothelium, particularly capillaries. We found that FAM3A and FAM3B protein were both localized to the islets of Langerhans of the endocrine pancreas. Recombinant FAM3B protein has delayed effects on beta-cell function, inhibiting basal insulin secretion from a beta-cell line in a dose-dependent manner.     

Analysis of the multi-copy gene family FAM90A as a copy number variant in different ethnic backgrounds

Copy number variants contribute extensively to inter-individual genomic differences, but little is known about their inter-population variability and diversity. In a previous study (Bosch et al., 2007; 16:2572-2582), we reported that the primate-specific gene family FAM90A, which accounts for as many as 25 members in the human reference assembly, has expanded the number of FAM90A clusters across the hominoid lineage. Here we examined the copy number variability of FAM90A genes in 260 HapMap samples of European, African, and Asian ancestry, and showed significant inter-population differences (p<0.0001). Based on the recent study of Stranger et al. (2007; 315:848-853), we also explored the correlation between copy number variability and expression levels of the FAM90A gene family. Despite the high genomic variability, we found a low correlation between FAM90A copy number and expression levels, which could be due to the action of independent trans-acting factors. Our results show that FAM90A is highly variable in copy number between individuals and between populations. However, this variability has little impact on gene expression levels, thus highlighting the importance of genomic variability for genes located in regions containing segmental duplications.     

The Raine Syndrome Protein FAM20C Is a Golgi Kinase That Phosphorylates Bio-Mineralization Proteins

Raine syndrome is caused by mutations in FAM20C, which had been reported to encode a secreted component of bone and teeth. We found that FAM20C encodes a Golgi-localized protein kinase, distantly related to the Golgi-localized kinase Four-jointed. Drosophila also encode a Golgi-localized protein kinase closely related to FAM20C. We show that FAM20C can phosphorylate secreted phosphoproteins, including both Casein and members of the SIBLING protein family, which modulate biomineralization, and we find that FAM20C phosphorylates a biologically active peptide at amino acids essential for inhibition of biomineralization. We also identify autophosphorylation of FAM20C, and characterize parameters of FAM20C's kinase activity, including its Km, pH and cation dependence, and substrate specificity. The biochemical properties of FAM20C match those of an enzymatic activity known as Golgi casein kinase. Introduction of point mutations identified in Raine syndrome patients into recombinant FAM20C impairs its normal localization and kinase activity. Our results identify FAM20C as a kinase for secreted phosphoproteins and establish a biochemical basis for Raine syndrome.     

RTN4B interacting protein FAM134C promotes ER membrane curvature and has a functional role in autophagy

The endoplasmic reticulum (ER) is composed of a controlled ratio of sheets and tubules, which are maintained by several proteins with multiple functions. Reticulons (RTNs), especially RTN4, and DP1/Yop1p family members are known to induce ER membrane curvature. RTN4B is the main RTN4 isoform expressed in nonneuronal cells. In this study, we identified FAM134C as a RTN4B interacting protein in mammalian, nonneuronal cells. FAM134C localized specifically to the ER tubules and sheet edges. Ultrastructural analysis revealed that overexpression of FAM134C induced the formation of unbranched, long tubules or dense globular structures composed of heavily branched narrow tubules. In both cases, tubules were nonmotile. ER tubulation was dependent on the reticulon homology domain (RHD) close to the N-terminus. FAM134C plays a role in the autophagy pathway as its level elevated significantly upon amino acid starvation but not during ER stress. Moreover, FAM134C depletion reduced the number and size of autophagic structures and the amount of ER as a cargo within autophagic structures under starvation conditions. Dominant-negative expression of FAM134C forms with mutated RHD or LC3 interacting region also led to a reduced number of autophagic structures. Our results suggest that FAM134C provides a link between regulation of ER architecture and ER turnover by promoting ER tubulation required for subsequent ER fragmentation and engulfment into autophagosomes.