退火解旋酶SMARCAL1在维持基因组稳定中的作用与机制

SMARCAL1是属于SWI/SNF (SWItch/Sucrose Non-Fermentable)相关、基质相关和激动蛋白依赖的染色质调节因子家族成员ATP驱动的DNA退火解旋酶。SMARCAL1在体外和体内能催化单链结合蛋白RPA结合的DNA单链与其互补链退火成双链DNA。人Smarcal1基因的突变与Schimke免疫骨性发育不良(Schimke immuno-osseous dysplasia, SIOD)所能表现出的临床症状呈高度相关。本文对SMARCAL1在DNA损伤部位DNA复制叉的重塑、在DNA双链断裂(double-stranded DNA, dsDNA)处参与经典的非同源末端连接(non-homologous end joining, NHEJ)修复,以及在人染色体端粒完整性维护等方面的作用与机制进行了梳理,对Smarcal1基因突变类型与SIOD症状之间的对应关系进行了更新,并对SMARCAL1在三核苷酸重复序列扩增关联的神经–肌肉退行性病变过程中的可能作用进行了分析和讨论,旨在更好地理解该退火解旋酶在维持基因组稳定中的作用和机制。     

APOBEC3F蛋白的结构与功能

载脂蛋白B mRNA编辑酶催化多肽样蛋白3F(apolipoprotin B mRNA-editing catalytic polypeptide 3protein F,APOBEC3F,简称A3F)是一种天然抗病毒活性的胞嘧啶脱氨基酶。在HIV病毒复制过程中,A3F蛋白能被整合进入病毒颗粒内部,诱导病毒c DNA胞嘧啶脱氨基化变为尿嘧啶,阻断病毒复制。近几年,科研工作者开展了一系列A3F蛋白的结构生物学和脱氨基化反应的研究,以及与单链DNA(single-stranded DNA,ss-DNA)的结合位点、病毒感染因子(viral infectivity factor,Vif)作用界面的探索。本文通过对这些工作进行总结,以期为艾滋病、乙肝的防治提供新的理论基础。     

BTR复合物在DNA损伤修复中的研究进展

Bloom综合征(Bloom syndrome,BS)是一种染色体紊乱型遗传病,BS患者具有基因组不稳定性、癌症易患性以及姐妹染色单体交换增多等重要特征。BS是由人体中BLM基因突变所致,该基因编码的BLM蛋白是一种Rec Q DNA解旋酶。BLM蛋白与DNA拓扑异构酶Topo Ⅲα、Rec Q介导的基因组不稳定蛋白1和2(Rec Q-mediated genome instability protein,RMI1和RMI2)紧密结合形成BTR复合物。该复合物能够抑制姐妹染色单体交换,维持基因组稳定性,在DNA复制、重组以及修复过程中发挥重要作用。现介绍BLM蛋白,并在此基础上对BTR复合物成员之间的相互作用以及其在DNA损伤修复中的作用进行阐述。     

人乳头状瘤病毒复制机制的研究进展

人乳头状瘤病毒(human papillomavirus,HPV)DNA以游离和整合两种形式存在于感染细胞中。游离形式HPVs的复制依赖于上皮细胞的分化,病毒E1、E2蛋白和复制起始位点(origin,Ori)为复制必需元件,E1和E2蛋白与Ori结合起始病毒DNA的复制。随后,病毒DNA通过E2蛋白与Brd4(bromodomain-containing protein 4)等细胞蛋白的互作而与染色体结合,并随细胞分裂平均分配到子代细胞中。在肿瘤中,高危型HPVs的基因组通常以整合形式存在,并随细胞的增殖而复制。     

单纯疱疹病毒1型单链结合蛋白ICP8研究进展

在单纯疱疹病毒1型（Herpes simplex virus 1,HSV-1）中，感染细胞蛋白8(Infected cell protein 8,ICP8)是由UL29基因编码的一种单链DNA结合蛋白（Single strand DNA-binding protein,SSBP），该蛋白在病毒复制中必不可缺，具有维持单链DNA的稳定性，并与其他病毒蛋白相互结合，促进病毒复制室的形成，介导晚期基因的表达。除此之外，ICP8还具有促进UL9编码的起源结合蛋白（Origin binding protein,OBP）和UL5/UL8/UL52蛋白的酶活性，与UL12蛋白共同介导链交换等功能。本文就上述目前国内外对HSV-1 ICP8的研究进展作一综述，以期为后续研究ICP8的作用机制提供参考。     

RNA聚合酶监视的DNA修复机制

生物体在正常生命过程中面临内/外因来源的DNA损伤,DNA损伤不仅影响基因正确复制,也阻碍其正常转录.为避免DNA损伤带来的灾难性后果,生物体进化出一整套修复机制,以保证复制和转录的正确性、基因组的完整性和遗传的稳定性.本文重点综述了RNA聚合酶监视(RNA polymerase-surveilled,RNAP-S)的DNA修复机制.首先从RNA聚合酶(RNA polymerase,RNAP)的结构出发介绍了RNAP对DNA损伤的感知机制;其次讨论了滞留RNAP的回溯、与其模板DNA的解离以及后续修复机制的启动,真核细胞科凯恩综合征B蛋白(Cockayne syndrome protein B,CSB)及其泛素化和8-氧代鸟嘌呤DNA糖基化酶1 (8-oxoguanine DNA glycosylase1,OGG1)介导的RNAP-S修复;最后探讨了RNAP-S损伤修复的生物学意义并展望其前景.     

几种核糖体失活蛋白对超螺旋环状DNA的切割与解旋作用

天花粉蛋白(trichosanthin)是一种单链核糖体失活蛋白(ribosome-inactivating protein,RIP),它失活核糖体的机制属于RNA N-糖苷酶型。最近Li等发现天花粉蛋白可作用于超螺旋环状DNA,将其切割与解旋成缺口及线状分子,但并不作用于线状DNA。为了     

RNA表观遗传修饰:N~6-甲基腺嘌呤

N6-甲基腺嘌呤(N6-methyladenosine,m6A)是真核生物信使RNA(Messenger RNA,m RNA)上含量最多的化学修饰之一。类似于DNA和组蛋白化学修饰,m6A修饰也同样是动态可逆的,可在时间和空间上被甲基转移酶和去甲基酶调控。哺乳动物体内m6A甲基转移酶复合物中有一部分成分已被解析,主要有METTL3(Methyltransferase-like protein 3)、METTL14(Methyltransferase-like protein 14)和WTAP(Wilms tumor 1-associating protein)。m6A去甲基酶肥胖蛋白FTO(Fat mass and obesity associated protein)和ALKBH5(Alk B homolog 5)依赖α-酮戊二酸(α-Ketoglutaric acid,α-KG)和Fe(Ⅱ)对m6A进行氧化去甲基化反应。m6A在生物体内由m6A结合蛋白识别,并介导其行使功能。目前发现的m6A结合蛋白有YTH结构域蛋白YTHDF1(YTH domain-containing family protein 1)、YTHDF2(YTH domain-containing family protein 2)、YTHDC1(YTH domain-containing protein1)和核内HNRNPA2B1(Heterogeneous nuclear ribonucleoproteins A2B1)。本文综述了m6A的分布和相关蛋白介导的m6A功能研究,以期全面理解m6A这一RNA表观遗传新修饰在生命进程中的重要调控作用。     

乙酰转移酶MYST家族的生物学功能

组蛋白乙酰化是表观遗传修饰的重要方式,主要受到组蛋白乙酰转移酶（histone acetyltransferases, HATs)和组蛋白去乙酰化酶（histone deacetylase, HDACs）催化. MYST是人类HATs的4大家族之一,包括MOF(males absent on the first),TIP60 (tat interacting protein 60 kD),结合ORC1的组蛋白乙酰转移酶（histone acetyltransferase binding to ORC1, HBO1),单核细胞白血病锌指蛋白(monocytic leukemia zinc finger protein, MOZ)和MOZ相关蛋白（MOZ related factor, MORF）等,均具有典型的MYST结构域.MYST介导的乙酰化是重要的翻译后修饰,其催化底物包括组蛋白和非组蛋白,如组蛋白H3, H4, H2A, H2A突变体,以及许多参与DNA代谢、细胞增殖和发育调控的蛋白因子. MYST蛋白家族参与许多细胞的生理过程,本文主要综述其在调节基因转录、DNA损伤修复和肿瘤发生发展等方面的生物学功能.     

家蚕细小病毒样病毒的研究进展

家蚕细小病毒样病毒(Bombyx mori parvo-like virus,BmPLV)是一种二分病毒,该病毒在家蚕中肠柱状细胞核内复制和包装,感染的细胞核呈现过分膨胀、细胞核孚尔根浓染等细胞病理学特征。病毒粒子直径20~24 nm,无囊膜呈球型。基因组为单链线性双分子DNA(VD1、VD2),分别独立包装在各自的衣壳中。病毒编码四个非结构蛋白NS1、NS2、NS3和pol(DNA聚合酶),一个主要结构蛋白VP及次要结构蛋白P133。其基因组末端反向重复序列可形成与BmPLV复制有关的"锅柄形"结构,以及含自身编码的DNA聚合酶的序列,推测该病毒与腺病毒复制方式相类似,依靠共价蛋白为起始物完成复制。     

HARP preferentially co-purifies with RPA bound to DNA-PK and blocks RPA phosphorylation

The HepA-related protein (HARP/SMARCAL1) is an ATP-dependent annealing helicase that is capable of rewinding DNA structures that are stably unwound due to binding of the single-stranded DNA (ssDNA)-binding protein Replication Protein A (RPA). HARP has been implicated in maintaining genome integrity through its role in DNA replication and repair, two processes that generate RPA-coated ssDNA. In addition, mutations in HARP cause a rare disease known as Schimke immuno-osseous dysplasia. In this study, we purified HARP containing complexes with the goal of identifying the predominant factors that stably associate with HARP. We found that HARP preferentially interacts with RPA molecules that are bound to the DNA-dependent protein kinase (DNA-PK). We also found that RPA is phosphorylated by DNA-PK in vitro, while the RPA-HARP complexes are not. Our results suggest that, in addition to its annealing helicase activity, which eliminates the natural binding substrate for RPA, HARP blocks the phosphorylation of RPA by DNA-PK.     

The HARP domain dictates the annealing helicase activity of HARP/SMARCAL1

Mutations in HepA-related protein (HARP, or SMARCAL1) cause Schimke immunoosseous dysplasia (SIOD). HARP has ATP-dependent annealing helicase activity, which helps to stabilize stalled replication forks and facilitate DNA repair during replication. Here, we show that the conserved tandem HARP (2HP) domain dictates this annealing helicase activity. Furthermore, chimeric proteins generated by fusing the 2HP domain of HARP with the SNF2 domain of BRG1 or HELLS show annealing helicase activity in vitro and, when targeted to replication forks, mimic the functions of HARP in vivo. We propose that the HARP domain endows HARP with this ATP-driven annealing helicase activity.     

HARP preferentially co-purifies with RPA bound to DNA-PK and blocks RPA phosphorylation

The HepA-related protein (HARP/SMARCAL1) is an ATP-dependent annealing helicase that is capable of rewinding DNA structures that are stably unwound due to binding of the single-stranded DNA (ssDNA)-binding protein Replication Protein A (RPA). HARP has been implicated in maintaining genome integrity through its role in DNA replication and repair, two processes that generate RPA-coated ssDNA. In addition, mutations in HARP cause a rare disease known as Schimke immuno-osseous dysplasia. In this study, we purified HARP containing complexes with the goal of identifying the predominant factors that stably associate with HARP. We found that HARP preferentially interacts with RPA molecules that are bound to the DNA-dependent protein kinase (DNA-PK). We also found that RPA is phosphorylated by DNA-PK in vitro, while the RPA-HARP complexes are not. Our results suggest that, in addition to its annealing helicase activity, which eliminates the natural binding substrate for RPA, HARP blocks the phosphorylation of RPA by DNA-PK.     

The Annealing Helicase and Branch Migration Activities of Drosophila HARP

HARP (SMARCAL1, MARCAL1) is an annealing helicase that functions in the repair and restart of damaged DNA replication forks through its DNA branch migration and replication fork regression activities. HARP is conserved among metazoans. HARP from invertebrates differs by the absence of one of the two HARP-specific domain repeats found in vertebrates. The annealing helicase and branch migration activity of invertebrate HARP has not been documented. We found that HARP from Drosophila melanogaster retains the annealing helicase activity of human HARP, the ability to disrupt D-loops and to branch migrate Holliday junctions, but fails to regress model DNA replication fork structures. A comparison of human and Drosophila HARP on additional substrates revealed that both HARPs are competent in branch migrating a bidirectional replication bubble composed of either DNA:DNA or RNA:DNA hybrid. Human, but not Drosophila, HARP is also capable of regressing a replication fork structure containing a highly stable poly rG:dC hybrid. Persistent RNA:DNA hybrids in vivo can lead to replication fork arrest and genome instability. The ability of HARP to strand transfer hybrids may signify a hybrid removal function for this enzyme, in vivo.     

The role of SMARCAL1 in replication fork stability and telomere maintenance

SMARCAL1 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily A-Like 1), also known as HARP, is an ATP-dependent annealing helicase that stabilizes replication forks during DNA damage. Mutations in this gene are the cause of Schimke immune-osseous dysplasia (SIOD), an autosomal recessive disorder characterized by T-cell immunodeficiency and growth dysfunctions. In this review, we summarize the main roles of SMARCAL1 in DNA repair, telomere maintenance and replication fork stability in response to DNA replication stress.     

Identification of SMARCAL1 as a Component of the DNA Damage Response

SMARCAL1 (also known as HARP) is a SWI/SNF family protein with an ATPase activity stimulated by DNA containing both single-stranded and double-stranded regions. Mutations in SMARCAL1 are associated with the disease Schimke immuno-osseous dysplasia, a multisystem autosomal recessive disorder characterized by T cell immunodeficiency, growth inhibition, and renal dysfunction. The cellular function of SMARCAL1, however, is unknown. Here, using Xenopus egg extracts and mass spectrometry, we identify SMARCAL1 as a protein recruited to double-stranded DNA breaks. SMARCAL1 binds to double-stranded breaks and stalled replication forks in both egg extract and human cells, specifically colocalizing with the single-stranded DNA binding factor RPA. In addition, SMARCAL1 interacts physically with RPA independently of DNA. SMARCAL1 is phosphorylated in a caffeine-sensitive manner in response to double-stranded breaks and stalled replication forks. It has been suggested that stalled forks can be stabilized by a mechanism involving caffeine-sensitive kinases, or they collapse and subsequently recruit Rad51 to promote homologous recombination repair. We show that depletion of SMARCAL1 from U2OS cells leads to increased frequency of RAD51 foci upon generation of stalled replication forks, indicating that fork breakdown is more prevalent in the absence of SMARCAL1. We propose that SMARCAL1 is a novel DNA damage-binding protein involved in replication fork stabilization.     

Effect of herparin on bovine epithelial lens cell proliferation induced by heparin affin regulatory peptide

HARP (heparin affin regultory peptide) is an 18 kDa heparin binding protein, also known as HB-GAM or pleiotrophin (PTN) which has been primarily isolated from brain and uterus, and displays neurite outgrowth, angiogenic and mitogenic activities. Previously, we have expressed the human cDNA encoding human HARP in NIH 3T3 cells. Purified recombinant HARP displayed mitogenic activity for endothelial cells. Its NH2-terminal sequence indicates that the HARP molecule possesses a three amino acid extension from the signal peptide more than the NH2-terminal described. For HB-GAM or PTN, these three amino acids may be essential for the stability and the mitogenic activity of this growth factor. In an attempt to further study the mode of action of this growth factor, we have investigated the mitogenic effect of HARP on various cell types. In contrast to FGF-2, HARP failed to induce stimulation of DNA synthesis on a CCL39 cell line. However, we found that in quiescent bovine epithelial lens (BEL) cells, the stimulation of DNA synthesis induced by HARP is dose-dependent (EC₅₀: 2.5 ng/ml) and maximal stimulation is as potent as that induced by FGF-2 (EC₅₀: 25 pg/ml). Interestingly, when BEL cells were allowed to quiesce in the presence of serum, the stimulation induced by HARP is considerably less potent. In this highly responsive cell system, heparin could potentiate the mitogenic activity of HARP at very low doses (0.1-1 m?g/ml) and inhibit this activity at concentrations of 10 m?g/ml. In contrast to its protective effect on FGF-1 and -2, heparin was unable to preserve HARP from tryptic and chymotryptic degradations. © 1995 Wiley-Liss, Inc.     

Glycosaminoglycans differentially bind HARP and modulate its biological activity

Heparin affin regulatory peptide (HARP) is a polypeptide belonging to a family of heparin binding growth/differentiation factors. The high affinity of HARP for heparin suggests that this secreted polypeptide should also bind to heparan sulfate proteoglycans derived from cell surface and extracellular matrix defined as extracellular compartments. Using Western blot analysis, we detected HARP bound to heparan sulfate proteoglycans in the extracellular compartments of MDA-MB 231 and MC 3T3-E1 as well as NIH3T3 cells overexpressing HARP protein. Heparitinase treatment of BEL cells inhibited HARP-induced cell proliferation, and the biological activity of HARP in this system was restored by the addition of heparin. We report that heparan sulfate, dermatan sulfate, and to a lesser extent, chondroitin sulfate A, displaced HARP bound to the extracellular compartment. Binding analyses with a biosensor showed that HARP bound heparin with fast association and dissociation kinetics (kass = 1.6 x 10(6) M-1 s-1; kdiss = 0.02 s-1), yielding a Kd value of 13 nM; the interaction between HARP and dermatan sulfate was characterized by slower association kinetics (kass = 0.68 x 10(6) M-1 s-1) and a lower affinity (Kd = 51 nM). Exogenous heparin, heparan sulfate, and dermatan sulfate potentiated the growth-stimulatory activity of HARP, suggesting that corresponding proteoglycans could be involved in the regulation of the mitogenic activity of HARP.     

PriC-mediated DNA Replication Restart Requires PriC Complex Formation with the Single-stranded DNA-binding Protein

Frequent collisions between cellular DNA replication complexes (replisomes) and obstacles such as damaged DNA or frozen protein complexes make DNA replication fork progression surprisingly sporadic. These collisions can lead to the ejection of replisomes prior to completion of replication, which, if left unrepaired, results in bacterial cell death. As such, bacteria have evolved DNA replication restart mechanisms that function to reload replisomes onto abandoned DNA replication forks. Here, we define a direct interaction between PriC, a key Escherichia coli DNA replication restart protein, and the single-stranded DNA-binding protein (SSB), a protein that is ubiquitously associated with DNA replication forks. PriC/SSB complex formation requires evolutionarily conserved residues from both proteins, including a pair of Arg residues from PriC and the C terminus of SSB. In vitro, disruption of the PriC/SSB interface by sequence changes in either protein blocks the first step of DNA replication restart, reloading of the replicative DnaB helicase onto an abandoned replication fork. Consistent with the critical role of PriC/SSB complex formation in DNA replication restart, PriC variants that cannot bind SSB are non-functional in vivo. Single-molecule experiments demonstrate that PriC binding to SSB alters SSB/DNA complexes, exposing single-stranded DNA and creating a platform for other proteins to bind. These data lead to a model in which PriC interaction with SSB remodels SSB/DNA structures at abandoned DNA replication forks to create a DNA structure that is competent for DnaB loading.     

Poly(ADP-ribose) polymerase-1: A Regulator of Protein–Nucleic Acid Interactions in Processes Responding to Genotoxic Impact

Poly(ADP-ribose) polymerase-1 (PARP-1), a nuclear protein of higher eukaryotes, specifically detects strand breaks in DNA. The enzyme is activated in the presence of such breaks and synthesizes poly(ADP-ribose) covalently bound to certain proteins, with PARP-1 itself being the main acceptor. This protein is involved in the majority of DNA-dependent processes, including replication, recombination, repair, and cell death (apoptosis and necrosis). Poly(ADP-ribosyl)ation of proteins is regarded as a mechanism which induces a signal of DNA damage and modulates the function of proteins in response to genotoxic actions. Attention in this review is focused on the role of PARP-1 and poly(ADP-ribosyl)ation in base excision repair (BER), the main process of DNA break repair. The main putative functions of PARP-1 in this process are also considered, namely, its functions as a factor initiating the BER protein complex, a temporary protector of DNA ends, a factor modulating chromatin structure through poly(ADP-ribosyl)ation of histones, and a signal in the mechanism recognizing the degree of DNA damage in the cell.