Molecular Mechanisms of DNA Damage and Repair: Progress in Plants

Dedicated to Prof. Jan H. J. Hoeijmakers.

Referee: Dr. Nawin C. Mishra, Professor of Genetics, University of South Carolina, Department of Biological Sciences, Columbia, SC 29208

Despite stable genomes of all living organisms, they are subject to damage by chemical and physical agents in the environment (e.g., UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. The DNA lesions produced by these damaging agents could be altered base, missing base, mismatch base, deletion or insertion, linked pyrimidines, strand breaks, intra- and inter-strand cross-links.     

DNA损伤修复过程表观遗传学改变

多种化学、物理及生物因素可诱发细胞DNA损伤,损伤后DNA损伤位点被相关损伤感受器识别,激活相应的修复通路进行DNA修复。越来越多的证据表明DNA甲基化状态、蛋白翻译后修饰、染色质重塑、miRNA等修饰方式参与了DNA的损伤修复。文章通过不同损伤修复通路中这些修饰的特点,阐述表观遗传学改变在DNA损伤修复发展过程中的作用机制。     

DNA修复的分子机制

ＤＮＡ是遗传信息的载体,需要有极高的保真度,这不仅有赖于完善的复制体系,而且还需要有能纠正已存在错误的修复系统。对于不同的ＤＮＡ损伤,生物体内存在许多不同的修复系统。本文介绍三种主要修复系统即核苷酸切割修复,错配修复及转录偶联修复的分子机制,深入研究ＤＮＡ修复作用对了解某些癌症成因及细胞衰老等过程有重要意义 。     

Unraveling DNA Repair in Human: Molecular Mechanisms and Consequences of Repair Defect

Cellular genomes are vulnerable to an array of DNA-damaging agents, of both endogenous and environmental origin. Such damage occurs at a frequency too high to be compatible with life. As a result cell death and tissue degeneration, aging and cancer are caused. To avoid this and in order for the genome to be reproduced, these damages must be corrected efficiently by DNA repair mechanisms. Eukaryotic cells have multiple mechanisms for the repair of damaged DNA. These repair systems in humans protect the genome by repairing modified bases, DNA adducts, crosslinks and double-strand breaks. The lesions in DNA are eliminated by mechanisms such as direct reversal, base excision and nucleotide excision. The base excision repair eliminates single damaged-base residues by the action of specialized DNA glycosylases and AP endonucleases. Nucleotide excision repair excises damage within oligomers that are 25 to 32 nucleotides long. This repair utilizes many proteins to remove the major UV-induced photoproducts from DNA, as well as other types of modified nucleotides. Different DNA polymerases and ligases are utilized to complete the separate pathways. The double-strand breaks in DNA are repaired by mechanisms that involve DNA protein kinase and recombination proteins. The defect in one of the repair protein results in three rare recessive syndromes: xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy. This review describes the biochemistry of various repair processes and summarizes the clinical features and molecular mechanisms underlying these disorders.     

DNA Repair Mechanisms and the Bypass of DNA Damage in Saccharomyces cerevisiae

DNA repair mechanisms are critical for maintaining the integrity of genomic DNA, and their loss is associated with cancer predisposition syndromes. Studies in Saccharomyces cerevisiae have played a central role in elucidating the highly conserved mechanisms that promote eukaryotic genome stability. This review will focus on repair mechanisms that involve excision of a single strand from duplex DNA with the intact, complementary strand serving as a template to fill the resulting gap. These mechanisms are of two general types: those that remove damage from DNA and those that repair errors made during DNA synthesis. The major DNA-damage repair pathways are base excision repair and nucleotide excision repair, which, in the most simple terms, are distinguished by the extent of single-strand DNA removed together with the lesion. Mistakes made by DNA polymerases are corrected by the mismatch repair pathway, which also corrects mismatches generated when single strands of non-identical duplexes are exchanged during homologous recombination. In addition to the true repair pathways, the postreplication repair pathway allows lesions or structural aberrations that block replicative DNA polymerases to be tolerated. There are two bypass mechanisms: an error-free mechanism that involves a switch to an undamaged template for synthesis past the lesion and an error-prone mechanism that utilizes specialized translesion synthesis DNA polymerases to directly synthesize DNA across the lesion. A high level of functional redundancy exists among the pathways that deal with lesions, which minimizes the detrimental effects of endogenous and exogenous DNA damage.     

肝细胞极性与膜蛋白分选的分子机制

肝细胞是高度特化的极性上皮细胞,细胞质膜蛋白的分选和极性转运对于肝细胞极性的建立与维持至关重要.首先,膜蛋白在内质网中合成,随后经高尔基体加工修饰,再由反面高尔基体进一步分选,最后通过膜泡运输等不同的机制分别转运到胆汁腔面或窦状隙面,行使其特殊的功能.近些年来,细胞内负责转运的细胞器和主要的分选信号已逐步被揭示.特别是循环内体也被证明参与了胆汁腔面和窦状隙面膜蛋白的极性分选和转运.肝细胞的极性一旦遭到破坏,将会引起胆汁分泌障碍以及其他肝脏功能的损伤,从而可能导致肝脏糖脂代谢紊乱,甚至丧失正常的生理功能.因此,深入研究肝脏细胞极性的形成与维持机制,将为多种肝脏疾病的预防和治疗寻找到新的方向和靶点,具有重要的理论和临床实践意义.     

线粒体未折叠蛋白反应分子机制的研究进展

线粒体未折叠蛋白反应(UPR~(mt))作为新发现的细胞内应激机制,直接影响老化、神经退行性疾病、癌症等疾病的发生发展.UPR~(mt)是线粒体为了维持其内部蛋白质的平衡,启动由核DNA编码的线粒体热休克蛋白和蛋白酶等基因群转录活化程序的应激反应.深入探究UPR~(mt)的作用机制对阐明老化和线粒体相关疾病的发病机理具有指导意义.本文主要阐述了线粒体未折叠蛋白反应的诱导因素、线虫和哺乳动物细胞中最新的未折叠蛋白应激反应的信号传导通路、调控因子、具体作用机制以及线粒体未折叠蛋白反应与衰老、免疫等疾病的联系,旨在为这些疾病提供新的理论基础和治疗靶点.     

DNA Damage Levels Determine Cyclobutyl Pyrimidine Dimer Repair Mechanisms in Alfalfa Seedlings

Ultraviolet radiation in sunlight damages DNA in plants, but little is understood about the types, lesion capacity, and coordination of repair pathways. We challenged intact alfalfa seedlings with UV doses that induced different initial levels of cyclobutyl pyrimidine dimers and measured repair by excision and photoreactivation. By using alkaline gel electrophoresis of nonradioactive DNAs treated with a cyclobutyl pyrimidine dimer-specific UV endonuclease, we quantitated ethidium-stained DNA by electronic imaging and calculated lesion frequencies from the number average molecular lengths. At low initial dimer frequencies (less than ~30 dimers per million bases), the seedlings used only photoreactivation to repair dimers; excision repair was not significant. At higher damage levels, both excision and photorepair contributed significantly. This strategy would allow plants with low damage levels to use error-free repair requiring only an external light energy source, whereas seedlings subjected to higher damage frequencies could call on additional repair processes requiring cellular energy. Characterization of repair in plants thus requires an investigation of a range of conditions, including the level of initial damage.     

酵母细胞自然衰老分子作用机理的研究进展

衰老是任何生物都无法避免的生理现象,它由多种因素引起,其过程极其复杂.酵母细胞是目前衰老研究领域公认的模式生物,一系列影响衰老的分子作用机理及调控因素的发现均源自于对酵母细胞的研究.自然衰老是酵母细胞的衰老模式之一,由于该衰老过程与其他高等真核细胞(特别是哺乳动物细胞)极为相似,近年来受到广泛关注.全面比较酵母细胞衰老的两种模式,详细介绍自然衰老过程中分子作用机理的研究进展,重点阐述其复杂的自然寿命调控通路,包括卡路里限制以及药物添加对Ras/PKA、Sch9、Tor等营养依赖型调控通路的影响,并展望未来该领域需要解决的重要科学问题,为全面深入了解高等生物,特别是人类自身的衰老机理提供参考.     

Molecular Mechanisms of Radiation Induced DNA Damage: H-Abstraction and β-Cleavage

Quantum mechanical simulations of hydrogen abstraction by hydroxyl radical from methanol and ethanol yield barriers that agree very well with those measured experimentally. Analysis of the multi configurationally wave function indicates that the strength of the C-H bond is the electronic parameter that has a major contribution to the barrier for H-abstraction. Similar analysis applied to 2-deoxy-D-ribose shows that the strength of a C-H bond together with the steric accessibility of the hydrogen determine that H₄ is the most susceptible hydrogen for abstraction by a hydroxyl radical. Quantum mechanical simulations of β-cleavage show that a concerted mechanism in which a water molecule assists in the bond breaking process is more likely than a Sⁱ_n mechanism. However, the polar transition state suggests that the environment of the DNA and the surrounding water will have an important effect on the reaction.     

Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations

Molecular dynamics (MD) simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein’s constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery—the fact that the two sites involved influence one another in a symmetrical manner—can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest.     

FHL2 蛋白在肿瘤中的转录调控及其分子生物学机制

FHL2是仅有四个半LIM结构域(FHL)蛋白家族的成员,目前在FHL蛋白家族中研究最为广泛。FHL2作为重要的衔接蛋白和支架蛋白,主要通过LIM结构域介导蛋白分子间的相互作用以实现其生物学功能。Fhl2基因在转录水平受多种肿瘤相关基因的调控,如p53,血清应答因子等。FHL2与恶性肿瘤的关系是近年来的研究热点,目前认为FHL2能够作为癌蛋白及抑癌蛋白通过不同机制广泛影响乳腺癌、胃肠道肿瘤、肝癌、前列腺癌等肿瘤的发生发展,并且在不同肿瘤中的表达具有组织特异性。本文就FHL2的结构特点、功能、转录调控及与肿瘤的关系几个方面展开综述,从而明确FHL2在不同肿瘤中所发挥的作用及其分子生物学机制将会为治疗相关肿瘤提供新的干预靶点。     

大气颗粒物致细胞损伤效应的分子机制

大气颗粒物(PM)是大气中各种具有不同化学组分的颗粒状物质的混合体。其中,空气动力学直径≤10μm和≤2.5μm的可吸入颗粒物(PM10和PM2.5)由于吸附有重金属、多环芳烃等有机物及细菌、病毒等有害成分,并能够通过呼吸系统进入体内,因此对人体健康具有极大的危害作用。流行病学研究数据显示,大气中PM含量增加会显著提高呼吸道和心血管疾病的发病率和致死率。因此,揭示PM诱导呼吸系统和心血管系统损伤的分子机制,对于制定相应防治策略、减低环境相关疾病的危害具有重要意义和医学价值。我们根据目前有限的研究线索,对PM诱导细胞损伤反应中涉及的氧化应激、内质网应激和炎性反应等机制做一综述。