Protein Dynamics in Complex DNA Lesions

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Replication-Dependent DNA Damage Response Triggered by Roscovitine Induces an Uncoupling of DNA Replication Proteins

The cyclin-dependent kinase (CDK) inhibitor roscovitine is under evaluation in clinical trials for its antiproliferative properties. Roscovitine arrests cell cycle progression in G1 and in G2 phase by inhibiting CDK2 and CDK1, and possibly CDK7 and CDK9. However, the effects of CDK2 inhibition in S-phase cells have been not fully investigated. Here, we show that a short-term treatment with roscovitine is sufficient to inhibit DNA synthesis, and to activate a DNA damage checkpoint response, as indicated by phosphorylation of p53-Ser15, replication protein A, and histone H2AX. Analysis of DNA replication proteins loaded onto DNA during S phase showed that the amount of proliferating cell nuclear antigen (PCNA), a cofactor of DNA replication enzymes, was significantly reduced by roscovitine. In contrast, chromatin-bound levels of DNA polymerase δ, DNA ligase I and CDK2, were stabilized. Checkpoint inhibition with caffeine could rescue PCNA disassembly only partially, pointing to additional effects due to CDK2 inhibition and the presence of replication stress. These results suggest that in S-phase cells, roscovitine induces checkpoint-dependent and -independent effects, leading to stabilization of replication forks and an uncoupling between PCNA and PCNA-interacting proteins.     

DNA Damage Response in Nucleoli

Molecular Biology - Nucleoli, the largest subnuclear compartments, are formed around arrays of ribosomal gene repeats transcribed by RNA polymerase I. The primary function of nucleoli is ribosome...     

SUMO化修饰在DNA损伤响应中的作用

物理或化学等多种因素均可以引起DNA损伤。为维持机体基因组的稳定性,机体形成了精确完整的机制来修复损伤的／DNA。SUMO（smallubiquitin-relatedmodifier,SUMO）化修饰与其他蛋白翻译后修饰一样,具有多种生物学功能。近年来的研究表明,其在DNA损伤修复中也具有非常重要的作用。该文就DNA损伤修复、SUMO,96修饰系统及其二者关系的最新研究进展作了较为全面的介绍和总结。     

Increased Sensitivity of DNA Damage Response-Deficient Cells to Stimulated Microgravity-Induced DNA Lesions

Microgravity is a major stress factor that astronauts have to face in space. In the past, the effects of microgravity on genomic DNA damage were studied, and it seems that the effect on genomic DNA depends on cell types and the length of exposure time to microgravity or simulated microgravity (SMG). In this study we used mouse embryonic stem (MES) and mouse embryonic fibroblast (MEF) cells to assess the effects of SMG on DNA lesions. To acquire the insight into potential mechanisms by which cells resist and/or adapt to SMG, we also included Rad9-deleted MES and Mdc1-deleted MEF cells in addition to wild type cells in this study. We observed significant SMG-induced DNA double strand breaks (DSBs) in Rad9 ^-/- MES and Mdc1 ^-/- MEF cells but not in their corresponding wild type cells. A similar pattern of DNA single strand break or modifications was also observed in Rad9 ^-/- MES. As the exposure to SMG was prolonged, Rad9 ^-/- MES cells adapted to the SMG disturbance by reducing the induced DNA lesions. The induced DNA lesions in Rad9 ^-/- MES were due to SMG-induced reactive oxygen species (ROS). Interestingly, Mdc1 ^-/- MEF cells were only partially adapted to the SMG disturbance. That is, the induced DNA lesions were reduced over time, but did not return to the control level while ROS returned to a control level. In addition, ROS was only partially responsible for the induced DNA lesions in Mdc1 ^-/- MEF cells. Taken together, these data suggest that SMG is a weak genomic DNA stress and can aggravate genomic instability in cells with DNA damage response (DDR) defects.     

c-Abl在DNA损伤反应中的功能

非受体酪氨酸激酶c-Abl在正常生理及病理条件下具有多种生物学功能。当电离辐射、顺铂、丝裂霉素C等DNA损伤诱导剂诱导DNA损伤反应后,c-Abl可参与DNA损伤反应后的细胞周期调控、基因重组修复及细胞凋亡调控等,进而决定细胞在DNA损伤反应条件下的状态。简要介绍了c-Abl在DNA损伤反应中的作用及其进展。     

Deubiquitylating Enzymes and DNA Damage Response Pathways

Covalent post-translational modification of proteins by ubiquitin and ubiquitin-like factors has emerged as a general mechanism to regulate myriad intra-cellular processes. The addition and removal of ubiquitin or ubiquitin-like proteins from factors has recently been demonstrated as a key mechanism to modulate DNA damage response (DDR) pathways. It is thus, timely to evaluate the potential for ubiquitin pathway enzymes as DDR drug targets for therapeutic intervention. The synthetic lethal approach provides exciting opportunities for the development of targeted therapies to treat cancer: most tumours have lost critical DDR pathways, and thus rely more heavily on the remaining pathways, while normal tissues are still equipped with all DDR pathways. Here, we review key deubiquitylating enzymes (DUBs) involved in DDR pathways, and describe how targeting DUBs may lead to selective therapies to treat cancer patients.     

DNA Damage Response: Three Levels of DNA Repair Regulation

Genome integrity is challenged by DNA damage from both endogenous and environmental sources. This damage must be repaired to allow both RNA and DNA polymerases to accurately read and duplicate the information in the genome. Multiple repair enzymes scan the DNA for problems, remove the offending damage, and restore the DNA duplex. These repair mechanisms are regulated by DNA damage response kinases including DNA-PKcs, ATM, and ATR that are activated at DNA lesions. These kinases improve the efficiency of DNA repair by phosphorylating repair proteins to modify their activities, by initiating a complex series of changes in the local chromatin structure near the damage site, and by altering the overall cellular environment to make it more conducive to repair. In this review, we focus on these three levels of regulation to illustrate how the DNA damage kinases promote efficient repair to maintain genome integrity and prevent disease.The DNA in each of our cells accumulates thousands of lesions every day. This damaged DNA must be removed for the DNA code to be read properly. Fortunately, cells contain multiple DNA repair mechanisms including: base excision repair (BER) that removes damaged bases, mismatch repair (MMR) that recognizes base incorporation errors and base damage, nucleotide excision repair (NER) that removes bulky DNA adducts, and cross-link repair (ICL) that removes interstrand cross-links. In addition, breaks in the DNA backbone are repaired via double-strand break (DSB) repair pathways including homologous recombination (HR) and nonhomologous end joining (NHEJ). Some of these mechanisms can operate independently to repair simple lesions. However, the repair of more complex lesions involving multiple DNA processing steps is regulated by the DNA damage response (DDR). For the most difficult to repair lesions, the DDR can be essential for successful repair.The DDR consists of multiple pathways, but for the purposes of this review we will focus on the DDR kinase signaling cascades controlled by the phosphatidylinositol 3-kinase-related kinases (PIKK). These kinases include DNA-dependent protein kinase (DNA-PKcs), ataxia telangiectasia-mutated (ATM), and ATM and Rad3-related (ATR). DNA-PKcs and ATM are primarily involved in DSB repair, whereas ATR responds to a wide range of DNA lesions, especially those associated with DNA replication (Cimprich and Cortez 2008). ATR’s versatility makes it essential for the viability of replicating cells in mice and humans (Brown and Baltimore 2000; de Klein et al. 2000; Cortez et al. 2001). In the case of ATM, inherited biallelic mutations cause ataxia-telangiectasia—a disorder characterized by neurodegeneration, immunodeficiency, and cancer (Shiloh 2003; Lavin 2008). ATM mutations are also frequently found in several types of tumors (Negrini et al. 2010).The DDR kinases share several common regulatory mechanisms of activation (Lovejoy and Cortez 2009). All three DDR kinases sense damage through protein–protein interactions that serve to recruit the kinases to damage sites. Once localized, posttranslational modifications and other protein–protein interactions fully activate the kinases to initate a cascade of phosphorylation events. The best-studied substrate of DNA-PKcs is actually DNA-PKcs itself, and autophosphorylation is an important step in direct religation of the DSB via nonhomologous end joining (NHEJ) (Weterings and Chen 2007; Dobbs et al. 2010). ATM and ATR have both unique and shared substrates that participate in DNA repair, checkpoint signaling, and determining cell fate decisions such as apoptosis and sensescence.     

Protein Expression of DNA Damage Repair Proteins Dictates Response to Topoisomerase and PARP Inhibitors in Triple-Negative Breast Cancer

Patients with metastatic triple-negative breast cancer (TNBC) have a poor prognosis. New approaches for the treatment of TNBC are needed to improve patient survival. The concept of synthetic lethality, brought about by inactivating complementary DNA repair pathways, has been proposed as a promising therapeutic option for these tumors. The TNBC tumor type has been associated with BRCA mutations, and inhibitors of Poly (ADP-ribose) polymerase (PARP), a family of proteins that facilitates DNA repair, have been shown to effectively kill BRCA defective tumors by preventing cells from repairing DNA damage, leading to a loss of cell viability and clonogenic survival. Here we present preclinical efficacy results of combining the PARP inhibitor, ABT-888, with CPT-11, a topoisomerase I inhibitor. CPT-11 binds to topoisomerase I at the replication fork, creating a bulky adduct that is recognized as damaged DNA. When DNA damage was stimulated with CPT-11, protein expression of the nucleotide excision repair enzyme ERCC1 inversely correlated with cell viability, but not clonogenic survival. However, 4 out of the 6 TNBC cells were synergistically responsive by cell viability and 5 out of the 6 TNBC cells were synergistically responsive by clonogenic survival to the combination of ABT-888 and CPT-11. In vivo, the BRCA mutant cell line MX-1 treated with CPT-11 alone demonstrated significant decreased tumor growth; this decrease was enhanced further with the addition of ABT-888. Decrease in tumor growth correlated with an increase in double strand DNA breaks as measured by γ-H2AX phosphorylation. In summary, inhibiting two arms of the DNA repair pathway simultaneously in TNBC cell lines, independent of BRCA mutation status, resulted in un-repairable DNA damage and subsequent cell death.     

Chlamydia Infection Promotes Host DNA Damage and Proliferation but Impairs the DNA Damage Response

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Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins

SH3 domains are peptide recognition modules that mediate the assembly of diverse biological complexes. We scanned billions of phage-displayed peptides to map the binding specificities of the SH3 domain family in the budding yeast, Saccharomyces cerevisiae. Although most of the SH3 domains fall into the canonical classes I and II, each domain utilizes distinct features of its cognate ligands to achieve binding selectivity. Furthermore, we uncovered several SH3 domains with specificity profiles that clearly deviate from the two canonical classes. In conjunction with phage display, we used yeast two-hybrid and peptide array screening to independently identify SH3 domain binding partners. The results from the three complementary techniques were integrated using a Bayesian algorithm to generate a high-confidence yeast SH3 domain interaction map. The interaction map was enriched for proteins involved in endocytosis, revealing a set of SH3-mediated interactions that underlie formation of protein complexes essential to this biological pathway. We used the SH3 domain interaction network to predict the dynamic localization of several previously uncharacterized endocytic proteins, and our analysis suggests a novel role for the SH3 domains of Lsb3p and Lsb4p as hubs that recruit and assemble several endocytic complexes.     

脆性组氨酸三联体突变体在 DNA 损伤应答中的作用机制

目的:用建立的稳定表达脆性组氨酸三联体(Fhit)突变体的细胞株,研究 Fhit 与复制蛋白 A(RPA)之间的相互作用对细胞在 DNA 损伤后的影响.方法:用电离辐射或 DNA 损伤诱导剂喜树碱处理稳定表达 Fhit 突变体的阳性细胞株 HeLa-FhitA/D/F 后,通过流式细胞技术、MTT 比色法及克隆形成实验,检测这些细胞系的细胞周期变化情况以及对 DNA 损伤诱导剂的敏感性.结果:DNA 损伤诱导剂处理后,Fhit 突变体基的高表达可以使细胞表现出更强的G2期阻滞及对 DNA 损伤诱导剂更耐受.结论:Fhit 与 RPA 相互作用的改变影响了细胞对 DNA 损伤诱导剂的耐受性,为阐明 Fhit 在维持基组完整性方面的机理提供了线索.     

Causes and Consequences of the DNA Damage Response

A prerequisite for maintaining genome stability in all cell types is the accurate repair and efficient signaling of DNA double strand breaks (DSBs). It is believed that DSBs are initially detected by damage sensors that trigger the activation of transducing kinases. These transducers amplify the damage signal, which is then relayed to effector proteins, which regulate the progression of the cell cycle, DNA repair and apoptosis. Errors in the execution of the repair and/or signaling of DSBs can give rise to multi-systemic disorders characterized by tissue degeneration, infertility, immune system dysfunction, age-related pathologies and cancer. This special Spotlight issue of Cell Cycle highlights recent advances in our understanding of the biology and significance of the DNA damage response. A range of issues are addressed including mechanistic ones: what is the aberrant DNA structure that triggers the activation of the checkpoint - how does chromatin structure influence the recruitment of repair and checkpoint proteins- how does chromosomal instability contribute to the evolution of cancer. In addition, questions related to the physiology of the DNA damage response in normal and abnormal cells is explored: what is the in vivo consequence of altering specific amino acids in a DNA damage sensor- does DNA damage accumulation in stem cells cause aging- how is neurodegeneration linked to deficiencies in specific DNA repair pathways, and finally, what is the biological basis for selection of aberrant DNA damage responses in cancer cells?     

Inner Nuclear Envelope Proteins SUN1 and SUN2 Play a Prominent Role in the DNA Damage Response

The DNA damage response (DDR) and DNA repair are critical for maintaining genomic stability and evading many human diseases [1, 2]. Recent findings indicate that accumulation of?SUN1, a nuclear envelope (NE) protein, is a significant pathogenic event in Emery-Dreifuss muscular dystrophy and Hutchinson-Gilford progeria syndrome, both caused by mutations in LMNA [3, 4]. However, roles of mammalian SUN proteins in mitotic cell division and genomic stability are unknown. Here we report that the inner NE proteins SUN1 and SUN2 may play a redundant role in DDR. Mouse embryonic fibroblasts from Sun1(-/-)Sun2(-/-) mice displayed premature proliferation arrest in S phase of cell cycle, increased apoptosis and DNA damage, and decreased perinuclear heterochromatin, indicating genome instability. Furthermore, activation of ATM and H2A.X, early events in?DDR, were impaired in Sun1(-/-)Sun2(-/-) fibroblasts. A biochemical screen identified interactions between SUN1 and SUN2 and DNA-dependent protein kinase (DNAPK) complex that functions in DNA nonhomologous end joining repair and possibly in DDR [2, 5, 6]. Knockdown of DNAPK reduced ATM activation in NIH 3T3 cells, consistent with a potential role of SUN1- and SUN2-DNAPK interaction during DDR. SUN1 and SUN2 could affect DDR by localizing certain nuclear factors to the NE or by mediating communication between nuclear and cytoplasmic events.     

Spatiotemporal Dynamics of Actomyosin Networks

Rhodamine–phalloidin-labeled actin filaments were visualized gliding over a skeletal heavy meromyosin (HMM)-coated surface. Experiments at low filament densities showed that when two filaments collided, their paths were affected in a manner that depended on collision angle. Some collisions resulted in complete alignment of the filament paths; in others, the filaments crossed over one another. Filament crossover or alignment was equally probable at ∼40° contact angle. Filaments often underwent significant bending during collision and analysis of filament shape indicated an energy requirement of ∼13 k_BT. Experiments were performed over a wide range of HMM surface density and actin filament bulk concentration. Actin filament gliding speed and path persistence plateaued above a critical HMM surface density, and at high (micromolar) actin filament concentrations, filament motion became dramatically aligned in a common direction. Spatiotemporal features of alignment behavior were determined by correlation analysis, supported by simulations. The thermal drift of individual filament tracks was suppressed as the population became more oriented. Spatial correlation analysis revealed that long-range alignment was due to incremental recruitment rather than fusion of locally ordered seed domains. The global alignment of filament movement, described by an “order parameter,” peaked at optimal actin concentrations and myosin surface densities, in contrast to previous predictions of a critical phase transition. Either hydrodynamic coupling or exchange of filaments between the surface bound and adjacent bulk phase layers might degrade order at high actin filament concentration, and high HMM surface densities might decrease alignment probability during collisions. Our results are compatible with generation of long-range order from mechanical interaction between individual actin filaments. Furthermore, we show that randomly oriented myosin motors align relatively short, submicrometer actin filaments into motile surface domains that extend over many tens of micrometers and these patterns persist for several minutes.