Specialized mismatch repair function of Glu339 in the Phe-X-Glu motif of yeast Msh6

The major eukaryotic mismatch repair (MMR) pathway requires Msh2-Msh6, which, like Escherichia coli MutS, binds to and participates in repair of the two most common replication errors, single base-base and single base insertion-deletion mismatches. For both types of mismatches, the side chain of E. coli Glu38 in a conserved Phe-X-Glu motif interacts with a mismatched base. The Ovarepsilon of Glu38 forms a hydrogen bond with either the N7 of purines or the N3 of pyrimidines. We show here that changing E. coli Glu38 to alanine results in nearly complete loss of repair of both single base-base and single base deletion mismatches. In contrast, a yeast strain with alanine replacing homologous Glu339 in Msh6 has nearly normal repair for insertion-deletion and most base-base mismatches, but is defective in repairing base-base mismatches characteristic of oxidative stress, e.g. 8-oxo-G.A mismatches. The results suggest that bacterial MutS and yeast Msh2-Msh6 differ in how they recognize and/or process replication errors involving undamaged bases, and that Glu339 in Msh6 may have a specialized role in repairing mismatches containing oxidized bases.     

Mismatch Repair Protein Deficiency Compromises Cisplatin-induced Apoptotic Signaling

Mismatch repair (MMR) proteins participate in cytotoxicity induced by certain DNA damage-inducing agents, including cisplatin (cis-diamminedichloroplatinum(II), CDDP), a cancer chemotherapeutic drug utilized clinically to treat a variety of malignancies. MMR proteins have been demonstrated to bind to CDDP-DNA adducts and initiate MMR protein-dependent cell death in cells treated with CDDP; however, the molecular events underlying this death remain unclear. As MMR proteins have been suggested to be important in clinical responses to CDDP, a clear understanding of MMR protein-dependent, CDDP-induced cell death is critical. In this report, we demonstrate MMR protein-dependent relocalization of cytochrome c to the cytoplasm and cleavage of caspase-9, caspase-3, and poly(ADP-ribose) polymerase upon treatment of cells with CDDP. Chemical inhibition of caspases specifically attenuates CDDP/MMR protein-dependent cytotoxicity, suggesting that a caspase-dependent signaling mechanism is required for the execution of this cell death. p53 protein levels were up-regulated independently of MMR protein status, suggesting that p53 is not a mediator of MMR-dependent, CDDP-induced death. This work is the first indication of a required signaling mechanism in CDDP-induced, MMR protein-dependent cytotoxicity, which can be uncoupled from other CDDP response pathways, and defines a critical contribution of MMR proteins to the control of cell death.The MMR² system of proteins plays roles in diverse cellular processes, perhaps most notably in preserving genomic integrity by recognizing and facilitating the repair of post-DNA replication base pairing errors. Recognition of these errors and recruitment of repair machinery is performed by the MutSα complex (consisting of the MMR proteins MSH2 and MSH6) or MutSβ complex (consisting of MSH2 and MSH3). Defects in MMR proteins render cells hypermutable and promote microsatellite instability, a hallmark of MMR defects. MMR protein defects are found in a wide variety of sporadic cancers, as well as in hereditary non-polyposis colorectal cancer (1).In addition to their role in DNA repair, MMR proteins also play a role in cytotoxicity induced by specific types of DNA-damaging chemotherapeutic drugs, such as CDDP, which is utilized clinically to treat a number of different cancer types. MutSα recognizes multiple types of DNA damage, including 1,2-intrastrand CDDP adducts and O⁶-methylguanine lesions (2). Treatment of cells with compounds that induce these types of lesions, including CDDP and methylating agents such as N-methyl-N′-nitro-N-nitrosoguanidine (MNNG), results in MMR protein-dependent cell cycle arrest and cell death (3–7). This suggests that MMR proteins, in addition to their role in DNA repair, are also capable of initiating cell death in response to certain types of DNA damage.Cells treated with DNA-damaging agents frequently activate an apoptotic cell death pathway mediated by the mitochondria. This intrinsic death signaling pathway predominantly involves the coordinated activity of two groups of proteins: pro-death members of the Bcl-2 family that control the integrity of mitochondrial membranes, and members of the caspase family of cysteinyl proteases that proteolytically cleave intracellular substrates, giving rise to apoptotic morphology and destruction of the cell (8, 9). Pro-death Bcl-2 family members, such as Bax and Bak, target the outer mitochondrial membrane and cause the cytosolic release of pro-death factors residing within the mitochondria of unstressed cells (8). Predominant among these factors is cytochrome c, whose cytoplasmic localization results in the formation of a caspase-activating platform known as the apoptosome (10). This complex includes the adaptor protein Apaf-1, and when formed the apoptosome promotes the cleavage and activation of caspase-9 (11, 12). Once activated, this apical caspase proceeds to cleave and activate caspase-3, the predominant effector protease of apoptosis.A significant amount of evidence has been gathered illustrating MMR protein-dependent pro-death signaling in response to methylating agents (13–16, 3). In contrast, the MMR protein-dependent cytotoxic response to CDDP is largely unknown, with only the p53-related transactivator protein p73 and the c-Abl kinase clearly implicated as potential mediators of CDDP/MMR protein-dependent cell death in human cells (17, 18). Interestingly, ATM, Chk1, Chk2, and p53, which are activated in an MMR protein-dependent manner after treatment of cells with MNNG (3, 13), are not involved in the MMR-dependent response to CDDP (7, 17). In addition, the magnitude of MMR protein-dependent cell death induced by methylating agents and CDDP differs (4). These findings suggest that unique signaling pathways may be engaged by MMR proteins depending upon the type of recognized lesion. As such, there is a requirement for further study of the molecular events underlying MMR protein-dependent cell death and cell cycle arrest for each type of recognized DNA lesion. This is particularly relevant in the case of CDDP, as evidence from a limited number of retrospective clinical studies suggests that MMR proteins play an important role in patient response to CDDP. Several studies examining immunohistochemical staining against MSH2 or MLH1 have demonstrated that levels of these proteins are reduced in ovarian and esophageal tumor samples following CDDP-based chemotherapy (19, 20). Low levels of MMR protein post-chemotherapy seem to be predictive of lower overall survival in a certain subset of tumors (esophageal cancer), but not others (ovarian and non-small cell lung cancer) (19–21). Two recent studies examining MMR protein levels and microsatellite instability in germ cell tumors from patients receiving platinum-based chemotherapy have suggested a prognostic value for pre-chemotherapy MMR protein status in these tumors (22, 23). This potential clinical relevance underscores the need for a greater understanding of MMR protein-dependent mechanisms of CDDP-induced cell death.In this study, we report that CDDP induces an MMR protein-dependent decrease in cell viability and MMR protein-dependent signaling in the form of cytochrome c release to the cytoplasm and cleavage of caspase-9, caspase-3, and PARP. Chemical inhibition of caspases specifically attenuates CDDP/MMR protein-dependent loss of cell viability, indicating a requirement for caspase activation in this process and uncoupling MMR protein-dependent cytotoxic signaling from other CDDP response pathways. Additionally, the CDDP-induced, MMR protein-dependent cytotoxic response is independent of p53 signaling. Our results demonstrate for the first time an MMR protein-dependent pro-death signaling pathway in cells treated with CDDP.     

Similarities in Restriction Fragment Patterns of Mitochondrial DNAs of PhytophthoraSpecies Strongly Depend on the Restriction Enzyme Used Due to Heterogeneous Base Distribution and Sequence Conservation

Mitochondrial DNAs of six morphologically different Phytophthora species were digested with 15 restriction enzymes. The numbers of restriction fragments obtained differed considerably from those theoretically expected for random base distribution. Enzymes with relatively many G and C in their recognition sequences produced significantly larger numbers of fragments. Moreover, fragments generated by most of these enzymes were more often shared by two or more species than those from enzymes with more A and T in their recognition sequence. It is concluded that base distribution in mitochondrial DNA of Phytophthora is heterogeneous,AT-rich stretches occurring scattered over the mitochondrial genome and GC-rich regions present in conserved sequences, presumably genes. A practical consequence for taxonomic RFLP studies is that optimal enzymes can be selected, depending on the desired level of resolution.     

Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for amniote relationships [published erratum appears in Mol Biol Evol 1991 May;8(3):398]

The 18S ribosomal RNAs of 21 tetrapods were sequenced and aligned with five published tetrapod sequences. When the coelacanth was used as an outgroup, Lissamphibia (living amphibians) and Amniota (amniotes) were found to be statistically significant monophyletic groups. Although little resolution was obtained among the lissamphibian taxa, the amniote sequences support a sister-group relationship between birds and mammals. Portions of the 28S ribosomal RNA (rRNA) molecule in 11 tetrapods also were sequenced, although the phylogenetic results were inconclusive. In contrast to previous studies, deletion or down- weighting of base-paired sites were found to have little effect on phylogenetic relationships. Molecular evidence for amniote relationships is reviewed, showing that three genes (beta-hemoglobin, myoglobin, and 18S rRNA) unambiguously support a bird-mammal relationship, compared with one gene (histone H2B) that favors a bird- crocodilian clade. Separate analyses of four other genes (alpha- crystallin A, alpha-hemoglobin, insulin, and 28S rRNA) and a combined analysis of all sequence data are inconclusive, in that different groups are defined in different analyses and none are strongly supported. It is suggested that until sequences become available from a broader array of taxa, the molecular evidence is best evaluated at the level of individual genes, with emphasis placed on those studies with the greatest number of taxa and sites. When this is done, a bird-mammal relationship is most strongly supported. When regarded in combination with the morphological evidence for this association, it must be considered at least as plausible as a bird-crocodilian relationship.      

Cooperative nuclear localization sequences lend a novel role to the N-terminal region of MSH6

Human mismatch repair proteins MSH2-MSH6 play an essential role in maintaining genetic stability and preventing disease. While protein functions have been extensively studied, the substantial amino-terminal region (NTR*) of MSH6 that is unique to eukaryotic proteins, has mostly evaded functional characterization. We demonstrate that a cluster of three nuclear localization signals (NLS) in the NTR direct nuclear import. Individual NLSs are capable of partially directing cytoplasmic protein into the nucleus; however only cooperative effects between all three NLSs efficiently transport MSH6 into the nucleus. In striking contrast to yeast and previous assumptions on required heterodimerization, human MSH6 does not determine localization of its heterodimeric partner, MSH2. A cancer-derived mutation localized between two of the three NLS significantly decreases nuclear localization of MSH6, suggesting altered protein localization can contribute to carcinogenesis. These results clarify the pending speculations on the functional role of the NTR in human MSH6 and identify a novel, cooperative nuclear localization signal.     

Evaluation of the <Emphasis Type="Italic">OPTC</Emphasis> gene in primary open angle glaucoma: functional significance of a silent change

Background  

We investigated the molecular basis of primary open-angle glaucoma (POAG) using Opticin (OPTC) as a candidate gene on the basis of its expression in the trabecular meshwork cells involved in the disease pathogenesis. Two hundred POAG patients and 100 controls were enrolled in this study. The coding sequence of OPTC was amplified by PCR from genomic DNA of POAG patients, followed by SSCP, DHPLC and DNA sequencing. Subsequent bioinformatic analysis, site-directed mutagenesis, quantitative RT-PCR and western blot experiments were performed to address the functional significance of a 'silent' change in the OPTC coding region while screening for mutations in POAG patients.     

The molecular mechanism of DNA damage recognition by MutS homologs and its consequences for cell death response

We determined the molecular mechanism of cell death response by MutS homologs in distinction to the repair event. Key protein–DNA contacts differ in the interaction of MutS homologs with cisplatinated versus mismatched DNA. Mutational analyses of protein–DNA contacts, which were predicted by molecular dynamics (MD) simulations, were performed. Mutations in suggested interaction sites can affect repair and cell death response independently, and to different extents. A glutamate residue is identified as the key contact with cisplatin-DNA. Mutation of the residue increases cisplatin resistance due to increased non-specific DNA binding. In contrast, the conserved phenylalanine that is instrumental and indispensable for mismatch recognition during repair is not required for cisplatin cytotoxicity. These differences in protein–DNA interactions are translated into localized conformational changes that affect nucleotide requirements and inter-subunit interactions. Specifically, the ability for ATP binding/hydrolysis has little consequence for the MMR-dependent damage response. As a consequence, intersubunit contacts are altered that most likely affect the interaction with downstream proteins. We here describe the interaction of MutS homologs with DNA damage, as it differs from the interaction with a mismatch, and its structural translation into all other functional regions of the protein as a mechanism to initiate cell death response and concomitantly inhibit repair.