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      Nuclear DNA Replication in Trypanosomatids: There Are No Easy Methods for Solving Difficult Problems

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          Abstract

          In trypanosomatids, etiological agents of devastating diseases, replication is robust and finely controlled to maintain genome stability and function in stressful environments. However, these parasites encode several replication protein components and complexes that show potentially variant composition compared with model eukaryotes. This review focuses on the advances made in recent years regarding the differences and peculiarities of the replication machinery in trypanosomatids, including how such divergence might affect DNA replication dynamics and the replication stress response. Comparing the DNA replication machinery and processes of parasites and their hosts may provide a foundation for the identification of targets that can be used in the development of chemotherapies to assist in the eradication of diseases caused by these pathogens.

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          In trypanosomatids, DNA replication is tightly controlled by protein complexes that diverge from those of model eukaryotes.

          There is no consensus for the number of replication origins used by trypanosomatids; how their replication dynamics compares with that of model organisms is the subject of debate.

          The DNA replication rate in trypanosomatids is similar to, but slightly higher than, that of model eukaryotes, which may be related to chromatin structure and function.

          Recent data suggest that the origin recognition complex in trypanosomatids closely resembles the multisubunit eukaryotic model.

          The absence of fundamental replication-associated proteins in trypanosomatids suggests that new signaling pathways may be present in these parasites to direct DNA replication and the replicative stress response.

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          Most cited references94

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          ATR prohibits replication catastrophe by preventing global exhaustion of RPA.

          ATR, activated by replication stress, protects replication forks locally and suppresses origin firing globally. Here, we show that these functions of ATR are mechanistically coupled. Although initially stable, stalled forks in ATR-deficient cells undergo nucleus-wide breakage after unscheduled origin firing generates an excess of single-stranded DNA that exhausts the nuclear pool of RPA. Partial reduction of RPA accelerated fork breakage, and forced elevation of RPA was sufficient to delay such "replication catastrophe" even in the absence of ATR activity. Conversely, unscheduled origin firing induced breakage of stalled forks even in cells with active ATR. Thus, ATR-mediated suppression of dormant origins shields active forks against irreversible breakage via preventing exhaustion of nuclear RPA. This study elucidates how replicating genomes avoid destabilizing DNA damage. Because cancer cells commonly feature intrinsically high replication stress, this study also provides a molecular rationale for their hypersensitivity to ATR inhibitors. Copyright © 2013 Elsevier Inc. All rights reserved.
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            Comparative genomics of trypanosomatid parasitic protozoa.

            A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that-along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions-have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.
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              ATR-mediated checkpoint pathways regulate phosphorylation and activation of human Chk1.

              Chk1 is an evolutionarily conserved protein kinase that regulates cell cycle progression in response to checkpoint activation. In this study, we demonstrated that agents that block DNA replication or cause certain forms of DNA damage induce the phosphorylation of human Chk1. The phosphorylated form of Chk1 possessed higher intrinsic protein kinase activity and eluted more quickly on gel filtration columns. Serines 317 and 345 were identified as sites of phosphorylation in vivo, and ATR (the ATM- and Rad3-related protein kinase) phosphorylated both of these sites in vitro. Furthermore, phosphorylation of Chk1 on serines 317 and 345 in vivo was ATR dependent. Mutants of Chk1 containing alanine in place of serines 317 and 345 were poorly activated in response to replication blocks or genotoxic stress in vivo, were poorly phosphorylated by ATR in vitro, and were not found in faster-eluting fractions by gel filtration. These findings demonstrate that the activation of Chk1 in response to replication blocks and certain forms of genotoxic stress involves phosphorylation of serines 317 and 345. In addition, this study implicates ATR as a direct upstream activator of Chk1 in human cells.
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                Author and article information

                Contributors
                Journal
                Trends Parasitol
                Trends Parasitol
                Trends in Parasitology
                Elsevier Science
                1471-4922
                1471-5007
                1 November 2017
                November 2017
                : 33
                : 11
                : 858-874
                Affiliations
                [1 ]Laboratório Especial de Ciclo Celular (LECC), Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, SP, Brazil
                [2 ]Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, SP, Brazil
                [3 ]Division of Biological Chemistry and Drug Discovery, School of Life Sciences, Dow Street, University of Dundee, Dundee, UK
                [4 ]The Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
                Author notes
                Article
                S1471-4922(17)30190-3
                10.1016/j.pt.2017.08.002
                5662062
                28844718
                65806005-af4c-44e4-aad2-bde3ebbe8fe2
                © 2017 The Authors

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

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                Categories
                Article

                Parasitology
                dna replication,origin recognition complex,replication fork,replication origins,replication stress,trypanosomatid emergence

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