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  1. Article ; Online: The unstructured C-terminal tail of yeast Dpb11 (human TopBP1) protein is dispensable for DNA replication and the S phase checkpoint but required for the G2/M checkpoint.

    Navadgi-Patil, Vasundhara M / Kumar, Sandeep / Burgers, Peter M

    The Journal of biological chemistry

    2011  Volume 286, Issue 47, Page(s) 40999–41007

    Abstract: ... compromised for the G(2)/M DNA damage checkpoint. These data suggest that replication checkpoint defects ... terminus of Dpb11 are critical for Mec1 activation in vitro and for the G(2)/M checkpoint in yeast ...

    Abstract Budding yeast Dpb11 (human TopBP1, fission yeast Cut5) is an essential protein required for replisome assembly and for the DNA damage checkpoint. Previous studies with the temperature-sensitive dpb11-1 allele, truncated at amino acid 583 of the 764-amino acid protein, have suggested the model that Dpb11 couples DNA replication to the replication checkpoint. However, the dpb11-1 allele shows distinct replication defects even at permissive temperatures. Here, we determine that the 1-600-amino acid domain of DPB11 is both required and sufficient for full replication function of Dpb11 but that this domain is defective for activation of the principal checkpoint kinase Mec1 (human ataxia telangiectasia and Rad3-related) in vitro and in vivo. Remarkably, mutants of DPB11 that leave its replication function intact but abrogate its ability to activate Mec1 are proficient for the replication checkpoint, but they are compromised for the G(2)/M DNA damage checkpoint. These data suggest that replication checkpoint defects may result indirectly from defects in replisome assembly. Two conserved aromatic amino acids in the C terminus of Dpb11 are critical for Mec1 activation in vitro and for the G(2)/M checkpoint in yeast. Together with aromatic motifs identified previously in the Ddc1 subunit of 9-1-1, another activator of Mec1 kinase, they define a consensus structure for Mec1 activation.
    MeSH term(s) Alleles ; Amino Acid Motifs ; Amino Acid Sequence ; Cell Cycle Checkpoints ; Cell Cycle Proteins/chemistry ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; DNA Damage/genetics ; DNA Replication/genetics ; DNA, Fungal/biosynthesis ; Enzyme Activation ; G2 Phase Cell Cycle Checkpoints/genetics ; Humans ; Intracellular Signaling Peptides and Proteins/metabolism ; M Phase Cell Cycle Checkpoints/genetics ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Mutation ; Protein-Serine-Threonine Kinases/metabolism ; S Phase Cell Cycle Checkpoints/genetics ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
    Chemical Substances Cell Cycle Proteins ; DNA, Fungal ; DPB11 protein, S cerevisiae ; Intracellular Signaling Peptides and Proteins ; Saccharomyces cerevisiae Proteins ; MEC1 protein, S cerevisiae (EC 2.7.11.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1)
    Language English
    Publishing date 2011-09-28
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.M111.283994
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Cell-cycle-specific activators of the Mec1/ATR checkpoint kinase.

    Navadgi-Patil, Vasundhara M / Burgers, Peter M

    Biochemical Society transactions

    2011  Volume 39, Issue 2, Page(s) 600–605

    Abstract: Mec1 [ATR (ataxia telangiectasia mutated- and Rad3-related) in humans] is the principle kinase responsible for checkpoint activation in response to replication stress and DNA damage in Saccharomyces cerevisiae. The heterotrimeric checkpoint clamp, 9-1-1 ( ...

    Abstract Mec1 [ATR (ataxia telangiectasia mutated- and Rad3-related) in humans] is the principle kinase responsible for checkpoint activation in response to replication stress and DNA damage in Saccharomyces cerevisiae. The heterotrimeric checkpoint clamp, 9-1-1 (checkpoint clamp of Rad9, Rad1 and Hus1 in humans and Ddc1, Rad17 and Mec3 in S. cerevisiae; Ddc1-Mec3-Rad17) and the DNA replication initiation factor Dpb11 (human TopBP1) are the two known activators of Mec1. The 9-1-1 clamp functions in checkpoint activation in G1- and G2-phase, but its employment differs between these two phases of the cell cycle. The Ddc1 (human Rad9) subunit of the clamp directly activates Mec1 in G1-phase, an activity identified only in S. cerevisiae so far. However, in G2-phase, the 9-1-1 clamp activates the checkpoint by two mechanisms. One mechanism includes direct activation of Mec1 by the unstructured C-terminal tail of Ddc1. The second mech-anism involves the recruitment of Dpb11 by the phosphorylated C-terminal tail of Ddc1. The latter mechanism is highly conserved and also functions in response to replication stress in higher eukaryotes. In S. cerevisiae, however, both the 9-1-1 clamp and the Dpb11 are partially redundant for checkpoint activation in response to replication stress, suggesting the existence of additional activators of Mec1.
    MeSH term(s) Animals ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; Cell Cycle Proteins/physiology ; DNA Damage/genetics ; DNA Damage/physiology ; Genes, cdc/physiology ; Humans ; Intracellular Signaling Peptides and Proteins/genetics ; Intracellular Signaling Peptides and Proteins/metabolism ; Intracellular Signaling Peptides and Proteins/physiology ; Models, Biological ; Protein-Serine-Threonine Kinases/genetics ; Protein-Serine-Threonine Kinases/metabolism ; Protein-Serine-Threonine Kinases/physiology ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae/physiology ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Saccharomyces cerevisiae Proteins/physiology ; Substrate Specificity ; Trans-Activators/metabolism ; Trans-Activators/physiology
    Chemical Substances Cell Cycle Proteins ; DPB11 protein, S cerevisiae ; Ddc1 protein, S cerevisiae ; Intracellular Signaling Peptides and Proteins ; Saccharomyces cerevisiae Proteins ; Trans-Activators ; MEC1 protein, S cerevisiae (EC 2.7.11.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1)
    Language English
    Publishing date 2011-04
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 184237-7
    ISSN 1470-8752 ; 0300-5127
    ISSN (online) 1470-8752
    ISSN 0300-5127
    DOI 10.1042/BST0390600
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Probing the Mec1ATR Checkpoint Activation Mechanism with Small Peptides.

    Wanrooij, Paulina H / Tannous, Elias / Kumar, Sandeep / Navadgi-Patil, Vasundhara M / Burgers, Peter M

    The Journal of biological chemistry

    2015  Volume 291, Issue 1, Page(s) 393–401

    Abstract: Yeast Mec1, the ortholog of human ATR, is the apical protein kinase that initiates the cell cycle checkpoint in response to DNA damage and replication stress. The basal activity of Mec1 kinase is activated by cell cycle phase-specific activators. Three ... ...

    Abstract Yeast Mec1, the ortholog of human ATR, is the apical protein kinase that initiates the cell cycle checkpoint in response to DNA damage and replication stress. The basal activity of Mec1 kinase is activated by cell cycle phase-specific activators. Three distinct activators stimulate Mec1 kinase using an intrinsically disordered domain of the protein. These are the Ddc1 subunit of the 9-1-1 checkpoint clamp (ortholog of human and Schizosaccharomyces pombe Rad9), the replication initiator Dpb11 (ortholog of human TopBP1 and S. pombe Cut5), and the multifunctional nuclease/helicase Dna2. Here, we use small peptides to determine the requirements for Mec1 activation. For Ddc1, we identify two essential aromatic amino acids in a hydrophobic environment that when fused together are proficient activators. Using this increased insight, we have been able to identify homologous motifs in S. pombe Rad9 that can activate Mec1. Furthermore, we show that a 9-amino acid Dna2-based peptide is sufficient for Mec1 activation. Studies with mutant activators suggest that binding of an activator to Mec1 is a two-step process, the first step involving the obligatory binding of essential aromatic amino acids to Mec1, followed by an enhancement in binding energy through interactions with neighboring sequences.
    MeSH term(s) Amino Acid Motifs ; Amino Acid Sequence ; Cell Cycle Checkpoints/drug effects ; Cell Cycle Proteins/chemistry ; Cell Cycle Proteins/metabolism ; DNA Helicases/chemistry ; Enzyme Activation/drug effects ; Enzyme Activators/pharmacology ; Intracellular Signaling Peptides and Proteins/metabolism ; Models, Molecular ; Molecular Sequence Data ; Peptides/pharmacology ; Proline/metabolism ; Protein-Serine-Threonine Kinases/metabolism ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/drug effects ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/metabolism
    Chemical Substances Cell Cycle Proteins ; Ddc1 protein, S cerevisiae ; Enzyme Activators ; Intracellular Signaling Peptides and Proteins ; Peptides ; Saccharomyces cerevisiae Proteins ; rad9 protein (139691-42-2) ; Proline (9DLQ4CIU6V) ; MEC1 protein, S cerevisiae (EC 2.7.11.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; DNA Helicases (EC 3.6.4.-) ; DNA2 protein, S cerevisiae (EC 3.6.4.12)
    Language English
    Publishing date 2015-10-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.M115.687145
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: A tale of two tails: activation of DNA damage checkpoint kinase Mec1/ATR by the 9-1-1 clamp and by Dpb11/TopBP1.

    Navadgi-Patil, Vasundhara M / Burgers, Peter M

    DNA repair

    2009  Volume 8, Issue 9, Page(s) 996–1003

    Abstract: The DNA damage and replication checkpoint kinase Mec1/ATR is a member of the PI3-kinase related kinases that function in response to various genotoxic stresses. The checkpoint clamp 9-1-1 (Rad9-Rad1-Hus1 in S. pombe and mammals; Ddc1-Rad17-Mec3 in S. ... ...

    Abstract The DNA damage and replication checkpoint kinase Mec1/ATR is a member of the PI3-kinase related kinases that function in response to various genotoxic stresses. The checkpoint clamp 9-1-1 (Rad9-Rad1-Hus1 in S. pombe and mammals; Ddc1-Rad17-Mec3 in S. cerevisiae) executes two distinct checkpoint functions. In S. cerevisiae, DNA-bound 9-1-1 directly activates Mec1 kinase activity, a function that has not been demonstrated in other organisms. A second, conserved activity of 9-1-1 is that of TopBP1/Cut5/Dpb11 recruitment to stalled replication sites; subsequent activation of Mec1/ATR is carried out by TopBP1/Cut5/Dpb11. Biochemical studies indicate that the mode of Mec1/ATR activation by S. cerevisiae 9-1-1 is analogous to activation by S. cerevisiae Dpb11 or by vertebrate TopBP1: activation is mediated by the intrinsically disordered C-terminal tail of each activator. The relative contributions made by multiple activators of Mec1/ATR are discussed.
    MeSH term(s) Cell Cycle Proteins/metabolism ; DNA Damage ; Enzyme Activation ; Intracellular Signaling Peptides and Proteins/metabolism ; Protein-Serine-Threonine Kinases/metabolism ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae Proteins/metabolism
    Chemical Substances Cell Cycle Proteins ; DPB11 protein, S cerevisiae ; Intracellular Signaling Peptides and Proteins ; Saccharomyces cerevisiae Proteins ; MEC1 protein, S cerevisiae (EC 2.7.11.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1)
    Language English
    Publishing date 2009-05-22
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2071608-4
    ISSN 1568-7856 ; 1568-7864
    ISSN (online) 1568-7856
    ISSN 1568-7864
    DOI 10.1016/j.dnarep.2009.03.011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The unstructured C-terminal tail of the 9-1-1 clamp subunit Ddc1 activates Mec1/ATR via two distinct mechanisms.

    Navadgi-Patil, Vasundhara M / Burgers, Peter M

    Molecular cell

    2009  Volume 36, Issue 5, Page(s) 743–753

    Abstract: DNA damage checkpoint pathways operate to prevent cell-cycle progression in response to DNA damage and replication stress. In S. cerevisiae, Mec1-Ddc2 (human ATR-ATRIP) is the principal checkpoint protein kinase. Biochemical studies have identified two ... ...

    Abstract DNA damage checkpoint pathways operate to prevent cell-cycle progression in response to DNA damage and replication stress. In S. cerevisiae, Mec1-Ddc2 (human ATR-ATRIP) is the principal checkpoint protein kinase. Biochemical studies have identified two factors, the 9-1-1 checkpoint clamp and the Dpb11/TopBP1 replication protein, as potential activators of Mec1/ATR. Here, we show that G1 phase checkpoint activation of Mec1 is achieved by the Ddc1 subunit of 9-1-1, while Dpb11 is dispensable. However, in G2, 9-1-1 activates Mec1 by two distinct mechanisms. One mechanism involves direct activation of Mec1 by Ddc1, while the second proceeds by Dpb11 recruitment mediated through Ddc1 T602 phosphorylation. Two aromatic residues, W352 and W544, localized to two widely separated, conserved motifs of Ddc1, are essential for Mec1 activation in vitro and checkpoint function in G1. Remarkably, small peptides that fuse the two tryptophan-containing motifs together are proficient in activating Mec1.
    MeSH term(s) Amino Acid Motifs ; Amino Acid Sequence ; Cell Cycle/physiology ; Cell Cycle Proteins/chemistry ; Cell Cycle Proteins/metabolism ; Cell Cycle Proteins/physiology ; Enzyme Activation/physiology ; Intracellular Signaling Peptides and Proteins/chemistry ; Intracellular Signaling Peptides and Proteins/genetics ; Intracellular Signaling Peptides and Proteins/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Interaction Mapping ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/chemistry ; Protein-Serine-Threonine Kinases/genetics ; Protein-Serine-Threonine Kinases/metabolism ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Saccharomyces cerevisiae Proteins/physiology
    Chemical Substances Cell Cycle Proteins ; Ddc1 protein, S cerevisiae ; Intracellular Signaling Peptides and Proteins ; Saccharomyces cerevisiae Proteins ; MEC1 protein, S cerevisiae (EC 2.7.11.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1)
    Language English
    Publishing date 2009-12-14
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2009.10.014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Yeast DNA replication protein Dpb11 activates the Mec1/ATR checkpoint kinase.

    Navadgi-Patil, Vasundhara M / Burgers, Peter M

    The Journal of biological chemistry

    2008  Volume 283, Issue 51, Page(s) 35853–35859

    Abstract: The Saccharomyces cerevisiae Mec1-Ddc2 protein kinase (human ATR-ATRIP) initiates a signal transduction pathway in response to DNA damage and replication stress to mediate cell cycle arrest. The yeast DNA damage checkpoint clamp Ddc1-Mec3-Rad17 (human ... ...

    Abstract The Saccharomyces cerevisiae Mec1-Ddc2 protein kinase (human ATR-ATRIP) initiates a signal transduction pathway in response to DNA damage and replication stress to mediate cell cycle arrest. The yeast DNA damage checkpoint clamp Ddc1-Mec3-Rad17 (human Rad9-Hus1-Rad1: 9-1-1) is loaded around effector DNA and thereby activates Mec1 kinase. Dpb11 (Schizosaccharomyces pombe Cut5/Rad4 or human TopBP1) is an essential protein required for the initiation of DNA replication and has a role in checkpoint activation. In this study, we demonstrate that Dpb11 directly activates the Mec1 kinase in phosphorylating the downstream effector kinase Rad53 (human Chk1/2) and DNA bound RPA. However, DNA was not required for Dpb11 to function as an activator. Dpb11 and yeast 9-1-1 independently activate Mec1, but substantial synergism in activation was observed when both activators were present. Our studies suggest that Dpb11 and 9-1-1 may partially compensate for each other during yeast checkpoint function.
    MeSH term(s) Cell Cycle/physiology ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; DNA Damage/physiology ; DNA Replication/physiology ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Enzyme Activation/physiology ; Humans ; Intracellular Signaling Peptides and Proteins ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Protein Serine-Threonine Kinases ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Schizosaccharomyces
    Chemical Substances Cell Cycle Proteins ; DNA-Binding Proteins ; DPB11 protein, S cerevisiae ; Intracellular Signaling Peptides and Proteins ; MEC3 protein, S cerevisiae ; Nuclear Proteins ; RAD17 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; MEC1 protein, S cerevisiae (EC 2.7.11.1) ; Protein Serine-Threonine Kinases (EC 2.7.11.1)
    Language English
    Publishing date 2008-10-15
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.M807435200
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Yeast DNA Replication Protein Dpb11 Activates the Mec1/ATR Checkpoint Kinase

    Navadgi-Patil, Vasundhara M / Burgers, Peter M

    Journal of biological chemistry. 2008 Dec. 19, v. 283, no. 51

    2008  

    Abstract: The Saccharomyces cerevisiae Mec1-Ddc2 protein kinase (human ATR-ATRIP) initiates a signal transduction pathway in response to DNA damage and replication stress to mediate cell cycle arrest. The yeast DNA damage checkpoint clamp Ddc1-Mec3-Rad17 (human ... ...

    Abstract The Saccharomyces cerevisiae Mec1-Ddc2 protein kinase (human ATR-ATRIP) initiates a signal transduction pathway in response to DNA damage and replication stress to mediate cell cycle arrest. The yeast DNA damage checkpoint clamp Ddc1-Mec3-Rad17 (human Rad9-Hus1-Rad1: 9-1-1) is loaded around effector DNA and thereby activates Mec1 kinase. Dpb11 (Schizosaccharomyces pombe Cut5/Rad4 or human TopBP1) is an essential protein required for the initiation of DNA replication and has a role in checkpoint activation. In this study, we demonstrate that Dpb11 directly activates the Mec1 kinase in phosphorylating the downstream effector kinase Rad53 (human Chk1/2) and DNA bound RPA. However, DNA was not required for Dpb11 to function as an activator. Dpb11 and yeast 9-1-1 independently activate Mec1, but substantial synergism in activation was observed when both activators were present. Our studies suggest that Dpb11 and 9-1-1 may partially compensate for each other during yeast checkpoint function.
    Language English
    Dates of publication 2008-1219
    Size p. 35853-35859.
    Publishing place American Society for Biochemistry and Molecular Biology
    Document type Article
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    Database NAL-Catalogue (AGRICOLA)

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