Biological Responses to DNA Damage

Symposium Participants v Foreword xxi

Mutation Response and Error Bypass

Understanding the Complexity of an Organism's Responses to DNA Damage G.C. Walker 1 DNA Repair Systems and Bacterial Evolution M. Radman, F. Taddei, and I. Matic 11 Adaptive Mutation in Escherichia coli P.L. Foster 21 The Biochemical Basis and In Vivo Regulation of SOS-induced Mutagenesis Promoted by Escherichia coli DNA Polymerase V (UmuD´2C) M.F. Goodman and R. Woodgate 31 Human DNA Polymerase k: A Novel DNA Polymerase of Unknown Biological Function Encoded by the DINB1 Gene V.L. Gerlach, W.J. Feaver, P.L. Fischhaber, J.A. Richardson, L. Aravind, E.V. Koonin, K. Bebenek, T.A. Kunkel, and E.C. Friedber 41 Role of Yeast and Human DNA Polymerase h in Error-free Replication of Damaged DNA S. Prakash, R.E. Johnson, M.T. Washington, L. Haracska, C.M. Kondratick, and L. Prakash 51 Roles of DNA Polymerase z and Rev1 Protein in Eukaryotic Mutagenesis and Translesion Replication C.W. Lawrence, P.E.M. Gibbs, R.S. Murante, X.-D. Wang, Z. Li, T.P. McManus, W.G. McGregor, J.R. Nelson, D.C. Hinkle, and V.M. Maher 61 Xeroderma Pigmentosum Variant: From a Human Genetic Disorder to a Novel DNA Polymerase C. Masutani, R. Kusumoto, A. Yamada, M. Yuasa, M. Araki, T. Nogimori, M. Yokoi, T. Eki, S. Iwai, and F. Hanaoka 71 Streisinger Revisited: DNA Synthesis Errors Mediated by Substrate Misalignments K. Bebenek and T.A. Kunkel 81

Base Recognition and Excision Repair

Roles of Watson-Crick and Minor Groove Hydrogen Bonds in DNA Replication E.T. Kool 93 Structural and Mechanistic Studies on Repair of 8-Oxoguanine in Mammalian Cells S.D. Bruner, D.P.G. Norman, J.C. Fromme, and G.L. Verdine 103 Envisioning the Fourth Dimension of the Genetic Code: The Structural Biology of Macromolecular Recognition and Conformational Switching in DNA Repair K.-P. Hopfner, S.S. Parikh, and J.A. Tainer 113 Repair of Endogenous DNA Damage T. Lindahl and D.E. Barnes 127 Base Removers and Strand Scissors: Different Strategies Employed in Base Excision and Strand Incision at Modified Base Residues in DNA E. Seeberg, L. Luna, I. Morland, L. Eide, B. Johnsen, E. Larsen, I. Alseth, F. Dantzer, K. Baynton, R. Aamodt, K.I. Kristiansen, T. Rognes, A. Klungland, and M. Bjørås 135 DNA Polymerase b and Mammalian Base Excision Repair S.H. Wilson, R.W. Sobol, W.A. Beard, J.K. Horton, R. Prasad, and B.J. Vande Berg 143 Photolyase/Cryptochrome Family Blue-light Photoreceptors Use Light Energy to Repair DNA or Set the Circadian Clock A. Sancar, C. Thompson, R.J. Thresher, F. Araujo, J. Mo, S. Ozgur, E. Vagas, L. Dawut, and C.P. Selby 157

Nucleotide Excision Repair

DNA Damage Recognition and Nucleotide Excision Repair in Mammalian Cells R.D. Wood, S.J. Araújo, R.R. Ariza, D.P. Batty, M. Biggerstaff, E. Evans, P.-H. Gaillard, D. Gunz, B. Köberle, I. Kuraoka, J.G. Moggs, J.K. Sandall, and M.K.K. Shivji 173 Regulation of Nucleotide Excision Repair in Bacteria and Mammalian Cells P.C. Hanawalt, D.J. Crowley, J.M. Ford, A.K. Ganesan, D.R. Lloyd, T. Nouspikel, C.A. Smith, G. Spivak, and S. Tornaletti 183 Three-dimensional Structure and Function of Replication Protein A G. Mer, A. Bochkarev, W.J. Chazin, and A.M. Edwards 193 Transcription-coupled Repair of Oxidative DNA Damage in Human Cells: Mechanisms and Consequences S. Tsutakawa and P.K. Cooper 201

Mismatch Repair

Signaling Mismatch Repair: The Mechanics of an Adenosine-Nucleotide Molecular Switch R. Fishel, S. Acharya, M. Berardini, T. Bocker, N. Charbonneau, A. Cranston, S. Gradia, S. Guerrette, C.D. Heinen, A. Mazurek, T. Snowden, C. Schmutte, K.-S. Shim, G. Tombline, and T. Wilson 217 DNA Mismatch Repair: From Structure to Mechanism W. Yang, M.S. Junop, C. Ban, G. Obmolova, and P. Hsieh 225 New Recognition Mode for a TG Mismatch: The Atomic Structure of a Very Short Patch Repair Endonuclease-DNA Complex S.E. Tsutakawa and K. Morikawa 233 Temporary and Permanent Mutators Lacking the Mismatch Repair System: The Enhancement of Mutators in Cell Populations J.H. Miller, A. Yeung, P. Funchain, E. Mao, J. Stewart, W.M. Clendenin, and M.M. Slupska 241 Telomeres and the Stability of DNA Ends Molecular Manifestations and Molecular Determinants of Telomere Capping E.H. Blackburn, S. Chan, J. Chang, T.B. Fulton, A. Krauskopf, M. McEachern, J. Prescott, J. Roy, C. Smith, and H. Wang 253 A New Connection at Human Telomeres: Association of the Mre11 Complex with TRF2 T. de Lange and J.H.J. Petrini 265 Telomere Length, Telomere-binding Proteins, and DNA Damage Signaling M.T. Hemann, J. Hackett, A. IJpma, and C.W. Greider 275 All Things Must End: Telomere Dynamics in Yeast M.L. DuBois, S.J. Diede, A.E. Stellwagen, and D.E. Gottschling 281 Sir2: An NAD-dependent Histone Deacetylase That Connects Chromatin Silencing, Metabolism, and Aging S. Imai, F.B. Johnson, R.A. Marciniak, M. McVey, P.U. Park, and L. Guarente 297 Arrest, Adaptation, and Recovery following a Chromosome Double-strand Break in Saccharomyces cerevisiae S.E. Lee, A. Pellicioli, J. Demeter, M.P. Vaze, A.P. Gasch, A. Malkova, P.O. Brown, D. Botstein, T. Stearns, M. Foiani, and J.E. Haber 303 Double-strand Break Repair in Human Cells S.C. West, C. Chappell, L.A. Hanakahi, J.-Y. Masson, M.J. McIlwraith, and E. Van Dyck 315

Damage Control during Replication and Mitosis

Controlling S-phase Onset in Fission Yeast Z. Lygerou and P. Nurs 323 Coping with and Recovering from Hydroxyurea-induced Replication Fork Arrest in Budding Yeast J.F.X. Diffley, K. Bousset, K. Labib, E.A. Noton, C. Santocanale, and J.A. Tercero 333 Damage Response and dNTP Regulation: The Interaction between Ribonucleotide Reductase and Its Inhibitor, Sml1 B. Georgieva, X. Zhao, and R. Rothstein 343 Is Rad9p Upstream or Downstream from Mec1p? E.J. Foss 347 DNA Damage Checkpoint Control of Mitosis in Fission Yeast N. Rhind, B.A. Baber-Furnari, A. Lopez-Girona, M.N. Boddy, J.-M. Brondello, B. Moser, P. Shanahan, A. Blasina, C. McGowan, and P. Russell 353 Mitotic Checkpoints, Genetic Instability, and Cancer M. Dobles and P.K. Sorger 361 Microscopy-induced Radiation Damage, Microtubules, and Progression through the Terminal Stage of G2 (Prophase) in Vertebrate Somatic Cells C.L. Rieder and R. Cole 369

Genome Stability and Checkpoint Control

Complexity of Damage Produced by Ionizing Radiation J.F. Ward 377 Complex Transcriptional Responses to Macromolecular Damaging Agents: Regulatory Responses Specific for SN2 Alkylation and the MAG1 Gene T.J. Begley, S.A. Jelinsky, and L.D. Samson 383 The Interplay between Nonhomologous End-joining and Cell Cycle Checkpoint Factors in Development, Genomic Stability, and Tumorigenesis D.O. Ferguson, J.M. Sekiguchi, K.M. Frank, Y. Gao, N.E. Sharpless, Y. Gu, J. Manis, R.A. DePinho, and F.W. Al 395 S-phase Functions of the Mre11 Complex J.H.J. Petrini 405 The FHA Domain, a Phosphoamino Acid Binding Domain Involved in the DNA Damage Response Pathway M. Huang and S.J. Elledge 413 The FHA Domain in DNA Repair and Checkpoint Signaling D. Durocher, S.J. Smerdon, M.B. Yaffe, and S.P. Jackson 423 Details and Concerns Regarding the G2/M DNA Damage Checkpoint in Budding Yeast T. Weinert, E. Little, L. Shanks, A. Admire, R. Gardner, C. Putnam, R. Michelson, K. Nyberg, and P. Sundareshan 433 Establishment of and Recovery from Damage Checkpoint Requires Sequential Interactions of Crb2 with Protein Kinases Rad3, Chk1, and Cdc2 F. Esashi, S. Mochida, T. Matsusaka, T. Obara, A. Ogawa, K. Tamai, and M. Yanagida 443 Analysis of the Fission Yeast Checkpoint Rad Proteins T. Caspari, C. Davies, and A.M. Carr 451 A Conserved Role for the Hus1 Checkpoint Protein in Eukaryotic Genome Maintenance R.S. Weiss, P. Leder, and T. Enoch 457 DNA-damage-induced Checkpoint Pathways in the Nematode Caenorhabditis elegans E.R. Hofmann, S. Milstein, and M.O. Hengartner 467

53 and the DNA Damage Response

The Transcriptional Program following p53 Activation R. Zhao, K. Gish, M. Murphy, Y. Yin, D. Notterman, W.H. Hoffman, E. Tom, D.H. Mack, and A.J. Levine 475 Regulation of p53 after Different Forms of Stress and at Different Cell Cycle Stages V. Gottifredi, S.Y. Shieh, and C. Prives 483 The DNA Damage Checkpoint and Human Cancer L.B. Schultz, N.H. Chehab, A. Malikzay, R.A. DiTullio, Jr., E.S. Stavridi, and T.D. Halazonetis 489 DNA Damage Responses and Chemosensitivity in the Em-myc Mouse Lymphoma Model C.A. Schmitt, R.R. Wallace-Brodeur, C.T. Rosenthal, M.E. McCurrach, and S.W. Lowe 499 Genetic Instability, Oncogenes, and the p53 Pathway G. Wahl and O. Vafa 511

DNA Damage and Cancer Progression

Multiple Signaling Pathways Involving ATM M.B. Kastan, D.-S. Lim, S.-T. Kim, B. Xu, and C. Canman 521 ATM: Sounding the Double-strand Break Alarm Y. Shiloh 527 Interactions of the Nijmegen Breakage Syndrome Protein with ATM and BRCA1 X. Wu, G. Rathbun, W.S. Lane, D.T. Weaver, and D.M. Livingston 535 The Function of BRCA1 in DNA Damage Response J.-S. Lee, K. Collins, A. Brown, C.-H. Lee, and J.H. Chung 547 Recombination between Two Chromosomes: Implications for Genomic Integrity in Mammalian Cells C. Richardson and M. Jasin 553 Transcription-coupled Repair: A Multifunctional Signaling Pathway S.A. Leadon 561 Chromosomal Instability and Cancer Predisposition: Insights from Studies on the Breast Cancer Susceptibility Gene, BRCA2 A.R. Venkitaraman 567 Roles of RecQ Family Helicases in the Maintenance of Genome Stability L. Wu, S.L. Davies, and I.D. Hickson 573 Dole of DNA Break-sensing Molecule Poly(ADP-ribose) Polymerase (PARP) in Cellular Function and Radiation Toxicity W.-M. Tong, D. Galendo, and Z.-Q. Wang 583 Summary: Biological Responses to DNA Damage: A Perspective in the New Millennium E.C. Friedberg 593