| [1] | Kitano H (2004) Biological robustness. Nat Rev Genet 5: 826–837.
|
| [2] | Stelling J, Sauer U, Szallasi Z, Doyle F. J 3rd, Doyle J (2004) Robustness of cellular functions. Cell 118: 675–685.
|
| [3] | Eldar A, Dorfman R, Weiss D, Ashe H, Shilo B. Z, et al. (2002) Robustness of the BMP morphogen gradient in Drosophila embryonic patterning. Nature 419: 304–308.
|
| [4] | Newman J. R, Ghaemmaghami S, Ihmels J, Breslow D. K, Noble M, et al. (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441: 840–846.
|
| [5] | Wagner A (2005) Distributed robustness versus redundancy as causes of mutational robustness. Bioessays 27: 176–188.
|
| [6] | Barkai N, Shilo B. Z (2007) Variability and robustness in biomolecular systems. Mol Cell 28: 755–760.
|
| [7] | Edelman G. M, Gally J. A (2001) Degeneracy and complexity in biological systems. Proc Natl Acad Sci U S A 98: 13763–13768.
|
| [8] | Moldovan G. L, Pfander B, Jentsch S (2007) PCNA, the maestro of the replication fork. Cell 129: 665–679.
|
| [9] | Maga G, Hubscher U (2003) Proliferating cell nuclear antigen (PCNA): a dancer with many partners. J Cell Sci 116: 3051–3060.
|
| [10] | Warbrick E (2000) The puzzle of PCNA's many partners. Bioessays 22: 997–1006.
|
| [11] | Vivona J. B, Kelman Z (2003) The diverse spectrum of sliding clamp interacting proteins. FEBS Lett 546: 167–172.
|
| [12] | Hoege C, Pfander B, Moldovan G. L, Pyrowolakis G, Jentsch S (2002) RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature 419: 135–141.
|
| [13] | Stelter P, Ulrich H. D (2003) Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation. Nature 425: 188–191.
|
| [14] | Gomes X. V, Burgers P. M (2000) Two modes of FEN1 binding to PCNA regulated by DNA. EMBO J 19: 3811–3821.
|
| [15] | Haracska L, Kondratick C. M, Unk I, Prakash S, Prakash L (2001) Interaction with PCNA is essential for yeast DNA polymerase eta function. Mol Cell 8: 407–415.
|
| [16] | Johansson E, Garg P, Burgers P. M (2004) The Pol32 subunit of DNA polymerase delta contains separable domains for processive replication and proliferating cell nuclear antigen (PCNA) binding. J Biol Chem 279: 1907–1915.
|
| [17] | Jin Y. H, Obert R, Burgers P. M, Kunkel T. A, Resnick M. A, et al. (2001) The 3′→5′ exonuclease of DNA polymerase delta can substitute for the 5′ flap endonuclease Rad27/Fen1 in processing Okazaki fragments and preventing genome instability. Proc Natl Acad Sci U S A 98: 5122–5127.
|
| [18] | Arnold F. H, Wintrode P. L, Miyazaki K, Gershenson A (2001) How enzymes adapt: lessons from directed evolution. Trends Biochem Sci 26: 100–106.
|
| [19] | Tao H, Cornish V. W (2002) Milestones in directed enzyme evolution. Curr Opin Chem Biol 6: 858–864.
|
| [20] | Hoogenboom H. R (2005) Selecting and screening recombinant antibody libraries. Nat Biotechnol 23: 1105–1116.
|
| [21] | Aharoni A, Griffiths A. D, Tawfik D. S (2005) High-throughput screens and selections of enzyme-encoding genes. Curr Opin Chem Biol 9: 210–216.
|
| [22] | Chao G, Lau W. L, Hackel B. J, Sazinsky S. L, Lippow S. M, et al. (2006) Isolating and engineering human antibodies using yeast surface display. Nat Protoc 1: 755–768.
|
| [23] | Fields S, Sternglanz R (1994) The two-hybrid system: an assay for protein-protein interactions. Trends Genet 10: 286–292.
|
| [24] | Piehler J (2005) New methodologies for measuring protein interactions in vivo and in vitro. Curr Opin Struct Biol 15: 4–14.
|
| [25] | Krishna T. S, Kong X. P, Gary S, Burgers P. M, Kuriyan J (1994) Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA. Cell 79: 1233–1243.
|
| [26] | Chapados B. R, Hosfield D. J, Han S, Qiu J, Yelent B, et al. (2004) Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair. Cell 116: 39–50.
|
| [27] | Gulbis J. M, Kelman Z, Hurwitz J, O'Donnell M, Kuriyan J (1996) Structure of the C-terminal region of p21(WAF1/CIP1) complexed with human PCNA. Cell 87: 297–306.
|
| [28] | Heltzel J. M, Maul R. W, Scouten Ponticelli S. K, Sutton M. D (2009) A model for DNA polymerase switching involving a single cleft and the rim of the sliding clamp. Proc Natl Acad Sci U S A 106: 12664–12669.
|
| [29] | Vijayakumar S, Chapados B. R, Schmidt K. H, Kolodner R. D, Tainer J. A, et al. (2007) The C-terminal domain of yeast PCNA is required for physical and functional interactions with Cdc9 DNA ligase. Nucleic Acids Res 35: 1624–1637.
|
| [30] | Bruning J. B, Shamoo Y (2004) Structural and thermodynamic analysis of human PCNA with peptides derived from DNA polymerase-delta p66 subunit and flap endonuclease-1. Structure 12: 2209–2219.
|
| [31] | Eissenberg J. C, Ayyagari R, Gomes X. V, Burgers P. M (1997) Mutations in yeast proliferating cell nuclear antigen define distinct sites for interaction with DNA polymerase delta and DNA polymerase epsilon. Mol Cell Biol 17: 6367–6378.
|
| [32] | Chockalingam K, Chen Z, Katzenellenbogen J. A, Zhao H (2005) Directed evolution of specific receptor-ligand pairs for use in the creation of gene switches. Proc Natl Acad Sci U S A 102: 5691–5696.
|
| [33] | Sporbert A, Domaing P, Leonhardt H, Cardoso M. C (2005) PCNA acts as a stationary loading platform for transiently interacting Okazaki fragment maturation proteins. Nucleic Acids Res 33: 3521–3528.
|
| [34] | Ayyagari R, Impellizzeri K. J, Yoder B. L, Gary S. L, Burgers P. M (1995) A mutational analysis of the yeast proliferating cell nuclear antigen indicates distinct roles in DNA replication and DNA repair. Mol Cell Biol 15: 4420–4429.
|
| [35] | Tishkoff D. X, Filosi N, Gaida G. M, Kolodner R. D (1997) A novel mutation avoidance mechanism dependent on S. cerevisiae RAD27 is distinct from DNA mismatch repair. Cell 88: 253–263.
|
| [36] | Debrauwere H, Loeillet S, Lin W, Lopes J, Nicolas A (2001) Links between replication and recombination in Saccharomyces cerevisiae: a hypersensitive requirement for homologous recombination in the absence of Rad27 activity. Proc Natl Acad Sci U S A 98: 8263–8269.
|
| [37] | Northam M. R, Garg P, Baitin D. M, Burgers P. M, Shcherbakova P. V (2006) A novel function of DNA polymerase zeta regulated by PCNA. EMBO J 25: 4316–4325.
|
| [38] | Scott A. D, Neishabury M, Jones D. H, Reed S. H, Boiteux S, et al. (1999) Spontaneous mutation, oxidative DNA damage, and the roles of base and nucleotide excision repair in the yeast Saccharomyces cerevisiae. Yeast 15: 205–218.
|
| [39] | Tran H. T, Degtyareva N. P, Koloteva N. N, Sugino A, Masumoto H, et al. (1995) Replication slippage between distant short repeats in Saccharomyces cerevisiae depends on the direction of replication and the RAD50 and RAD52 genes. Mol Cell Biol 15: 5607–5617.
|
| [40] | Stith C. M, Sterling J, Resnick M. A, Gordenin D. A, Burgers P. M (2008) Flexibility of eukaryotic Okazaki fragment maturation through regulated strand displacement synthesis. J Biol Chem 283: 34129–34140.
|
| [41] | Burgers P. M (2009) Polymerase dynamics at the eukaryotic DNA replication fork. J Biol Chem 284: 4041–4045.
|
| [42] | Lawrence C. W (2002) Cellular roles of DNA polymerase zeta and Rev1 protein. DNA Repair (Amst) 1: 425–435.
|
| [43] | Huh W. K, Falvo J. V, Gerke L. C, Carroll A. S, Howson R. W, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425: 686–691.
|
| [44] | Gal-Tanamy M, Zemel R, Berdichevsky Y, Bachmatov L, Tur-Kaspa R, et al. (2005) HCV NS3 serine protease-neutralizing single-chain antibodies isolated by a novel genetic screen. J Mol Biol 347: 991–1003.
|
| [45] | Pfander B, Moldovan G. L, Sacher M, Hoege C, Jentsch S (2005) SUMO-modified PCNA recruits Srs2 to prevent recombination during S phase. Nature 436: 428–433.
|
| [46] | Sopko R, Huang D, Preston N, Chua G, Papp B, et al. (2006) Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell 21: 319–330.
|
| [47] | Lea D. E, Coulson C. A (1949) The distribution of the numbers of mutants in bacterial populations. J Genet 49: 264–285.
|
| [48] | Reenan R. A, Kolodner R. D (1992) Characterization of insertion mutations in the Saccharomyces cerevisiae MSH1 and MSH2 genes: evidence for separate mitochondrial and nuclear functions. Genetics 132: 975–985.
|
| [49] | Hall B. M, Ma C. X, Liang P, Singh K. K (2009) Fluctuation analysis CalculatOR: a web tool for the determination of mutation rate using Luria-Delbruck fluctuation analysis. Bioinformatics 25: 1564–1565.
|
