In silico analyses of a new group of fungal and plant RecQ4-homologous proteins

Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389 Bachrati, 2003, RecQ helicases: suppressors of tumorigenesis and premature aging, Biochem. J., 374, 577, 10.1042/bj20030491 Bañuelos, 2003, Activation mechanism of the nuclear chaperone nucleoplasmin: role of the core domain, J. Mol. Biol., 334, 585, 10.1016/j.jmb.2003.09.067 Bernstein, 2003, High-resolution structure of the E. coli RecQ helicase catalytic core, EMBO J., 22, 4910, 10.1093/emboj/cdg500 Bystroff, 2000, HMMSTR: a hidden Markov model for local sequence–structure correlations in proteins, J. Mol. Biol., 301, 173, 10.1006/jmbi.2000.3837 Chen, 2003, Werner syndrome, J. Biomed. Biotechnol., 2, 46, 10.1155/S1110724302201011 Duguet, 1997, When helicase and topoisomerase meet!, J. Cell Sci., 110, 1345, 10.1242/jcs.110.12.1345 Ellis, 1995, The Bloom's syndrome gene product is homologous to RecQ helicases, Cell, 83, 655, 10.1016/0092-8674(95)90105-1 Gaboriaud, 1987, Hydrophobic cluster analysis: an efficient new way to compare and analyse amino acid sequences, FEBS Lett., 224, 149, 10.1016/0014-5793(87)80439-8 Gangloff, 1994, The yeast type I topoisomerase Top3 interacts with Sgs1, a DNA helicase homolog: a potential eukaryotic reverse gyrase, Mol. Cell. Biol., 14, 8391, 10.1128/MCB.14.12.8391 Gorbalenya, 1993, Helicases: amino acid sequence comparisons and structure–function relationships, Curr. Opin. Struct. Biol., 3, 419, 10.1016/S0959-440X(05)80116-2 Gouet, 2003, ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structure of proteins, Nucleic Acids Res., 31, 3320, 10.1093/nar/gkg556 Hall, 1999, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symp. Ser., 41, 95 Imbert, 1996, Integrated map of the chromosome 8p12–p21 region, a region involved in human cancers and Werner syndrome, Genomics, 32, 29, 10.1006/geno.1996.0073 Killoran, 2006, Sit down, relax and unwind: structural insights into RecQ helicase mechanisms, Nucleic Acids Res., 34, 4098, 10.1093/nar/gkl538 Kitao, 1999, Mutations in RECQL4 cause a subset of cases of Rothmund–Thomson syndrome, Nat. Genet., 22, 82, 10.1038/8788 Kumar, 2004, MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment, Brief. Bioinform., 5, 150, 10.1093/bib/5.2.150 Larizza, 2006, Rothmund–Thomson syndrome and RECQL4 defect: splitting and lumping, Cancer Lett., 232, 107, 10.1016/j.canlet.2005.07.042 Lindor, 2000, Rothmund–Thomson syndrome due to RECQ4 helicase mutations: report and clinical and molecular comparisons with Bloom syndrome and Werner syndrome, Am. J. Med. Genet., 90, 223, 10.1002/(SICI)1096-8628(20000131)90:3<223::AID-AJMG7>3.0.CO;2-Z Macris, 2006, Biochemical characterization of the RECQ4 protein, mutated in Rothmund–Thomson syndrome, DNA Repair, 5, 172, 10.1016/j.dnarep.2005.09.005 Morozov, 1997, A putative nucleic acid-binding domain in Bloom's and Werner's syndrome helicases, Trends Biochem. Sci., 22, 417, 10.1016/S0968-0004(97)01128-6 Myre, 2002, Nucleomorphin: a novel, acidic, nuclear calmodulin-binding protein from Dictyostelium that regulates nuclear number, J. Biol. Chem., 277, 19735, 10.1074/jbc.M109717200 Onoda, 2000, Elevation of sister chromatid exchange in Saccharomyces cerevisiae sgs1 disruptants and the relevance of the disruptants as a system to evaluate mutations in Bloom's syndrome gene, Mutat. Res., 459, 203, 10.1016/S0921-8777(99)00071-3 Pettersen, 2004, UCSF Chimera—a visualization system for exploratory research and analysis, J. Comput. Chem., 25, 1605, 10.1002/jcc.20084 Stewart, 1997, rqh1+, a fission yeast gene related to the Bloom's and Werner's syndrome genes, is required for reversible S phase arrest, EMBO J., 16, 2682, 10.1093/emboj/16.10.2682 Tatusova, 1999, BLAST 2 sequences, a new tool for comparing protein and nucleotide sequences, FEMS Microbiol. Lett., 174, 247, 10.1111/j.1574-6968.1999.tb13575.x Thompson, 1994, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res., 22, 4673, 10.1093/nar/22.22.4673 Tuteja, 2004, Prokaryotic and eukaryotic DNA helicases: essential molecular motor proteins for cellular machinery, Eur. J. Biochem., 271, 1835, 10.1111/j.1432-1033.2004.04093.x Vennos, 1995, Rothmund–Thomson syndrome, Dermatol. Clin., 13, 143, 10.1016/S0733-8635(18)30117-7 Wang, 2002, Intron-size constraint as a mutational mechanism in Rothmund–Thomson syndrome, Am. J. Hum. Genet., 71, 165, 10.1086/341234 Watt, 1996, SGS1, a homologue of the Bloom's and Werner's syndrome genes, is required for maintenance of genome stability in Saccharomyces cerevisiae, Genetics, 144, 935, 10.1093/genetics/144.3.935 Watt, 1995, SGS1: a eukaryotic homolog of E. coli RecQ that interacts with topoisomerase II in vivo and is required for faithful chromosome segregation, Cell, 81, 253, 10.1016/0092-8674(95)90335-6 Yu, 1996, Positional cloning of the Werner's syndrome gene, Science, 272, 258, 10.1126/science.272.5259.258