tailieunhanh - Báo cáo khoa học: DG-based prediction and experimental confirmation of SYCRP1-binding sites on the Synechocystis genome

DNA-binding sites for SYCRP1, which is a regulatory protein of the cyanobacterium Synechocystissp. PCC6803, were predicted for the whole genome sequence by estimating changes in the binding free energy (DDG A total ) for SYCRP1 for those sites. The DDG A total values were calculated by summingDDGvalues derived from systematic single base-pair substitu-tion experiments (symmetrical and cooperative binding model). | ễFEBS Journal DG-based prediction and experimental confirmation of SYCRPI-binding sites on the Synechocystis genome Katsumi Omagari1 Hidehisa Yoshimura2 Takayuki Suzuki2 Mitunori Takano3 Masayuki Ohmori2 4 and Akinori Sarai5 1 Department of Virology MedicalSchool Nagoya City University Japan 2 Department of Life Sciences Graduate Schoolof Arts and Sciences The University of Tokyo Japan 3 Department of Physics Schoolof Science and Engineering Waseda University Tokyo Japan 4 Department of BiologicalSciences Faculty of Science and Engineering Chuo University Tokyo Japan 5 Department of BiochemicalEngineering and Science Kyushu Institute of Technology KIT Fukuoka Japan Keywords additivity binding free energy change DNA-binding sites prediction regulatory protein Correspondence K. Omagari Department of Virology Medical School Nagoya City University 1 Kawasumi Mizuho Nagoya 467-8601 Japan Tel Fax 81 52 853 8191 3638 E-mail usagi525@ Received 13 April2008 revised 21 June 2008 accepted 30 July 2008 doi DNA-binding sites for SYCRP1 which is a regulatory protein of the cyanobacterium Synechocystis sp. PCC6803 were predicted for the whole genome sequence by estimating changes in the binding free energy AAG l for SYCRP1 for those sites. The AAGtotal values were calculated by summing AAG values derived from systematic single base-pair substitution experiments symmetrical and cooperative binding model . Of the calculated binding sites 23 sites with a AAGtotalvalue kcal-mol-1 located upstream or between the ORFs were selected as putative binding sites for SYCRP1. In order to confirm whether SYCRP1 actually binds to these binding sites or not 11 sites with the lowest AAGtotal values were tested experimentally and we confirmed that SYCRP1 binds to ten of the 11 sites with a AAGtotai value kcal-mol-1. The best correlation coefficient between AAGtotal and the observed DDGtotal for binding of SYCRP1 to those sites was . .