Noncanonical DNA-binding mode of repressor and its disassembly by antirepressor.
DNA-binding repressors are involved in transcriptional repression in many organisms. Disabling a repressor is a crucial step in activating expression of desired genes. Thus, several mechanisms have been identified for the removal of a stably bound repressor (Rep) from the operator. Here, we describe an uncharacterized mechanism of noncanonical DNA binding and induction by a Rep from the temperate Salmonella phage SPC32H; this mechanism was revealed using the crystal structures of homotetrameric Rep (92-198) and a hetero-octameric complex between the Rep and its antirepressor (Ant). The canonical method of inactivating a repressor is through the competitive binding of the antirepressor to the operator-binding site of the repressor; however, these studies revealed several noncanonical features. First, Ant does not compete for the DNA-binding region of Rep. Instead, the tetrameric Ant binds to the C-terminal domains of two asymmetric Rep dimers. Simultaneously, Ant facilitates the binding of the Rep N-terminal domains to Ant, resulting in the release of two Rep dimers from the bound DNA. Second, the dimer pairs of the N-terminal DNA-binding domains originate from different dimers of a Rep tetramer (trans model). This situation is different from that of other canonical Reps, in which two N-terminal DNA-binding domains from the same dimeric unit form a dimer upon DNA binding (cis model). On the basis of these observations, we propose a noncanonical model for the reversible inactivation of a Rep by an Ant.
Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea; Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Korea;
Minsik
M
Kim
Department of Bio and Nano Chemistry, Kookmin University, Seoul 02707, Korea;
Hee Jung
HJ
Kim
Department of Bio and Nano Chemistry, Kookmin University, Seoul 02707, Korea;
Sang Hyeon
SH
Son
Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea;
Hye Jin
HJ
Yoon
Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea;
Youngbin
Y
Lim
Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea;
Jong Woo
JW
Lee
Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea; Department of Biological Sciences, Seoul National University, Seoul 08826, Korea; Institute of Microbiology, Seoul National University, Seoul 08826, Korea;
Yeong-Jae
YJ
Seok
Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk 37673, Korea;
Kyeong Sik
KS
Jin
Department of Bio and Nano Chemistry, Kookmin University, Seoul 02707, Korea;
Yeon Gyu
YG
Yu
Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea; Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea;
Seong Keun
SK
Kim
Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea; Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Korea; Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea sangryu@snu.ac.kr hyungholee@snu.ac.kr.
Sangryeol
S
Ryu
Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea; sangryu@snu.ac.kr hyungholee@snu.ac.kr.
Hyung Ho
HH
Lee
D001435:Bacteriophages / Q000737:chemistry / Q000235:genetics; D001665:Binding Sites; D003198:Computer Simulation; D004279:DNA, Viral / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D012097:Repressor Proteins / Q000737:chemistry* / Q000648:ultrastructure*
D004279:DNA, Viral; D012097:Repressor Proteins
Salmonella; antirepressor; bacteriophage; repressor; transcription